(fix): update filter-fn docstring (#1589 )

Fix inconsistency for filter-fn in ref and node functions, and update docstrings to be consistent.
Org-roam V2 (#1401 )
2025-08-03 12:27:23 -05:00 · 2021-07-17 21:09:38 +08:00 · 2021-07-17 19:29:30 +08:00 · 2021-06-09 20:21:08 +08:00 · 2021-06-09 20:07:47 +08:00 · 2021-05-13 15:04:49 +07:00
50 changed files with 5924 additions and 7304 deletions
--- a/.dir-locals.el
+++ b/.dir-locals.el
@ -1,6 +1,13 @@
-;;; Directory Local Variables
-;;; For more information see (info "(emacs) Directory Variables")
-
 ((emacs-lisp-mode
-  (eval . (require 'org-roam-dev))
-  (eval . (org-roam-dev-mode))))
+  (fill-column . 110)
+  (indent-tabs-mode . nil)
+  (elisp-lint-ignored-validators . ("byte-compile" "package-lint"))
+  (elisp-lint-indent-specs . ((describe . 1)
+                              (it . 1)
+                              (org-element-map . defun)
+                              (org-roam-with-temp-buffer . 1)
+                              (org-with-point-at . 1)
+                              (magit-insert-section . defun)
+                              (magit-section-case . 0)
+                              (->> . 1)
+                              (org-roam-with-file . 2)))))
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@ -34,36 +34,28 @@ jobs:
  build:
    runs-on: ubuntu-latest
    strategy:
-      fail-fast: false
      matrix:
        emacs_version:
+          - 27.1
          - snapshot
    steps:
-    - uses: purcell/setup-emacs@master
-      with:
-        version: ${{ matrix.emacs_version }}
+      - uses: purcell/setup-emacs@master
+        with:
+          version: ${{ matrix.emacs_version }}

-    - uses: actions/checkout@v2
+      - uses: actions/checkout@v2

-    - name: Initialize sandbox
-      run: |
-        SANDBOX_DIR=$(mktemp -d) || exit 1
-        echo ::set-env name=SANDBOX_DIR::$SANDBOX_DIR
-        ./makem.sh -vv --sandbox $SANDBOX_DIR --install-deps --install-linters
+      - name: Install Eldev
+        run: curl -fsSL https://raw.github.com/doublep/eldev/master/webinstall/github-eldev | sh

-    # The "all" rule is not used, because it treats compilation warnings
-    # as failures, so linting and testing are run as separate steps.
+      - name: Install dependencies
+        run: make prepare

-    # org-roam-compat is excluded from linting because it contains
-    # symbols/aliases from other packages
-    - name: Lint
-      continue-on-error: false
-      run: ./makem.sh -vv --sandbox $SANDBOX_DIR --exclude org-roam-compat.el lint
-
-    - name: Test
-      if: always()  # Run test even if linting fails.
-      run: ./makem.sh -vv --sandbox $SANDBOX_DIR test
+      - name: Lint
+        run: make lint

+      - name: Test
+        run: make test
 # Local Variables:
 # eval: (outline-minor-mode)
 # End:
--- a/.gitignore
+++ b/.gitignore
@ -12,4 +12,5 @@
 /doc/mimetype
 /doc/stats/
 /config.mk
-/doc/manual/
+/doc/manual.html
+/.eldev/
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@ -1,5 +1,65 @@
 # Changelog

+## 1.2.4 (TBD)
+
+### Added
+
+- [#1396](https://github.com/org-roam/org-roam/pull/1396) add option to choose between prepending, appending, and omitting `roam_tags` in file completion
+- [#1270](https://github.com/org-roam/org-roam/pull/1270) capture: create OLP if it does not exist. Removes need for OLP setup in `:head`.
+- [#1353](https://github.com/org-roam/org-roam/pull/1353) support file-level property drawers
+
+### Changed
+
+- [#1352](https://github.com/org-roam/org-roam/pull/1352) prefer lower-case for roam_tag and roam_alias in interactive commands
+- [#1513](https://github.com/org-roam/org-roam/pull/1513) replaced hardcoded "svg" with defcustom org-roam-graph-filetype 
+- [#1540](https://github.com/org-roam/org-roam/pull/1540) allow `roam_tag` and `roam_alias` to be specified on multiple lines
+
+### Fixed
+
+- [#1281](https://github.com/org-roam/org-roam/pull/1281) fixed idle-timer not instantiated on `org-roam-mode`
+- [#1308](https://github.com/org-roam/org-roam/pull/1308) fixed file renames corrupting database
+- [#1325](https://github.com/org-roam/org-roam/pull/1325) make titles and tags extracted unique per note
+- [#1327](https://github.com/org-roam/org-roam/pull/1327) preserve existing link description during automatic replacement
+- [#1346](https://github.com/org-roam/org-roam/pull/1346) prevent malformed path to `org-roam-index-file`
+- [#1347](https://github.com/org-roam/org-roam/pull/1347) allow use of `%a` element in regular Org-roam captures
+- [#1352](https://github.com/org-roam/org-roam/pull/1352) fixed org-roam-{tag/alias}-{add/delete} altering the original case of the Org property
+- [#1374](https://github.com/org-roam/org-roam/pull/1374) fix headline completions erroring out
+- [#1375](https://github.com/org-roam/org-roam/pull/1375) fix org-roam-protocol to use existing ref file
+- [#1403](https://github.com/org-roam/org-roam/issues/1403) fixed inconsistency between how we write and read props like alias and tags
+- [#1409](https://github.com/org-roam/org-roam/issues/1398) prevent inclusion of non-org-roam files in `org-roam-dailies--list-files`
+- [#1542](https://github.com/org-roam/org-roam/issues/1542) fix files not excluded when `org-roam-list-files-commands` is nil
+
+## 1.2.3 (13-11-2020)
+
+Primarily a stabilization and bug-fix release.
+
+Org-roam-dailies has also been revamped to include new features, see [this video](https://www.youtube.com/watch?v=1q9x2aZCJJ4) for a quick overview.
+
+### Added
+
+- [#978](https://github.com/org-roam/org-roam/pull/978) Revamp org-roam-dailies
+- [#1183](https://github.com/org-roam/org-roam/pull/1183) Interactive functions for managing aliases and tags in Org-roam file, namely `org-roam-alias-add`, `org-roam-alias-delete`, `org-roam-tag-add`, and `org-roam-tag-delete`.
+- [#1215](https://github.com/org-roam/org-roam/pull/1215) Multiple `ROAM_KEY` keywords can now be specified in one file. This allows bibliographical entries to share the same note file.
+- [#1238](https://github.com/org-roam/org-roam/pull/1238) Add `org-roam-prefer-id-links` variable to select linking method
+- [#1239](https://github.com/org-roam/org-roam/pull/1239) Allow `org-roam-protocol` to capture the webpage's selection, and add a toggle for storing the links to the pages
+- [#1264](https://github.com/org-roam/org-roam/pull/1264) add `org-roam-db-update-method` to control when the cache is rebuilt.
+
+### Changed
+
+- [#1264](https://github.com/org-roam/org-roam/pull/1264) renamed `org-roam-update-db-idle-seconds` to `org-roam-db-idle-idle-seconds`
+
+### Fixed
+
+- [#1074](https://github.com/org-roam/org-roam/issues/1074) fix `org-roam--extract-links` to handle content boundaries.
+- [#1193](https://github.com/org-roam/org-roam/issues/1193) fix `org-roam-db-build-cache` by not killing temporary buffer in `org-roam--extract-links`.
+- [#1195](https://github.com/org-roam/org-roam/issues/1195) fix ID face showing as invalid if within Org ID files, but not Org-roam's.
+- [#1199](https://github.com/org-roam/org-roam/issues/1199) make Org-roam link insertions respect `org-roam-link-title-format` everywhere.
+- [#1201](https://github.com/org-roam/org-roam/issues/1201) fix `org-roam-db-build-cache` failing in scenarios involving duplicate IDs and deleted files.
+- [#1226](https://github.com/org-roam/org-roam/issues/1226) only update relative path of file links
+- [#1232](https://github.com/org-roam/org-roam/issues/1232) fix incorrect title extractions from narrowed buffers
+- [#1233](https://github.com/org-roam/org-roam/issues/1233) fixes bug where descriptive file links become plain links during update for relative paths
+- [#1252](https://github.com/org-roam/org-roam/issues/1252) respect original link type during automatic replacement
+
 ## 1.2.2 (06-10-2020)

 In this release we support fuzzy links of the form `[[roam:Title]]`, `[[roam:*Headline]]` and `[[roam:Title*Headline]]`. Completion for these fuzzy links is supported via `completion-at-point`.
@ -31,7 +91,7 @@ This change requires you to set `org-roam-directory` to the resolved path of a f
 - [#974](https://github.com/org-roam/org-roam/pull/974) Protect region targeted by `org-roam-insert`
 - [#994](https://github.com/org-roam/org-roam/pull/994) Simplify org-roam-store-link
 - [#1062](https://github.com/org-roam/org-roam/pull/1062) Variable `org-roam-completions-everywhere` allows for completions everywhere from word at point
- [#910](https://github.com/org-roam/org-roam/pull/910), [#1105](https://github.com/org-roam/org-roam/pull/1105) Support fuzzy links of the form [[roam:Title]], [[roam:*Headline]] and [[roam:Title*Headline]]
+- [#910](https://github.com/org-roam/org-roam/pull/910), [#1105](https://github.com/org-roam/org-roam/pull/1105) Support fuzzy links of the form `[[roam:Title]]`, `[[roam:*Headline]]` and `[[roam:Title*Headline]]`

 ### Bugfixes

--- a/29
+++ b/29
@ -0,0 +1,29 @@
+; -*- mode: emacs-lisp; lexical-binding: t; no-byte-compile: t -*-
+
+;; explicitly set main file
+(setf eldev-project-main-file "org-roam.el")
+
+(eldev-use-package-archive 'gnu)
+(eldev-use-package-archive 'melpa-unstable)
+
+;; allow to load test helpers
+(eldev-add-loading-roots 'test "test/utils")
+
+;; Tell checkdoc not to demand two spaces after a period.
+(setq sentence-end-double-space nil)
+
+(setf eldev-lint-default '(elisp))
+(setf eldev-standard-excludes `(:or ,eldev-standard-excludes "org-roam-macs.el"))
+
+(with-eval-after-load 'elisp-lint
+  ;; We will byte-compile with Eldev.
+  (setf elisp-lint-ignored-validators '("package-lint" "fill-column")
+        enable-local-variables        :all))
+
+;; Teach linter how to properly indent emacsql vectors
+(eldev-add-extra-dependencies 'lint 'emacsql)
+(add-hook 'eldev-lint-hook
+          (lambda ()
+            (eldev-load-project-dependencies 'lint nil t)
+            (require 'emacsql)
+            (call-interactively #'emacsql-fix-vector-indentation)))
--- a/73
+++ b/73
@ -1,70 +1,29 @@
-# * makem.sh/Makefile --- Script to aid building and testing Emacs Lisp packages
+.PHONY: clean
+clean:
+	eldev clean all

-# This Makefile is from the makem.sh repo: <https://github.com/alphapapa/makem.sh>.
+.PHONY: prepare
+prepare:
+	eldev -C --unstable -p -dtT prepare

-# * Arguments
+.PHONY: lint
+lint:
+	eldev -C --unstable -T lint

-# For consistency, we use only var=val options, not hyphen-prefixed options.
-
-# NOTE: I don't like duplicating the arguments here and in makem.sh,
-# but I haven't been able to find a way to pass arguments which
-# conflict with Make's own arguments through Make to the script.
-# Using -- doesn't seem to do it.
-
-ifdef install-deps
-	INSTALL_DEPS = "--install-deps"
-endif
-ifdef install-linters
-	INSTALL_LINTERS = "--install-linters"
-endif
-
-ifdef sandbox
-	ifeq ($(sandbox), t)
-		SANDBOX = --sandbox
-	else
-		SANDBOX = --sandbox $(sandbox)
-	endif
-endif
-
-ifdef debug
-	DEBUG = "--debug"
-endif
-
-# ** Verbosity
-
-# Since the "-v" in "make -v" gets intercepted by Make itself, we have
-# to use a variable.
-
-verbose = $(v)
-
-ifneq (,$(findstring vv,$(verbose)))
-	VERBOSE = "-vv"
-else ifneq (,$(findstring v,$(verbose)))
-	VERBOSE = "-v"
-endif
-
-# * Rules
-
-# TODO: Handle cases in which "test" or "tests" are called and a
-# directory by that name exists, which can confuse Make.
-
-%:
-	@./makem.sh $(DEBUG) $(VERBOSE) $(SANDBOX) $(INSTALL_DEPS) $(INSTALL_LINTERS) $(@)
-
-.DEFAULT: init
-init:
-	@./makem.sh $(DEBUG) $(VERBOSE) $(SANDBOX) $(INSTALL_DEPS) $(INSTALL_LINTERS)
+.PHONY: test
+test:
+	eldev -C --unstable -T test

 docs:
-	@$(MAKE) -C doc all
+	make -C doc all

 html:
-	@$(MAKE) -C doc html-dir
+	make -C doc html-dir

 install: install-docs

 install-docs: docs
-	@$(MAKE) -C doc install-docs
+	make -C doc install-docs

 install-info: info
-	@$(MAKE) -C doc install-info
+	make -C doc install-info
--- a/README.md
+++ b/README.md
@ -1,47 +1,35 @@
-[![License GPL 3][badge-license]](http://www.gnu.org/licenses/gpl-3.0.txt)
-[![GitHub Release](https://img.shields.io/github/v/release/org-roam/org-roam)](https://img.shields.io/github/v/release/org-roam/org-roam)
-[![MELPA](https://melpa.org/packages/org-roam-badge.svg)](https://melpa.org/#/org-roam)
+# Org-roam [![GitHub Release][release-badge]][release] [![MELPA][melpa-badge]][melpa] [![License GPL 3][gpl3-badge]][gpl3]

-## Synopsis
+<img src="https://www.orgroam.com/img/logo.svg" align="right" alt="Org-roam Logo" width="240">

-> **NOTE:** Org-roam builds upon Emacs and Org-mode, both of which are intricate
-> tools that require time investment for mastery. This makes Org-roam less
-> friendly for beginners, but extremely powerful for those familiar with the
-> ecosystem, or willing to invest effort in it.
+Org-roam is a plain-text knowledge management system. It brings some of
+[Roam's][roamresearch] more powerful features into the [Org-mode][org]
+ecosystem.

-Org-roam is a [Roam][roamresearch] replica built on top of the
-all-powerful [Org-mode][org].
+Org-roam borrows principles from the Zettelkasten method, providing a solution
+for non-hierarchical note-taking. It should also work as a plug-and-play
+solution for anyone already using Org-mode for their personal wiki.

-Org-roam is a solution for effortless non-hierarchical note-taking
-with Org-mode. With Org-roam, notes flow naturally, making note-taking
-fun and easy. Org-roam should also work as a plug-and-play solution
-for anyone already using Org-mode for their personal wiki.
+- **Private and Secure**: Edit your personal wiki completely offline, entirely
+  in your control. Encrypt your notes with GPG. Take lasting notes in
+  plain-text.
+- **Networked Thought**: Connect notes and thoughts together with ease using
+  backlinks. Discover surprising and previously unseen connections in your notes
+  with the built-in graph visualization.
+- **Extensible and Powerful**: Leverage Emacs' fantastic text-editing interface,
+  and the mature Emacs and Org-mode ecosystem of packages.
+- **Free and Open Source**: Org-roam is licensed under the GNU General Public
+  License version 3 or later.

-Org-roam aims to implement the core features of Roam, leveraging the
-mature ecosystem around Org-mode where possible. Eventually, we hope
-to further introduce features enabled by the Emacs ecosystem.
-
-[@technovangelist](https://github.com/technovangelist/) has produced a video
-describing Org-roam and the concepts behind it:
-
-[![Making Connections in your Notes](http://img.youtube.com/vi/Lg61ocfxk3c/0.jpg)](http://www.youtube.com/watch?v=Lg61ocfxk3c "Making Connections in your Notes")
-
-Important links:
+<p align="center">
+  <img src="https://www.orgroam.com/img/screenshot.png" alt="Org-roam Screenshot" width="738">
+</p>

 - **[Documentation][docs]**
 - **[Discourse][discourse]**
 - **[Slack][slack]**
-
-## A Preview
-
-Here's a screencast of Org-roam. The `org-roam-buffer` (window on the
-right) shows backlinks for the active Org-roam buffer (window on the
-left), as well as the surrounding content in the backlink file. The
-database is built once, and updated incrementally. The graph is
-generated from the link structure, and can be used to navigate to the
-respective files.
-
-![img](doc/images/org-roam-graph.gif)
+- **[Frequently Asked Questions][faq]**
+- **[Changelog](CHANGELOG.md)**

 ## Installation

@ -51,61 +39,53 @@ You can install `org-roam` using `package.el`:
 M-x package-install RET org-roam RET
 ```

-Here's a sample configuration with using `use-package`:
+Here's a sample configuration with `use-package`:

 ```emacs-lisp
 (use-package org-roam
      :ensure t
-      :hook
-      (after-init . org-roam-mode)
      :custom
-      (org-roam-directory "/path/to/org-files/")
-      :bind (:map org-roam-mode-map
-              (("C-c n l" . org-roam)
-               ("C-c n f" . org-roam-find-file)
-               ("C-c n g" . org-roam-graph))
-              :map org-mode-map
-              (("C-c n i" . org-roam-insert))
-              (("C-c n I" . org-roam-insert-immediate))))
+      (org-roam-directory (file-truename "/path/to/org-files/"))
+      :bind (("C-c n l" . org-roam-buffer-toggle)
+             ("C-c n f" . org-roam-node-find)
+             ("C-c n g" . org-roam-graph)
+             ("C-c n i" . org-roam-node-insert)
+             ("C-c n c" . org-roam-capture)
+             ;; Dailies
+             ("C-c n j" . org-roam-dailies-capture-today))
+      :config
+      (org-roam-setup)
+      ;; If using org-roam-protocol
+      (require 'org-roam-protocol))
 ```

-`org-roam-graph` by default expects to find the `dot` executable
-from the `graphviz` package in the `exec-path`.
-Ensure `graphviz` is installed and found if you want to use this
-feature or customize your configuration for `org-roam-graph` to use a
-different tool.
+The `file-truename` function is only necessary when you use symbolic links
+inside `org-roam-directory`: Org-roam does not resolve symbolic links.

-For more detailed installation and configuration instructions (including for
-Doom and Spacemacs users), please see [the
-documentation][docs].
-
-## Frequently-asked Questions
-
-Q: How do I create a note whose title already matches one of the candidates (e.g. creating `bar` when `barricade` already exists)?
-
-A: With `ivy`, you need to press `C-M-j` to use the current input instead of the nearest candidate. (Source: [`ivy`’s
-  FAQ](https://github.com/abo-abo/swiper#frequently-asked-questions))
+Org-roam requires sqlite to function. Org-roam optionally uses Graphviz for
+graph-related functionality. It is recommended to install PCRE-enabled ripgrep
+for better performance and extended functionality.

 ## Getting Help

-Before creating a new topic/issue, please be mindful of our time and ensure
-that it has not already been addressed on
-[GitHub][issues] or on
+Before creating a new topic/issue, please be mindful of our time and ensure that
+it has not already been addressed on [GitHub][issues] or on
 [Discourse][discourse].

- If you are new to Emacs and have problem setting up Org-roam, please ask your question on [Slack, channel #how-do-i][slack].
- For quick questions, please ask them on [Slack, channel #troubleshooting][slack].
- If something is not working as it should, or if you would like to suggest a new feature, please [create a new issue][issues].
- If you have questions about your workflow with the slip-box method, please find a relevant topic on [Discourse][discourse], or create a new one.
+- If you are new to Emacs and have problem setting up Org-roam, please ask your
+  question on [Slack, channel #how-do-i][slack].
+- For quick questions, please ask them on [Slack, channel
+  #troubleshooting][slack].
+- If something is not working as it should, or if you would like to suggest a
+  new feature, please [create a new issue][issues].
+- If you have questions about your workflow with the slip-box method, please
+  find a relevant topic on [Discourse][discourse], or create a new one.

 ## Knowledge Bases using Org-roam

 - [Jethro Kuan](https://braindump.jethro.dev/)
  ([Source](https://github.com/jethrokuan/braindump/tree/master/org))
-
-## Changelog
-
-A changelog is being maintained [here](CHANGELOG.md)
+- [Alexey Shmalko](https://braindump.rasen.dev/)

 ## Contributing

@ -116,12 +96,18 @@ request. Please also see [CONTRIBUTING.md](.github/CONTRIBUTING.md).
 ## License

 Copyright © Jethro Kuan and contributors. Distributed under the GNU
-General Public License, Version 3
+General Public License, Version 3.

 [roamresearch]: https://www.roamresearch.com/
 [org]: https://orgmode.org/
-[badge-license]: https://img.shields.io/badge/license-GPL_3-green.svg
-[docs]: https://www.orgroam.com/manual/
+[gpl3-badge]: https://img.shields.io/badge/license-GPL_3-green.svg
+[gpl3]: http://www.gnu.org/licenses/gpl-3.0.txt
+[melpa-badge]: https://melpa.org/packages/org-roam-badge.svg
+[melpa]: https://melpa.org/#/org-roam
+[release-badge]: https://img.shields.io/github/v/release/org-roam/org-roam
+[release]: https://github.com/org-roam/org-roam/releases
+[docs]: https://www.orgroam.com/manual.html
 [discourse]: https://org-roam.discourse.group/
 [slack]: https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg
 [issues]: https://github.com/org-roam/org-roam/issues
+[faq]: https://www.orgroam.com/manual.html#FAQ
--- a/doc/Makefile
+++ b/doc/Makefile
@ -27,12 +27,9 @@ dir: org-roam.info
 	@printf "Generating $@\n"
 	@$(MAKEINFO) --html --no-split $(MANUAL_HTML_ARGS) $<

-html-dir: 
-	@printf "Generating org-roam/*.html\n"
-	@$(MAKEINFO) --html $(MANUAL_HTML_ARGS) org-roam.texi
-	mv org-roam manual
-	cp -r assets manual
-	cp -r images manual
+html-dir:
+	@$(MAKEINFO) --html --no-split $(MANUAL_HTML_ARGS) org-roam.texi
+	mv org-roam.html manual.html

 %.pdf: %.texi
 	@printf "Generating $@\n"
--- a/doc/assets/page.css
+++ b/doc/assets/page.css
@ -1,442 +1,68 @@
-/* Import Inter font */
-/* More info at https://github.com/xz/fonts */
-@import url("https://fonts.xz.style/serve/inter.css");
-
 :root {
-  --nc-font-sans: "Inter", -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto,
-    Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif,
-    "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol";
-  --nc-font-mono: "Courier New", Courier, "Ubuntu Mono", "Liberation Mono",
-    monospace;
-  --nc-tx-1: #000000;
-  --nc-tx-2: #1a1a1a;
-  --nc-bg-1: #ffffff;
-  --nc-bg-2: #f6f8fa;
-  --nc-bg-3: #e5e7eb;
-  --nc-lk-1: #0070f3;
-  --nc-lk-2: #0366d6;
-  --nc-lk-tx: #ffffff;
-  --nc-ac-1: #79ffe1;
-  --nc-ac-tx: #0c4047;
-}
-
-@media (prefers-color-scheme: dark) {
-  :root {
-    --nc-tx-1: #ffffff;
-    --nc-tx-2: #eeeeee;
-    --nc-bg-1: #000000;
-    --nc-bg-2: #111111;
-    --nc-bg-3: #222222;
-    --nc-lk-1: #3291ff;
-    --nc-lk-2: #0070f3;
-    --nc-lk-tx: #ffffff;
-    --nc-ac-1: #7928ca;
-    --nc-ac-tx: #ffffff;
-  }
-}
-
-* {
-  /* Reset margins and padding */
-  margin: 0;
-  padding: 0;
-}
-
-address,
-area,
-article,
-aside,
-audio,
-blockquote,
-datalist,
-details,
-dl,
-fieldset,
-figure,
-form,
-input,
-iframe,
-img,
-meter,
-nav,
-ol,
-optgroup,
-option,
-output,
-p,
-pre,
-progress,
-ruby,
-section,
-table,
-textarea,
-ul,
-video {
-  /* Margins for most elements */
-  margin-bottom: 1rem;
-}
-
-html,
-input,
-select,
-button {
-  /* Set body font family and some finicky elements */
-  font-family: var(--nc-font-sans);
+  --border: #526980;
+  --code: #007;
 }

 body {
-  /* Center body in page */
-  margin: 0 auto;
-  max-width: 750px;
-  padding: 2rem;
-  border-radius: 6px;
-  overflow-x: hidden;
-  background: var(--nc-bg-1);
-
-  /* Main body text */
-  color: var(--nc-tx-2);
-  font-size: 1.03rem;
-  line-height: 1.5;
+    margin: 5ex 10ex;
+    max-width: 80ex;
+    line-height: 1.5;
+    font-family: sans-serif;
 }

-::selection {
-  /* Set background color for selected text */
-  background: var(--nc-ac-1);
-  color: var(--nc-ac-tx);
+h1, h2, h3 {
+    font-weight: normal;
 }

-p {
-  margin-bottom: 1rem;
-}
-
-h1,
-h2,
-h3,
-h4,
-h5,
-h6 {
-  line-height: 1;
-  color: var(--nc-tx-1);
-  padding-top: 0.875rem;
-}
-
-h1,
-h2,
-h3 {
-  color: var(--nc-tx-1);
-  padding-bottom: 2px;
-  margin-bottom: 8px;
-  border-bottom: 1px solid var(--nc-bg-2);
-}
-
-h4,
-h5,
-h6 {
-  margin-bottom: 0.3rem;
-}
-
-h1 {
-  font-size: 2.25rem;
-}
-
-h2 {
-  font-size: 1.85rem;
-}
-
-h3 {
-  font-size: 1.55rem;
-}
-
-h4 {
-  font-size: 1.25rem;
-}
-
-h5 {
-  font-size: 1rem;
-}
-
-h6 {
-  font-size: 0.875rem;
-}
-
-a {
-  color: var(--nc-lk-1);
-}
-
-a:hover {
-  color: var(--nc-lk-2);
-}
-
-abbr:hover {
-  /* Set the '?' cursor while hovering an abbreviation */
-  cursor: help;
-}
-
-blockquote {
-  padding: 1.5rem;
-  background: var(--nc-bg-2);
-  border-left: 5px solid var(--nc-bg-3);
-}
-
-abbr {
-  cursor: help;
-}
-
-blockquote *:last-child {
-  padding-bottom: 0;
-  margin-bottom: 0;
-}
-
-header {
-  background: var(--nc-bg-2);
-  border-bottom: 1px solid var(--nc-bg-3);
-  padding: 2rem 1.5rem;
-
-  /* This sets the right and left margins to cancel out the body's margins. It's width is still the same, but the background stretches across the page's width. */
-
-  margin: -2rem calc(0px - (50vw - 50%)) 2rem;
-
-  /* Shorthand for:
-
-	margin-top: -2rem;
-	margin-bottom: 2rem;
-
-	margin-left: calc(0px - (50vw - 50%));
-	margin-right: calc(0px - (50vw - 50%)); */
-
-  padding-left: calc(50vw - 50%);
-  padding-right: calc(50vw - 50%);
-}
-
-header h1,
-header h2,
-header h3 {
-  padding-bottom: 0;
-  border-bottom: 0;
-}
-
-header > *:first-child {
-  margin-top: 0;
-  padding-top: 0;
-}
-
-header > *:last-child {
-  margin-bottom: 0;
-}
-
-.button,
-button,
-input[type="submit"],
-input[type="reset"],
-input[type="button"] {
-  font-size: 1rem;
-  display: inline-block;
-  padding: 6px 12px;
-  text-align: center;
-  text-decoration: none;
-  white-space: nowrap;
-  background: var(--nc-lk-1);
-  color: var(--nc-lk-tx);
-  border: 0;
-  border-radius: 4px;
-  box-sizing: border-box;
-  cursor: pointer;
-  color: var(--nc-lk-tx);
-}
-
-.button[disabled],
-button[disabled],
-input[type="submit"][disabled],
-input[type="reset"][disabled],
-input[type="button"][disabled] {
-  cursor: default;
-  opacity: 0.5;
-
-  /* Set the [X] cursor while hovering a disabled link */
-  cursor: not-allowed;
-}
-
-.button:focus,
-.button:hover,
-button:focus,
-button:hover,
-input[type="submit"]:focus,
-input[type="submit"]:hover,
-input[type="reset"]:focus,
-input[type="reset"]:hover,
-input[type="button"]:focus,
-input[type="button"]:hover {
-  background: var(--nc-lk-2);
-}
-
-code,
-pre,
-kbd,
-samp {
-  /* Set the font family for monospaced elements */
-  font-family: var(--nc-font-mono);
-}
-
-code,
-samp,
-kbd,
-pre {
-  /* The main preformatted style. This is changed slightly across different cases. */
-  background: var(--nc-bg-2);
-  border: 1px solid var(--nc-bg-3);
-  border-radius: 4px;
-  padding: 3px 6px;
-  font-size: 0.9rem;
-}
-
-kbd {
-  /* Makes the kbd element look like a keyboard key */
-  border-bottom: 3px solid var(--nc-bg-3);
+pre, code {
+    font-family: x, monospace;
 }

 pre {
-  padding: 1rem 1.4rem;
-  max-width: 100%;
-  overflow: auto;
+    padding: 1ex;
+    background: #eee;
+    border: solid 1px #ddd;
+    min-width: 0;
+    font-size: 80%;
+    overflow: auto;
 }

-pre code {
-  /* When <code> is in a <pre>, reset it's formatting to blend in */
-  background: inherit;
-  font-size: inherit;
-  color: inherit;
-  border: 0;
-  padding: 0;
-  margin: 0;
-}
-
-code pre {
-  /* When <pre> is in a <code>, reset it's formatting to blend in */
-  display: inline;
-  background: inherit;
-  font-size: inherit;
-  color: inherit;
-  border: 0;
-  padding: 0;
-  margin: 0;
-}
-
-details {
-  /* Make the <details> look more "clickable" */
-  padding: 0.6rem 1rem;
-  background: var(--nc-bg-2);
-  border: 1px solid var(--nc-bg-3);
-  border-radius: 4px;
-}
-
-summary {
-  /* Makes the <summary> look more like a "clickable" link with the pointer cursor */
-  cursor: pointer;
-  font-weight: bold;
-}
-
-details[open] {
-  /* Adjust the <details> padding while open */
-  padding-bottom: 0.75rem;
-}
-
-details[open] summary {
-  /* Adjust the <details> padding while open */
-  margin-bottom: 6px;
-}
-
-details[open] > *:last-child {
-  /* Resets the bottom margin of the last element in the <details> while <details> is opened. This prevents double margins/paddings. */
-  margin-bottom: 0;
-}
-
-dt {
-  font-weight: bold;
-}
-
-dd::before {
-  /* Add an arrow to data table definitions */
-  content: "→ ";
-}
-
-hr {
-  /* Reset the border of the <hr> separator, then set a better line */
-  border: 0;
-  border-bottom: 1px solid var(--nc-bg-3);
-  margin: 1rem auto;
-}
-
-fieldset {
-  margin-top: 1rem;
-  padding: 2rem;
-  border: 1px solid var(--nc-bg-3);
-  border-radius: 4px;
-}
-
-legend {
-  padding: auto 0.5rem;
-}
-
-textarea {
-  /* Don't let the <textarea> extend off the screen naturally or when dragged by the user */
-  max-width: 100%;
-}
-
-ol,
-ul {
-  /* Replace the browser default padding */
-  padding-left: 2rem;
-}
-
-li {
-  margin-top: 0.4rem;
-}
-
-ul ul,
-ol ul,
-ul ol,
-ol ol {
-  margin-bottom: 0;
-}
-
-mark {
-  padding: 3px 6px;
-  background: var(--nc-ac-1);
-  color: var(--nc-ac-tx);
-}
-
-textarea,
-select,
-input {
-  padding: 6px 12px;
-  margin-bottom: 0.5rem;
-  background: var(--nc-bg-2);
-  color: var(--nc-tx-2);
-
-  /* Set a border of the same color as the main background. It isn't visible on idle, but prevents the cell from growing in size when a darker border is set on focus. */
-  border: 1px solid var(--nc-bg-2);
-  border-radius: 4px;
-  box-shadow: none;
-  box-sizing: border-box;
-}
-
-textarea:focus,
-select:focus,
-input[type]:focus {
-  border: 1px solid var(--nc-bg-3);
-
-  /* Reset any browser default outlines */
-  outline: 0;
+code {
+    color: var(--code);
 }

 img {
-  max-width: 100%;
+    max-width: 100%;
 }

-/* Customizations */
-.menu-comment {
-  font-weight: bold;
-  border: 0;
-  margin: 0;
-  padding: 0;
-  font-size: 1.2rem;
+table {
+  border-collapse: collapse;
+  width: 100%;
+}
+
+pre.menu-comment {
+  background: none;
+  border: none;
+  font-family: sans-serif;
+  padding: 0;
+  margin: 0;
+  font-size: 100%;
+}
+
+thead {
+  border-bottom: 1px solid var(--border);
+}
+
+tfoot {
+  border-top: 1px solid var(--border);
+}
+
+blockquote {
+  margin-left: 1rem;
+  font-style: italic;
+  font-family: serif;
+  border-left: 3px solid;
+  border-left-color: currentcolor;
+  border-color: var(--text-color);
+  padding-left: 1em;
 }
--- a/doc/index.html
+++ b/doc/index.html
@ -93,7 +93,7 @@
        You can find us on Discourse and Slack.
        
        <ul>
-            <li>Read our documentation within Emacs, or on the <a href="https://www.orgroam.com/manual/">Online Manual</a></li>
+            <li>Read our documentation within Emacs, or on the <a href="https://www.orgroam.com/manual.html">Online Manual</a></li>
            <li>Participate in our forum discussions on <a href="https://org-roam.discourse.group">Discourse</a></li>
            <li>Chat with us on <a href="https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg">Slack</a></li>
          </ul>
@ -120,13 +120,6 @@
            >org-roam-server</a
          >
        </div>
-        <div class="row">
-          <a
-            class="content footer-links"
-            href="https://github.com/org-roam/company-org-roam"
-            >company-org-roam</a
-          >
-        </div>
      </div>

      <div class="col">
--- a/doc/org-roam.org
+++ b/doc/org-roam.org
--- a/doc/org-roam.texi
+++ b/doc/org-roam.texi
--- a/makem.sh
+++ b/makem.sh
--- a/org-roam-buffer.el
+++ b/org-roam-buffer.el
@ -1,336 +0,0 @@
-;;; org-roam-buffer.el --- Metadata buffer -*- coding: utf-8; lexical-binding: t; -*-
-
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/org-roam/org-roam
-;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.2
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
-
-;; This file is NOT part of GNU Emacs.
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation; either version 3, or (at your option)
-;; any later version.
-;;
-;; This program is distributed in the hope that it will be useful,
-;; but WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;; GNU General Public License for more details.
-;;
-;; You should have received a copy of the GNU General Public License
-;; along with GNU Emacs; see the file COPYING.  If not, write to the
-;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
-;; Boston, MA 02110-1301, USA.
-
-;;; Commentary:
-;;
-;; This library provides the org-roam-buffer functionality for org-roam
-;;; Code:
-;;;; Library Requires
-(eval-when-compile (require 'subr-x))
-(require 'cl-lib)
-(require 'dash)
-(require 's)
-(require 'f)
-(require 'ol)
-
-(defvar org-roam-directory)
-(defvar org-link-frame-setup)
-(defvar org-return-follows-link)
-(defvar org-roam-backlinks-mode)
-(defvar org-roam-last-window)
-(defvar org-ref-cite-types) ;; in org-ref-core.el
-(defvar org-roam-mode)
-(defvar org-roam--org-link-bracket-typed-re)
-
-(declare-function org-roam-db--ensure-built   "org-roam-db")
-(declare-function org-roam--extract-ref       "org-roam")
-(declare-function org-roam--extract-titles    "org-roam")
-(declare-function org-roam--get-title-or-slug "org-roam")
-(declare-function org-roam--get-backlinks     "org-roam")
-(declare-function org-roam-backlinks-mode     "org-roam")
-(declare-function org-roam-mode               "org-roam")
-(declare-function org-roam--find-file         "org-roam")
-(declare-function org-roam-format-link        "org-roam")
-(declare-function org-roam-link-get-path      "org-roam-link")
-
-(defcustom org-roam-buffer-position 'right
-  "Position of `org-roam' buffer.
-Valid values are
- * left,
- * right,
- * top,
- * bottom."
-  :type '(choice (const left)
-                 (const right)
-                 (const top)
-                 (const bottom))
-  :group 'org-roam)
-
-(defcustom org-roam-buffer-width 0.33
-  "Width of `org-roam' buffer.
-Has an effect if and only if `org-roam-buffer-position' is `left' or `right'."
-  :type 'number
-  :group 'org-roam)
-
-(defcustom org-roam-buffer-height 0.27
-  "Height of `org-roam' buffer.
-Has an effect if and only if `org-roam-buffer-position' is `top' or `bottom'."
-  :type 'number
-  :group 'org-roam)
-
-
-(defcustom org-roam-buffer "*org-roam*"
-  "Org-roam buffer name."
-  :type 'string
-  :group 'org-roam)
-
-(defcustom org-roam-buffer-prepare-hook '(org-roam-buffer--insert-title
-                                          org-roam-buffer--insert-backlinks
-                                          org-roam-buffer--insert-ref-links)
-  "Hook run in the `org-roam-buffer' before it is displayed."
-  :type 'hook
-  :group 'org-roam)
-
-(defcustom org-roam-buffer-window-parameters nil
-  "Additional window parameters for the `org-roam-buffer' side window.
-For example: (setq org-roam-buffer-window-parameters '((no-other-window . t)))"
-  :type '(alist)
-  :group 'org-roam)
-
-(defvar org-roam-buffer--current nil
-  "Currently displayed file in `org-roam' buffer.")
-
-(defun org-roam-buffer--find-file (file)
-  "Open FILE in the window `org-roam' was called from."
-  (setq file (expand-file-name file))
-  (if (and org-roam-last-window (window-valid-p org-roam-last-window))
-      (progn (with-selected-window org-roam-last-window
-               (org-roam--find-file file))
-             (select-window org-roam-last-window))
-    (org-roam--find-file file)))
-
-(defun org-roam-buffer--insert-title ()
-  "Insert the org-roam-buffer title."
-  (insert (propertize (org-roam--get-title-or-slug
-                       (buffer-file-name org-roam-buffer--current))
-                      'font-lock-face
-                      'org-document-title)))
-
-(defun org-roam-buffer--pluralize (string number)
-  "Conditionally pluralize STRING if NUMBER is above 1."
-  (let ((l (pcase number
-             ((pred (listp)) (length number))
-             ((pred (integerp)) number)
-             (wrong-type (signal 'wrong-type-argument
-                                 `((listp integerp)
-                                   ,wrong-type))))))
-    (concat string (when (> l 1) "s"))))
-
-(defun org-roam-buffer-expand-links (content orig-path)
-  "Crawl CONTENT for relative links and corrects them to be correctly displayed.
-ORIG-PATH is the path where the CONTENT originated."
-  (with-temp-buffer
-    (insert content)
-    (goto-char (point-min))
-    (let (link link-type)
-      (while (re-search-forward org-roam--org-link-bracket-typed-re (point-max) t)
-        (setq link-type (match-string 1)
-              link (match-string 2))
-        (when (and (string-equal link-type "file")
-                   (f-relative-p link))
-          (replace-match (org-roam-link-get-path (expand-file-name link (file-name-directory orig-path)))
-                         nil t nil 2))))
-    (buffer-string)))
-
-(defun org-roam-buffer--insert-ref-links ()
-  "Insert ref backlinks for the current buffer."
-  (when-let ((path (cdr (with-temp-buffer
-                          (insert-buffer-substring org-roam-buffer--current)
-                          (org-roam--extract-ref)))))
-    (if-let* ((key-backlinks (org-roam--get-backlinks path))
-              (grouped-backlinks (--group-by (nth 0 it) key-backlinks)))
-        (progn
-          (insert (let ((l (length key-backlinks)))
-                    (format "\n\n* %d %s\n"
-                            l (org-roam-buffer--pluralize "Ref Backlink" l))))
-          (dolist (group grouped-backlinks)
-            (let ((file-from (car group))
-                  (bls (cdr group)))
-              (insert (format "** %s\n"
-                              (org-roam-format-link file-from
-                                                     (org-roam--get-title-or-slug file-from)
-                                                     "file")))
-              (dolist (backlink bls)
-                (pcase-let ((`(,file-from _ ,props) backlink))
-                  (insert (propertize (org-roam-buffer-expand-links (plist-get props :content) file-from)
-                           'help-echo "mouse-1: visit backlinked note"
-                           'file-from file-from
-                           'file-from-point (plist-get props :point)))
-                  (insert "\n\n"))))))
-      (insert "\n\n* No ref backlinks!"))))
-
-(defun org-roam-buffer--insert-backlinks ()
-  "Insert the org-roam-buffer backlinks string for the current buffer."
-  (if-let* ((file-path (buffer-file-name org-roam-buffer--current))
-            (titles (with-current-buffer org-roam-buffer--current
-                      (org-roam--extract-titles)))
-            (backlinks (org-roam--get-backlinks (push file-path titles)))
-            (grouped-backlinks (--group-by (nth 0 it) backlinks)))
-      (progn
-        (insert (let ((l (length backlinks)))
-                     (format "\n\n* %d %s\n"
-                             l (org-roam-buffer--pluralize "Backlink" l))))
-        (dolist (group grouped-backlinks)
-          (let ((file-from (car group))
-                (bls (mapcar (lambda (row)
-                                 (nth 2 row)) (cdr group))))
-            (insert (format "** %s\n"
-                            (org-roam-format-link file-from
-                                                   (org-roam--get-title-or-slug file-from)
-                                                   "file")))
-            ;; Sort backlinks according to time of occurrence in buffer
-            (setq bls (seq-sort-by (lambda (bl)
-                                     (plist-get bl :point))
-                                   #'<
-                                   bls))
-            (dolist (props bls)
-              (insert "*** "
-                      (if-let ((outline (plist-get props :outline)))
-                          (-> outline
-                              (string-join " > ")
-                              (org-roam-buffer-expand-links file-from))
-                        "Top")
-                      "\n"
-                      (propertize
-                       (s-trim (s-replace "\n" " "
-                                          (org-roam-buffer-expand-links (plist-get props :content) file-from)))
-                       'help-echo "mouse-1: visit backlinked note"
-                       'file-from file-from
-                       'file-from-point (plist-get props :point))
-                      "\n\n")))))
-    (insert "\n\n* No backlinks!")))
-
-(defun org-roam-buffer-update ()
-  "Update the `org-roam-buffer'."
-  (org-roam-db--ensure-built)
-  (let* ((source-org-roam-directory org-roam-directory))
-    (with-current-buffer org-roam-buffer
-      ;; When dir-locals.el is used to override org-roam-directory,
-      ;; org-roam-buffer should have a different local org-roam-directory and
-      ;; default-directory, as relative links are relative from the overridden
-      ;; org-roam-directory.
-      (setq-local org-roam-directory source-org-roam-directory)
-      (setq-local default-directory source-org-roam-directory)
-      ;; Locally overwrite the file opening function to re-use the
-      ;; last window org-roam was called from
-      (setq-local org-link-frame-setup
-                  (cons '(file . org-roam--find-file) org-link-frame-setup))
-      (let ((inhibit-read-only t))
-        (erase-buffer)
-        (unless (eq major-mode 'org-mode)
-          (org-mode))
-        (unless org-roam-backlinks-mode
-          (org-roam-backlinks-mode))
-        (make-local-variable 'org-return-follows-link)
-        (setq org-return-follows-link t)
-        (run-hooks 'org-roam-buffer-prepare-hook)
-        (read-only-mode 1)))))
-
-
-(cl-defun org-roam-buffer--update-maybe (&key redisplay)
-  "Reconstructs `org-roam-buffer'.
-This needs to be quick or infrequent, because this is run at
-`post-command-hook'.  If REDISPLAY, force an update of
-`org-roam-buffer'."
-  (let ((buffer (window-buffer)))
-    (when (and (or redisplay
-                   (not (eq org-roam-buffer--current buffer)))
-               (eq 'visible (org-roam-buffer--visibility))
-               (buffer-file-name buffer))
-      (setq org-roam-buffer--current buffer)
-      (org-roam-buffer-update))))
-
-;;;; Toggling the org-roam buffer
-(define-inline org-roam-buffer--visibility ()
-  "Return whether the current visibility state of the org-roam buffer.
-Valid states are 'visible, 'exists and 'none."
-  (declare (side-effect-free t))
-  (inline-quote
-   (cond
-    ((get-buffer-window org-roam-buffer) 'visible)
-    ((get-buffer org-roam-buffer) 'exists)
-    (t 'none))))
-
-(defun org-roam-buffer--set-width (width)
-  "Set the width of `org-roam-buffer' to `WIDTH'."
-  (unless (one-window-p)
-    (let ((window-size-fixed)
-          (w (max width window-min-width)))
-      (cond
-       ((> (window-width) w)
-        (shrink-window-horizontally  (- (window-width) w)))
-       ((< (window-width) w)
-        (enlarge-window-horizontally (- w (window-width))))))))
-
-(defun org-roam-buffer--set-height (height)
-  "Set the height of `org-roam-buffer' to `HEIGHT'."
-  (unless (one-window-p)
-    (let ((window-size-fixed)
-          (h (max height window-min-height)))
-      (cond
-       ((> (window-height) h)
-        (shrink-window  (- (window-height) h)))
-       ((< (window-height) h)
-        (enlarge-window (- h (window-height))))))))
-
-(defun org-roam-buffer--get-create ()
-  "Set up the `org-roam' buffer at `org-roam-buffer-position'."
-  (let ((position
-         (if (member org-roam-buffer-position '(right left top bottom))
-             org-roam-buffer-position
-           (let ((text-quoting-style 'grave))
-             (lwarn '(org-roam) :error
-                    "Invalid org-roam-buffer-position: %s. Defaulting to \\='right"
-                    org-roam-buffer-position))
-           'right)))
-    (save-selected-window
-      (-> (get-buffer-create org-roam-buffer)
-          (display-buffer-in-side-window
-           `((side . ,position)
-             (window-parameters . ,org-roam-buffer-window-parameters)))
-          (select-window))
-      (pcase position
-        ((or 'right 'left)
-         (org-roam-buffer--set-width
-          (round (* (frame-width)  org-roam-buffer-width))))
-        ((or 'top  'bottom)
-         (org-roam-buffer--set-height
-          (round (* (frame-height) org-roam-buffer-height))))))))
-
-(defun org-roam-buffer-activate ()
-  "Activate display of the `org-roam-buffer'."
-  (interactive)
-  (unless org-roam-mode (org-roam-mode))
-  (setq org-roam-last-window (get-buffer-window))
-  (org-roam-buffer--get-create))
-
-(defun org-roam-buffer-deactivate ()
-  "Deactivate display of the `org-roam-buffer'."
-  (interactive)
-  (setq org-roam-last-window (get-buffer-window))
-  (delete-window (get-buffer-window org-roam-buffer)))
-
-(defun org-roam-buffer-toggle-display ()
-  "Toggle display of the `org-roam-buffer'."
-  (interactive)
-  (pcase (org-roam-buffer--visibility)
-    ('visible (org-roam-buffer-deactivate))
-    ((or 'exists 'none) (org-roam-buffer-activate))))
-
-(provide 'org-roam-buffer)
-
-;;; org-roam-buffer.el ends here
--- a/org-roam-capture.el
+++ b/org-roam-capture.el
--- a/org-roam-compat.el
+++ b/org-roam-compat.el
@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.2
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))

 ;; This file is NOT part of GNU Emacs.

@ -34,69 +34,7 @@
 ;;;; Library Requires

 ;;; Obsolete aliases (remove after next major release)
-;;;; Functions
-(define-obsolete-function-alias 'org-roam--capture-get-point 'org-roam-capture--get-point
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-build-cache 'org-roam-db-build-cache
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-sql         'org-roam-db-query
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam--db-clear   'org-roam-db--clear
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-show-graph  'org-roam-graph-show
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam--maybe-update-buffer
-  'org-roam-buffer--update-maybe "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam--current-visibility
-  'org-roam-buffer--visibility "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-update         'org-roam-buffer-update
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam--set-width     'org-roam-buffer--set-width
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam--set-height    'org-roam-buffer--set-height
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam--set-up-buffer 'org-roam-buffer--get-create
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-today 'org-roam-dailies-today
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-tomorrow 'org-roam-dailies-tomorrow
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-yesterday 'org-roam-dailies-yesterday
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-date 'org-roam-dailies-date
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-graph-show  'org-roam-graph
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-graph-build 'org-roam-graph
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-find-index 'org-roam-jump-to-index
-  "org-roam 1.1.0")
-(define-obsolete-function-alias 'org-roam--pluralize 'org-roam-buffer--pluralize
-  "org-roam 1.1.0")
-(define-obsolete-function-alias 'org-roam--capture 'org-roam-capture--capture
-  "org-roam 1.1.0")
-(define-obsolete-function-alias 'org-roam-db--maybe-update 'org-roam-db--update-maybe
-  "org-roam 1.1.0")
-(define-obsolete-function-alias 'org-roam-db--clear 'org-roam-db-clear
-  "org-roam 1.2.0")
-
-;;;; Variables
-(define-obsolete-variable-alias 'org-roam-graphviz-extra-options
-  'org-roam-graph-extra-config "org-roam 1.0.0")
-(define-obsolete-variable-alias 'org-roam-grapher-extra-options
-  'org-roam-graph-extra-config "org-roam 1.0.0")
-(define-obsolete-variable-alias 'org-roam-graph-node-shape
-  'org-roam-graph-node-extra-config "org-roam 1.0.0")
-(define-obsolete-variable-alias 'org-roam--db-connection
-  'org-roam-db--connection "org-roam 1.0.0")
-(define-obsolete-variable-alias 'org-roam--current-buffer
-  'org-roam-buffer--current "org-roam 1.0.0")
-(define-obsolete-variable-alias 'org-roam-date-title-format
-  'org-roam-dailies-capture-templates "org-roam 1.0.0")
-(define-obsolete-variable-alias 'org-roam-date-filename-format
-  'org-roam-dailies-capture-templates "org-roam 1.0.0")
-(make-obsolete-variable 'org-roam-buffer-no-delete-other-windows
-  'org-roam-buffer-window-parameters "org-roam 1.1.1")
+;;; Obsolete functions

 (provide 'org-roam-compat)

--- a/org-roam-completion.el
+++ b/org-roam-completion.el
@ -5,9 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.2
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
-
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 ;; This file is NOT part of GNU Emacs.

 ;; This program is free software; you can redistribute it and/or modify
@ -27,89 +26,81 @@

 ;;; Commentary:
 ;;
-;; This library provides completion for org-roam.
+;; This library provides completion-at-point functions for Org-roam.
+;;
+;; The two main functions provided to capf are:
+;;
+;;    `org-roam-complete-link-at-point' provides completions to nodes
+;;    within link brackets
+;;
+;;    `org-roam-complete-everywhere' provides completions for nodes everywhere,
+;;    matching the symbol at point
+;;
 ;;; Code:
-;;;; Library Requires
 (require 'cl-lib)
-(require 's)
+(require 'org-element)

-(defvar helm-pattern)
-(declare-function helm "ext:helm")
-(declare-function helm-make-source "ext:helm-source" (name class &rest args) t)
+(declare-function org-roam--get-titles "org-roam")

-(defcustom org-roam-completion-system 'default
-  "The completion system to be used by `org-roam'."
-  :type '(radio
-          (const :tag "Default" default)
-          (const :tag "Ido" ido)
-          (const :tag "Ivy" ivy)
-          (const :tag "Helm" helm)
-          (function :tag "Custom function"))
-  :group 'org-roam)
-
-(defcustom org-roam-completion-ignore-case t
-  "Whether to ignore case in Org-roam `completion-at-point' completions."
+(defcustom org-roam-completion-everywhere nil
+  "When non-nil, provide link completion matching outside of Org links."
  :group 'org-roam
  :type 'boolean)

-(defun org-roam-completion--helm-candidate-transformer (candidates _source)
-  "Transforms CANDIDATES for Helm-based completing read.
-SOURCE is not used."
-  (let ((prefix (propertize "[?] "
-                            'face 'helm-ff-prefix)))
-    (cons (propertize helm-pattern
-                      'display (concat prefix helm-pattern))
-          candidates)))
+(defvar org-roam-completion-functions (list #'org-roam-complete-link-at-point
+                                            #'org-roam-complete-everywhere)
+  "List of functions to be used with `completion-at-point' for Org-roam.")

-(cl-defun org-roam-completion--completing-read (prompt choices &key
-                                                       require-match initial-input
-                                                       action)
-  "Present a PROMPT with CHOICES and optional INITIAL-INPUT.
-If REQUIRE-MATCH is t, the user must select one of the CHOICES.
-Return user choice."
-  (let (res)
-    (setq res
-          (cond
-           ((eq org-roam-completion-system 'ido)
-            (let ((candidates (mapcar #'car choices)))
-              (ido-completing-read prompt candidates nil require-match initial-input)))
-           ((eq org-roam-completion-system 'default)
-            (completing-read prompt choices nil require-match initial-input))
-           ((eq org-roam-completion-system 'ivy)
-            (if (fboundp 'ivy-read)
-                (ivy-read prompt choices
-                          :initial-input initial-input
-                          :require-match require-match
-                          :action (prog1 action
-                                    (setq action nil))
-                          :caller 'org-roam--completing-read)
-              (user-error "Please install ivy from \
-https://github.com/abo-abo/swiper")))
-           ((eq org-roam-completion-system 'helm)
-            (unless (and (fboundp 'helm)
-                         (fboundp 'helm-make-source))
-              (user-error "Please install helm from \
-https://github.com/emacs-helm/helm"))
-            (let ((source (helm-make-source prompt 'helm-source-sync
-                            :candidates (mapcar #'car choices)
-                            :filtered-candidate-transformer
-                            (and (not require-match)
-                                 #'org-roam-completion--helm-candidate-transformer)))
-                  (buf (concat "*org-roam "
-                               (s-downcase (s-chop-suffix ":" (s-trim prompt)))
-                               "*")))
-              (or (helm :sources source
-                        :action (if action
-                                    (prog1 action
-                                      (setq action nil))
-                                  #'identity)
-                        :prompt prompt
-                        :input initial-input
-                        :buffer buf)
-                  (keyboard-quit))))))
-    (if action
-        (funcall action res)
-      res)))
+(defconst org-roam-bracket-completion-re
+  "\\[\\[\\(\\(?:roam:\\)?\\)\\([^z-a]*\\)]]"
+  "Regex for completion within link brackets.
+We use this as a substitute for `org-link-bracket-re', because
+`org-link-bracket-re' requires content within the brackets for a match.")
+
+(defun org-roam-complete-everywhere ()
+  "Provides completions for links for any word at point.
+This is a `completion-at-point' function, and is active when
+`org-roam-completion-everywhere' is non-nil."
+  (when (and org-roam-completion-everywhere
+             (thing-at-point 'word)
+             (not (save-match-data (org-in-regexp org-link-any-re))))
+    (let ((bounds (bounds-of-thing-at-point 'word)))
+      (list (car bounds) (cdr bounds)
+            (completion-table-dynamic
+             (lambda (_)
+               (funcall #'org-roam--get-titles)))
+            :exit-function
+            (lambda (str _status)
+              (delete-char (- (length str)))
+              (insert "[[roam:" str "]]"))))))
+
+(defun org-roam-complete-link-at-point ()
+  "Do appropriate completion for the link at point."
+  (let (roam-p start end)
+    (when (org-in-regexp org-roam-bracket-completion-re 1)
+      (setq roam-p (not (string-blank-p (match-string 1)))
+            start (match-beginning 2)
+            end (match-end 2))
+      (list start end
+            (completion-table-dynamic
+             (lambda (_)
+               (funcall #'org-roam--get-titles)))
+            :exit-function
+            (lambda (str &rest _)
+              (delete-char (- 0 (length str)))
+              (insert (concat (unless roam-p "roam:")
+                              str))
+              (forward-char 2))))))
+
+(defun org-roam-complete-at-point ()
+  "."
+  (run-hook-with-args-until-success 'org-roam-completion-functions))
+
+(defun org-roam--register-completion-functions ()
+  "."
+  (add-hook 'completion-at-point-functions #'org-roam-complete-at-point nil t))
+
+(add-hook 'org-roam-find-file-hook #'org-roam--register-completion-functions)

 (provide 'org-roam-completion)

--- a/org-roam-dailies.el
+++ b/org-roam-dailies.el
@ -1,12 +1,14 @@
-;;; org-roam-dailies.el --- Daily notes for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
+;;; org-roam-dailies.el --- Daily-notes for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
 ;;;
 ;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020 Leo Vivier <leo.vivier+dev@gmail.com>

 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;;      Leo Vivier <leo.vivier+dev@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.2
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))

 ;; This file is NOT part of GNU Emacs.

@ -27,110 +29,322 @@

 ;;; Commentary:
 ;;
-;; This library provides functionality for creating daily notes. This is a
+;; This library provides functionality for creating daily-notes. This is a
 ;; concept borrowed from Roam Research.
 ;;
 ;;; Code:
 ;;; Library Requires
 (require 'org-capture)
 (require 'org-roam-capture)
-(require 'org-roam-macs)
+(require 'f)
+
+;;;; Declarations
+(defvar org-roam-directory)
+(defvar org-roam-file-extensions)
+(declare-function org-roam-file-p        "org-roam")
+
+;;;; Faces
+(defface org-roam-dailies-calendar-note
+  '((t :inherit (org-link) :underline nil))
+  "Face for dates with a daily-note in the calendar."
+  :group 'org-roam-faces)
+
+;;;; Customizable variables
+(defcustom org-roam-dailies-directory "daily/"
+  "Path to daily-notes.
+This path is relative to `org-roam-directory'."
+  :group 'org-roam
+  :type 'string)
+
+(defcustom org-roam-dailies-find-file-hook nil
+  "Hook that is run right after navigating to a daily-note."
+  :group 'org-roam
+  :type 'hook)

 (defcustom org-roam-dailies-capture-templates
-  '(("d" "daily" plain (function org-roam-capture--get-point)
-     ""
-     :immediate-finish t
-     :file-name "%<%Y-%m-%d>"
-     :head "#+title: %<%Y-%m-%d>"))
-  "Capture templates for daily notes in Org-roam."
+  `(("d" "default" entry
+     "* %?"
+     :if-new (file+head "%<%Y-%m-%d>.org"
+                        "#+title: %<%Y-%m-%d>\n")))
+  "Capture templates for daily-notes in Org-roam.
+See `org-roam-capture-templates' for the template documentation."
  :group 'org-roam
-  ;; Adapted from `org-capture-templates'
-  :type
-  '(repeat
-    (choice :value ("d" "daily" plain (function org-roam-capture--get-point)
-                    ""
-                    :immediate-finish t
-                    :file-name "%<%Y-%m-%d>"
-                    :head "#+title: %<%Y-%m-%d>")
-            (list :tag "Multikey description"
-                  (string :tag "Keys       ")
-                  (string :tag "Description"))
-            (list :tag "Template entry"
-                  (string :tag "Keys              ")
-                  (string :tag "Description       ")
-                  (const :format "" plain)
-                  (const :format "" (function org-roam-capture--get-point))
-                  (choice :tag "Template          "
-                          (string :tag "String"
-                                  :format "String:\n            \
-Template string   :\n%v")
-                          (list :tag "File"
-                                (const :format "" file)
-                                (file :tag "Template file     "))
-                          (list :tag "Function"
-                                (const :format "" function)
-                                (function :tag "Template function ")))
-                  (const :format "" :immediate-finish) (const :format "" t)
-                  (const :format "File name format  :" :file-name)
-                  (string :format " %v" :value "#+title: ${title}\n")
-                  (const :format "Header format     :" :head)
-                  (string :format "\n%v" :value "%<%Y%m%d%H%M%S>-${slug}")
-                  (plist :inline t
-                         :tag "Options"
-                         ;; Give the most common options as checkboxes
-                         :options
-                         (((const :format "%v " :prepend) (const t))
-                          ((const :format "%v " :jump-to-captured) (const t))
-                          ((const :format "%v " :empty-lines) (const 1))
-                          ((const :format "%v " :empty-lines-before) (const 1))
-                          ((const :format "%v " :empty-lines-after) (const 1))
-                          ((const :format "%v " :clock-in) (const t))
-                          ((const :format "%v " :clock-keep) (const t))
-                          ((const :format "%v " :clock-resume) (const t))
-                          ((const :format "%v " :time-prompt) (const t))
-                          ((const :format "%v " :tree-type) (const week))
-                          ((const :format "%v " :table-line-pos) (string))
-                          ((const :format "%v " :kill-buffer) (const t))
-                          ((const :format "%v " :unnarrowed) (const t))))))))
+  :type '(repeat
+          (choice (list :tag "Multikey description"
+                        (string :tag "Keys       ")
+                        (string :tag "Description"))
+                  (list :tag "Template entry"
+                        (string :tag "Keys           ")
+                        (string :tag "Description    ")
+                        (choice :tag "Capture Type   " :value entry
+                                (const :tag "Org entry" entry)
+                                (const :tag "Plain list item" item)
+                                (const :tag "Checkbox item" checkitem)
+                                (const :tag "Plain text" plain)
+                                (const :tag "Table line" table-line))
+                        (choice :tag "Template       "
+                                (string)
+                                (list :tag "File"
+                                      (const :format "" file)
+                                      (file :tag "Template file"))
+                                (list :tag "Function"
+                                      (const :format "" function)
+                                      (function :tag "Template function")))
+                        (plist :inline t
+                               ;; Give the most common options as checkboxes
+                               :options (((const :format "%v " :if-new)
+                                          (choice :tag "Node location"
+                                                  (list :tag "File"
+                                                        (const :format "" file)
+                                                        (string :tag "  File"))
+                                                  (list :tag "File & Head Content"
+                                                        (const :format "" file+head)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content"))
+                                                  (list :tag "File & Outline path"
+                                                        (const :format "" file+olp)
+                                                        (string :tag "  File")
+                                                        (list :tag "Outline path"
+                                                              (repeat (string :tag "Headline"))))
+                                                  (list :tag "File & Head Content & Outline path"
+                                                        (const :format "" file+head+olp)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content")
+                                                        (list :tag "Outline path"
+                                                              (repeat (string :tag "Headline"))))))
+                                         ((const :format "%v " :prepend) (const t))
+                                         ((const :format "%v " :immediate-finish) (const t))
+                                         ((const :format "%v " :jump-to-captured) (const t))
+                                         ((const :format "%v " :empty-lines) (const 1))
+                                         ((const :format "%v " :empty-lines-before) (const 1))
+                                         ((const :format "%v " :empty-lines-after) (const 1))
+                                         ((const :format "%v " :clock-in) (const t))
+                                         ((const :format "%v " :clock-keep) (const t))
+                                         ((const :format "%v " :clock-resume) (const t))
+                                         ((const :format "%v " :time-prompt) (const t))
+                                         ((const :format "%v " :tree-type) (const week))
+                                         ((const :format "%v " :unnarrowed) (const t))
+                                         ((const :format "%v " :table-line-pos) (string))
+                                         ((const :format "%v " :kill-buffer) (const t))))))))

-;; Declarations
-(defvar org-roam-mode)
-(declare-function org-roam--file-path-from-id "org-roam")
-(declare-function org-roam-mode               "org-roam")
-
-(defun org-roam-dailies--file-for-time (time)
-  "Create and find file for TIME."
-  (let ((org-roam-capture-templates org-roam-dailies-capture-templates)
-        (org-roam-capture--info (list (cons 'time time)))
-        (org-roam-capture--context 'dailies))
-    (setq org-roam-capture-additional-template-props (list :finalize 'find-file))
-    (org-roam-capture--capture)))
-
-(defun org-roam-dailies-today ()
-  "Create and find the daily note for today."
+;;;###autoload
+(defun org-roam-dailies-find-directory ()
+  "Find and open `org-roam-dailies-directory'."
  (interactive)
-  (unless org-roam-mode (org-roam-mode))
-  (org-roam-dailies--file-for-time (current-time)))
+  (find-file (expand-file-name org-roam-dailies-directory org-roam-directory)))

-(defun org-roam-dailies-tomorrow (n)
-  "Create and find the daily note for tomorrow.
-With numeric argument N, use N days in the future."
-  (interactive "p")
-  (unless org-roam-mode (org-roam-mode))
-  (org-roam-dailies--file-for-time (time-add (* n 86400) (current-time))))
+(defun org-roam-dailies--daily-note-p (&optional file)
+  "Return t if FILE is an Org-roam daily-note, nil otherwise.
+If FILE is not specified, use the current buffer's file-path."
+  (when-let ((path (expand-file-name
+                    (or file
+                        (buffer-file-name (buffer-base-buffer)))))
+             (directory (expand-file-name org-roam-dailies-directory org-roam-directory)))
+    (setq path (expand-file-name path))
+    (save-match-data
+      (and
+       (org-roam-file-p path)
+       (f-descendant-of-p path directory)))))

-(defun org-roam-dailies-yesterday (n)
-  "Create and find the file for yesterday.
-With numeric argument N, use N days in the past."
-  (interactive "p")
-  (unless org-roam-mode (org-roam-mode))
-  (org-roam-dailies-tomorrow (- n)))
+(defun org-roam-dailies--capture (time &optional goto)
+  "Capture an entry in a daily-note for TIME, creating it if necessary.
+When GOTO is non-nil, go the note without creating an entry."
+  (let ((org-roam-directory (expand-file-name org-roam-dailies-directory org-roam-directory)))
+    (org-roam-capture- :goto (when goto '(4))
+                       :node (org-roam-node-create)
+                       :templates org-roam-dailies-capture-templates
+                       :props (list :override-default-time time)))
+  (when goto (run-hooks 'org-roam-dailies-find-file-hook)))

-(defun org-roam-dailies-date ()
-  "Create the file for any date using the calendar interface."
+;;;; Commands
+;;; Today
+;;;###autoload
+(defun org-roam-dailies-capture-today (&optional goto)
+  "Create an entry in the daily-note for today.
+When GOTO is non-nil, go the note without creating an entry."
+  (interactive "P")
+  (org-roam-dailies--capture (current-time) goto))
+
+;;;###autoload
+(defun org-roam-dailies-goto-today ()
+  "Find the daily-note for today, creating it if necessary."
  (interactive)
-  (let ((time (org-read-date nil 'to-time nil "Date:  ")))
-    (org-roam-dailies--file-for-time time)))
+  (org-roam-dailies-capture-today t))
+
+;;; Tomorrow
+;;;###autoload
+(defun org-roam-dailies-capture-tomorrow (n &optional goto)
+  "Create an entry in the daily-note for tomorrow.
+
+With numeric argument N, use the daily-note N days in the future.
+
+With a `C-u' prefix or when GOTO is non-nil, go the note without
+creating an entry."
+  (interactive "p")
+  (org-roam-dailies--capture (time-add (* n 86400) (current-time)) goto))
+
+;;;###autoload
+(defun org-roam-dailies-goto-tomorrow (n)
+  "Find the daily-note for tomorrow, creating it if necessary.
+
+With numeric argument N, use the daily-note N days in the
+future."
+  (interactive "p")
+  (org-roam-dailies-capture-tomorrow n t))
+
+;;; Yesterday
+;;;###autoload
+(defun org-roam-dailies-capture-yesterday (n &optional goto)
+  "Create an entry in the daily-note for yesteday.
+
+With numeric argument N, use the daily-note N days in the past.
+
+When GOTO is non-nil, go the note without creating an entry."
+  (interactive "p")
+  (org-roam-dailies-capture-tomorrow (- n) goto))
+
+;;;###autoload
+(defun org-roam-dailies-goto-yesterday (n)
+  "Find the daily-note for yesterday, creating it if necessary.
+
+With numeric argument N, use the daily-note N days in the
+future."
+  (interactive "p")
+  (org-roam-dailies-capture-tomorrow (- n) t))
+
+;;; Calendar
+(defun org-roam-dailies-calendar--file-to-date (&optional file)
+  "Convert FILE to date.
+Return (MONTH DAY YEAR)."
+  (let ((file (or file
+                  (buffer-base-buffer (buffer-file-name)))))
+    (cl-destructuring-bind (_ _ _ d m y _ _ _)
+        (org-parse-time-string
+         (file-name-sans-extension
+          (file-name-nondirectory file)))
+      (list m d y))))
+
+(defun org-roam-dailies-calendar--date-to-time (date)
+  "Convert DATE as returned from then calendar (MONTH DAY YEAR) to a time."
+  (encode-time 0 0 0 (nth 1 date) (nth 0 date) (nth 2 date)))
+
+(defun org-roam-dailies-calendar-mark-entries ()
+  "Mark days in the calendar for which a daily-note is present."
+  (when (file-exists-p (expand-file-name org-roam-dailies-directory org-roam-directory))
+    (dolist (date (mapcar #'org-roam-dailies-calendar--file-to-date
+                          (org-roam-dailies--list-files)))
+      (when (calendar-date-is-visible-p date)
+        (calendar-mark-visible-date date 'org-roam-dailies-calendar-note)))))
+
+;;; Date
+;;;###autoload
+(defun org-roam-dailies-capture-date (&optional goto prefer-future)
+  "Create an entry in the daily-note for a date using the calendar.
+Prefer past dates, unless PREFER-FUTURE is non-nil.
+With a `C-u' prefix or when GOTO is non-nil, go the note without
+creating an entry."
+  (interactive "P")
+  (let ((time (let ((org-read-date-prefer-future prefer-future))
+                (org-read-date t t nil (if goto
+                                           "Find daily-note: "
+                                         "Capture to daily-note: ")))))
+    (org-roam-dailies--capture time goto)))
+
+;;;###autoload
+(defun org-roam-dailies-goto-date (&optional prefer-future)
+  "Find the daily-note for a date using the calendar, creating it if necessary.
+Prefer past dates, unless PREFER-FUTURE is non-nil."
+  (interactive)
+  (org-roam-dailies-capture-date t prefer-future))
+
+;;; Navigation
+(defun org-roam-dailies--list-files (&rest extra-files)
+  "List all files in `org-roam-dailies-directory'.
+EXTRA-FILES can be used to append extra files to the list."
+  (let ((dir (expand-file-name org-roam-dailies-directory org-roam-directory))
+        (regexp (rx-to-string `(and "." (or ,@org-roam-file-extensions)))))
+    (append (--remove (let ((file (file-name-nondirectory it)))
+                        (when (or (auto-save-file-name-p file)
+                                  (backup-file-name-p file)
+                                  (string-match "^\\." file))
+                          it))
+                      (directory-files-recursively dir regexp))
+            extra-files)))
+
+(defun org-roam-dailies-goto-next-note (&optional n)
+  "Find next daily-note.
+
+With numeric argument N, find note N days in the future. If N is
+negative, find note N days in the past."
+  (interactive "p")
+  (unless (org-roam-dailies--daily-note-p)
+    (user-error "Not in a daily-note"))
+  (setq n (or n 1))
+  (let* ((dailies (org-roam-dailies--list-files))
+         (position
+          (cl-position-if (lambda (candidate)
+                            (string= (buffer-file-name (buffer-base-buffer)) candidate))
+                          dailies))
+         note)
+    (unless position
+      (user-error "Can't find current note file - have you saved it yet?"))
+    (pcase n
+      ((pred (natnump))
+       (when (eq position (- (length dailies) 1))
+         (user-error "Already at newest note")))
+      ((pred (integerp))
+       (when (eq position 0)
+         (user-error "Already at oldest note"))))
+    (setq note (nth (+ position n) dailies))
+    (find-file note)
+    (run-hooks 'org-roam-dailies-find-file-hook)))
+
+(defun org-roam-dailies-goto-previous-note (&optional n)
+  "Find previous daily-note.
+
+With numeric argument N, find note N days in the past. If N is
+negative, find note N days in the future."
+  (interactive "p")
+  (let ((n (if n (- n) -1)))
+    (org-roam-dailies-goto-next-note n)))
+
+(add-hook 'calendar-today-visible-hook #'org-roam-dailies-calendar-mark-entries)
+(add-hook 'calendar-today-invisible-hook #'org-roam-dailies-calendar-mark-entries)
+
+;;;; Bindings
+(defvar org-roam-dailies-map (make-sparse-keymap)
+  "Keymap for `org-roam-dailies'.")
+
+(define-prefix-command 'org-roam-dailies-map)
+
+(define-key org-roam-dailies-map (kbd "d") #'org-roam-dailies-goto-today)
+(define-key org-roam-dailies-map (kbd "y") #'org-roam-dailies-goto-yesterday)
+(define-key org-roam-dailies-map (kbd "t") #'org-roam-dailies-goto-tomorrow)
+(define-key org-roam-dailies-map (kbd "n") #'org-roam-dailies-capture-today)
+(define-key org-roam-dailies-map (kbd "f") #'org-roam-dailies-goto-next-note)
+(define-key org-roam-dailies-map (kbd "b") #'org-roam-dailies-goto-previous-note)
+(define-key org-roam-dailies-map (kbd "c") #'org-roam-dailies-goto-date)
+(define-key org-roam-dailies-map (kbd "v") #'org-roam-dailies-capture-date)
+(define-key org-roam-dailies-map (kbd ".") #'org-roam-dailies-find-directory)
+
+(define-obsolete-function-alias
+  'org-roam-dailies-find-today
+  'org-roam-dailies-goto-today "org-roam 2.0")
+(define-obsolete-function-alias
+  'org-roam-dailies-find-yesterday
+  'org-roam-dailies-goto-yesterday "org-roam 2.0")
+(define-obsolete-function-alias
+  'org-roam-dailies-find-tomorrow
+  'org-roam-dailies-goto-tomorrow "org-roam 2.0")
+(define-obsolete-function-alias
+  'org-roam-dailies-find-next-note
+  'org-roam-dailies-goto-next-note "org-roam 2.0")
+(define-obsolete-function-alias
+  'org-roam-dailies-find-previous-note
+  'org-roam-dailies-goto-previous-note "org-roam 2.0")
+(define-obsolete-function-alias
+  'org-roam-dailies-find-date
+  'org-roam-dailies-goto-date "org-roam 2.0")

 (provide 'org-roam-dailies)

--- a/org-roam-db.el
+++ b/org-roam-db.el
@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.2
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))

 ;; This file is NOT part of GNU Emacs.

@ -27,32 +27,31 @@

 ;;; Commentary:
 ;;
-;; This library is provides the underlying database api to org-roam
+;; This library provides the underlying database api to org-roam.
 ;;
 ;;; Code:
 ;;;; Library Requires
 (eval-when-compile (require 'subr-x))
 (require 'emacsql)
-(require 'emacsql-sqlite3)
+(require 'emacsql-sqlite)
 (require 'seq)
-(require 'org-macs)
-(require 'org-roam-macs)

+(eval-and-compile
+  (require 'org-roam-macs)
+  ;; For `org-with-wide-buffer'
+  (require 'org-macs))
+(require 'org)
+(require 'ol)
+(require 'org-roam-utils)
+
+(defvar org-roam-find-file-hook)
 (defvar org-roam-directory)
-(defvar org-roam-enable-headline-linking)
 (defvar org-roam-verbose)
-(defvar org-roam-file-name)
+(defvar org-agenda-files)

-(declare-function org-roam--org-roam-file-p                "org-roam")
-(declare-function org-roam--extract-titles                 "org-roam")
-(declare-function org-roam--extract-ref                    "org-roam")
-(declare-function org-roam--extract-tags                   "org-roam")
-(declare-function org-roam--extract-ids                    "org-roam")
-(declare-function org-roam--extract-links                  "org-roam")
-(declare-function org-roam--list-all-files                 "org-roam")
-(declare-function org-roam--path-to-slug                   "org-roam")
-(declare-function org-roam--file-name-extension            "org-roam")
-(declare-function org-roam-buffer--update-maybe            "org-roam-buffer")
+(declare-function org-roam-id-at-point "org-roam")
+(declare-function org-roam--list-all-files "org-roam")
+(declare-function org-roam-node-at-point "org-roam")

 ;;;; Options
 (defcustom org-roam-db-location (expand-file-name "org-roam.db" user-emacs-directory)
@ -66,7 +65,7 @@ when used with multiple Org-roam instances."

 (defcustom org-roam-db-gc-threshold gc-cons-threshold
  "The value to temporarily set the `gc-cons-threshold' threshold to.
-During large, heavy operations like `org-roam-db-build-cache',
+During large, heavy operations like `org-roam-db-sync',
 many GC operations happen because of the large number of
 temporary structures generated (e.g. parsed ASTs). Temporarily
 increasing `gc-cons-threshold' will help reduce the number of GC
@ -79,7 +78,16 @@ value like `most-positive-fixnum'."
  :type 'int
  :group 'org-roam)

-(defconst org-roam-db--version 9)
+(defcustom org-roam-db-node-include-function (lambda () t)
+  "A custom function to check if the headline at point is a node."
+  :type 'function
+  :group 'org-roam)
+
+(defconst org-roam-db-version 16)
+(defconst org-roam--sqlite-available-p
+  (with-demoted-errors "Org-roam initialization: %S"
+    (emacsql-sqlite-ensure-binary)
+    t))

 (defvar org-roam-db--connection (make-hash-table :test #'equal)
  "Database connection to Org-roam database.")
@ -99,7 +107,7 @@ Performs a database upgrade when required."
               (emacsql-live-p (org-roam-db--get-connection)))
    (let ((init-db (not (file-exists-p org-roam-db-location))))
      (make-directory (file-name-directory org-roam-db-location) t)
-      (let ((conn (emacsql-sqlite3 org-roam-db-location)))
+      (let ((conn (emacsql-sqlite org-roam-db-location)))
        (set-process-query-on-exit-flag (emacsql-process conn) nil)
        (puthash (expand-file-name org-roam-directory)
                 conn
@ -107,74 +115,105 @@ Performs a database upgrade when required."
        (when init-db
          (org-roam-db--init conn))
        (let* ((version (caar (emacsql conn "PRAGMA user_version")))
-               (version (org-roam-db--update-maybe conn version)))
+               (version (org-roam-db--upgrade-maybe conn version)))
          (cond
-           ((> version org-roam-db--version)
+           ((> version org-roam-db-version)
            (emacsql-close conn)
            (user-error
             "The Org-roam database was created with a newer Org-roam version.  "
             "You need to update the Org-roam package"))
-           ((< version org-roam-db--version)
+           ((< version org-roam-db-version)
            (emacsql-close conn)
            (error "BUG: The Org-roam database scheme changed %s"
                   "and there is no upgrade path")))))))
  (org-roam-db--get-connection))

 ;;;; Entrypoint: (org-roam-db-query)
+(define-error 'emacsql-constraint "SQL constraint violation")
 (defun org-roam-db-query (sql &rest args)
  "Run SQL query on Org-roam database with ARGS.
 SQL can be either the emacsql vector representation, or a string."
-  (if  (stringp sql)
-      (emacsql (org-roam-db) (apply #'format sql args))
-    (apply #'emacsql (org-roam-db) sql args)))
+  (apply #'emacsql (org-roam-db) sql args))
+
+(defun org-roam-db-query! (handler sql &rest args)
+  "Run SQL query on Org-roam database with ARGS.
+SQL can be either the emacsql vector representation, or a string.
+The query is expected to be able to fail, in this situation, run HANDLER."
+  (condition-case err
+      (org-roam-db-query sql args)
+    (emacsql-constraint
+     (funcall handler err))))

 ;;;; Schemata
 (defconst org-roam-db--table-schemata
  '((files
     [(file :unique :primary-key)
      (hash :not-null)
-      (meta :not-null)])
+      (atime :not-null)
+      (mtime :not-null)])

-    (ids
-     [(id :unique :primary-key)
-      (file :not-null)
-      (level :not-null)])
+    (nodes
+     ([(id :not-null :primary-key)
+       (file :not-null)
+       (level :not-null)
+       (pos :not-null)
+       todo
+       priority
+       (scheduled text)
+       (deadline text)
+       title
+       properties
+       olp]
+      (:foreign-key [file] :references files [file] :on-delete :cascade)))

-    (links
-     [(from :not-null)
-      (to :not-null)
-      (type :not-null)
-      (properties :not-null)])
-
-    (tags
-     [(file :unique :primary-key)
-      (tags)])
-
-    (titles
-     [(file :not-null)
-      title])
+    (aliases
+     ([(node-id :not-null)
+       alias]
+      (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))

    (refs
-     [(ref :unique :not-null)
-      (file :not-null)
-      (type :not-null)])))
+     ([(node-id :not-null)
+       (ref :not-null)
+       (type :not-null)]
+      (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
+
+    (tags
+     ([(node-id :not-null)
+       tag]
+      (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
+
+    (links
+     ([(pos :not-null)
+       (source :not-null)
+       (dest :not-null)
+       (type :not-null)
+       (properties :not-null)]
+      (:foreign-key [source] :references nodes [id] :on-delete :cascade)))))
+
+(defconst org-roam-db--table-indices
+  '((alias-node-id aliases [node-id])
+    (refs-node-id refs [node-id])
+    (tags-node-id tags [node-id])))

 (defun org-roam-db--init (db)
  "Initialize database DB with the correct schema and user version."
  (emacsql-with-transaction db
-    (pcase-dolist (`(,table . ,schema) org-roam-db--table-schemata)
+    (emacsql db "PRAGMA foreign_keys = ON")
+    (pcase-dolist (`(,table ,schema) org-roam-db--table-schemata)
      (emacsql db [:create-table $i1 $S2] table schema))
-    (emacsql db (format "PRAGMA user_version = %s" org-roam-db--version))))
+    (pcase-dolist (`(,index-name ,table ,columns) org-roam-db--table-indices)
+      (emacsql db [:create-index $i1 :on $i2 $S3] index-name table columns))
+    (emacsql db (format "PRAGMA user_version = %s" org-roam-db-version))))

-(defun org-roam-db--update-maybe (db version)
+(defun org-roam-db--upgrade-maybe (db version)
  "Upgrades the database schema for DB, if VERSION is old."
  (emacsql-with-transaction db
    'ignore
-    (if (< version org-roam-db--version)
+    (if (< version org-roam-db-version)
        (progn
          (org-roam-message (format "Upgrading the Org-roam database from version %d to version %d"
-                                    version org-roam-db--version))
-          (org-roam-db-build-cache t))))
+                                    version org-roam-db-version))
+          (org-roam-db-sync t))))
  version)

 (defun org-roam-db--close (&optional db)
@ -192,190 +231,215 @@ the current `org-roam-directory'."
    (org-roam-db--close conn)))

 ;;;; Database API
-;;;;; Initialization
-(defun org-roam-db--initialized-p ()
-  "Whether the Org-roam cache has been initialized."
-  (and (file-exists-p org-roam-db-location)
-       (> (caar (org-roam-db-query [:select (funcall count) :from titles]))
-          0)))
-
-(defun org-roam-db--ensure-built ()
-  "Ensures that Org-roam cache is built."
-  (unless (org-roam-db--initialized-p)
-    (error "[Org-roam] your cache isn't built yet! Please run org-roam-db-build-cache")))
-
 ;;;;; Clearing
-(defun org-roam-db-clear ()
+(defun org-roam-db-clear-all ()
  "Clears all entries in the Org-roam cache."
  (interactive)
  (when (file-exists-p org-roam-db-location)
    (dolist (table (mapcar #'car org-roam-db--table-schemata))
      (org-roam-db-query `[:delete :from ,table]))))

-(defun org-roam-db--clear-file (&optional filepath)
-  "Remove any related links to the file at FILEPATH.
-This is equivalent to removing the node from the graph."
-  (let ((file (expand-file-name (or filepath
-                                    (buffer-file-name (buffer-base-buffer))))))
-    (dolist (table (mapcar #'car org-roam-db--table-schemata))
-      (org-roam-db-query `[:delete :from ,table
-                           :where (= ,(if (eq table 'links) 'from 'file) $s1)]
-                         file))))
+(defun org-roam-db-clear-file (&optional file)
+  "Remove any related links to the FILE.
+This is equivalent to removing the node from the graph.
+If FILE is nil, clear the current buffer."
+  (setq file (or file (buffer-file-name (buffer-base-buffer))))
+  (org-roam-db-query [:delete :from files
+                      :where (= file $s1)]
+                     file))

-;;;;; Insertion
-(defun org-roam-db--insert-meta (file hash meta)
-  "Insert HASH and META for a FILE into the Org-roam cache."
-  (org-roam-db-query
-   [:insert :into files
-    :values $v1]
-   (list (vector file hash meta))))
+;;;;; Updating tables
+(defun org-roam-db-insert-file ()
+  "Update the files table for the current buffer.
+If UPDATE-P is non-nil, first remove the file in the database."
+  (let* ((file (buffer-file-name))
+         (attr (file-attributes file))
+         (atime (file-attribute-access-time attr))
+         (mtime (file-attribute-modification-time attr))
+         (hash (org-roam-db--file-hash)))
+    (org-roam-db-query
+     [:insert :into files
+      :values $v1]
+     (list (vector file hash atime mtime)))))

-(defun org-roam-db--insert-links (links)
-  "Insert LINKS into the Org-roam cache."
-  (org-roam-db-query
-   [:insert :into links
-    :values $v1]
-   links))
+(defun org-roam-db-get-scheduled-time ()
+  "Return the scheduled time at point in ISO8601 format."
+  (when-let ((time (org-get-scheduled-time (point))))
+    (org-format-time-string "%FT%T%z" time)))

-(defun org-roam-db--insert-titles (file titles)
-  "Insert TITLES for a FILE into the Org-roam cache."
-  (org-roam-db-query
-   [:insert :into titles
-    :values $v1]
-   (mapcar (lambda (title)
-             (vector file title)) titles)))
+(defun org-roam-db-get-deadline-time ()
+  "Return the deadline time at point in ISO8601 format."
+  (when-let ((time (org-get-deadline-time (point))))
+    (org-format-time-string "%FT%T%z" time)))

-(defun org-roam-db--insert-ids (ids)
-  "Insert IDS into the Org-roam cache.
-Returns t if the insertion was successful, nil otherwise.
-Insertions can fail when there is an ID conflict."
-  (condition-case nil
-      (progn
+(defun org-roam-db-node-p ()
+  "Return t if headline at point is a node, else return nil."
+  (and (org-id-get)
+       (not (cdr (assoc "ROAM_EXCLUDE" (org-entry-properties))))
+       (funcall org-roam-db-node-include-function)))
+
+(defun org-roam-db-map-nodes (fns)
+  "Run FNS over all nodes in the current buffer."
+  (org-with-point-at 1
+    (org-map-entries
+     (lambda ()
+       (when (org-roam-db-node-p)
+         (dolist (fn fns)
+           (funcall fn)))))))
+
+(defun org-roam-db-map-links (fns)
+  "Run FNS over all links in the current buffer."
+  (org-with-point-at 1
+    (org-element-map (org-element-parse-buffer) 'link
+      (lambda (link)
+        (dolist (fn fns)
+          (funcall fn link))))))
+
+(defun org-roam-db-insert-file-node ()
+  "Insert the file-level node into the Org-roam cache."
+  (org-with-point-at 1
+    (when (and (= (org-outline-level) 0)
+               (org-roam-db-node-p))
+      (when-let ((id (org-id-get)))
+        (let* ((file (buffer-file-name (buffer-base-buffer)))
+               (title (org-link-display-format
+                       (or (cadr (assoc "TITLE" (org-collect-keywords '("title"))
+                                        #'string-equal))
+                           (file-relative-name file org-roam-directory))))
+               (pos (point))
+               (todo nil)
+               (priority nil)
+               (scheduled nil)
+               (deadline nil)
+               (level 0)
+               (aliases (org-entry-get (point) "ROAM_ALIASES"))
+               (tags org-file-tags)
+               (refs (org-entry-get (point) "ROAM_REFS"))
+               (properties (org-entry-properties))
+               (olp (org-get-outline-path)))
+          (org-roam-db-query!
+           (lambda (err)
+             (lwarn 'org-roam :warning "%s for %s (%s) in %s"
+                    (error-message-string err)
+                    title id file))
+           [:insert :into nodes
+            :values $v1]
+           (vector id file level pos todo priority
+                   scheduled deadline title properties olp))
+          (when tags
+            (org-roam-db-query
+             [:insert :into tags
+              :values $v1]
+             (mapcar (lambda (tag)
+                       (vector id (substring-no-properties tag)))
+                     tags)))
+          (when aliases
+            (org-roam-db-query
+             [:insert :into aliases
+              :values $v1]
+             (mapcar (lambda (alias)
+                       (vector id alias))
+                     (split-string-and-unquote aliases))))
+          (when refs
+            (setq refs (split-string-and-unquote refs))
+            (let (rows)
+              (dolist (ref refs)
+                (if (string-match org-link-plain-re ref)
+                    (progn
+                      (push (vector id (match-string 2 ref)
+                                    (match-string 1 ref)) rows))
+                  (lwarn '(org-roam) :warning
+                         "%s:%s\tInvalid ref %s, skipping..."
+                         (buffer-file-name) (point) ref)))
+              (when rows
+                (org-roam-db-query
+                 [:insert :into refs
+                  :values $v1]
+                 rows)))))))))
+
+(defun org-roam-db-insert-node-data ()
+  "Insert node data for headline at point into the Org-roam cache."
+  (when-let ((id (org-id-get)))
+    (let* ((file (buffer-file-name (buffer-base-buffer)))
+           (heading-components (org-heading-components))
+           (pos (point))
+           (todo (nth 2 heading-components))
+           (priority (nth 3 heading-components))
+           (level (nth 1 heading-components))
+           (scheduled (org-roam-db-get-scheduled-time))
+           (deadline (org-roam-db-get-deadline-time))
+           (title (org-link-display-format (nth 4 heading-components)))
+           (properties (org-entry-properties))
+           (olp (org-get-outline-path)))
+      (org-roam-db-query!
+       (lambda (err)
+         (lwarn 'org-roam :warning "%s for %s (%s) in %s"
+                (error-message-string err)
+                title id file))
+       [:insert :into nodes
+        :values $v1]
+       (vector id file level pos todo priority
+               scheduled deadline title properties olp)))))
+
+(defun org-roam-db-insert-aliases ()
+  "Insert aliases for node at point into Org-roam cache."
+  (when-let ((node-id (org-id-get))
+             (aliases (org-entry-get (point) "ROAM_ALIASES")))
+    (org-roam-db-query [:insert :into aliases
+                        :values $v1]
+                       (mapcar (lambda (alias)
+                                 (vector node-id alias))
+                               (split-string-and-unquote aliases)))))
+
+(defun org-roam-db-insert-tags ()
+  "Insert tags for node at point into Org-roam cache."
+  (when-let ((node-id (org-id-get))
+             (tags (org-get-tags)))
+    (org-roam-db-query [:insert :into tags
+                        :values $v1]
+                       (mapcar (lambda (tag)
+                                 (vector node-id (substring-no-properties tag))) tags))))
+
+(defun org-roam-db-insert-refs ()
+  "Insert refs for node at point into Org-roam cache."
+  (when-let* ((node-id (org-id-get))
+              (refs (org-entry-get (point) "ROAM_REFS"))
+              (refs (split-string-and-unquote refs)))
+    (let (rows)
+      (dolist (ref refs)
+        (save-match-data
+          (if (string-match org-link-plain-re ref)
+              (progn
+                (push (vector node-id (match-string 2 ref) (match-string 1 ref)) rows))
+            (lwarn '(org-roam) :warning
+                   "%s:%s\tInvalid ref %s, skipping..." (buffer-file-name) (point) ref))))
+      (org-roam-db-query [:insert :into refs
+                          :values $v1]
+                         rows))))
+
+(defun org-roam-db-insert-link (link)
+  "Insert link data for LINK at current point into the Org-roam cache."
+  (save-excursion
+    (goto-char (org-element-property :begin link))
+    (let ((type (org-element-property :type link))
+          (dest (org-element-property :path link))
+          (properties (list :outline (org-get-outline-path)))
+          (source (org-roam-id-at-point)))
+      (when source
        (org-roam-db-query
-         [:insert :into ids
+         [:insert :into links
          :values $v1]
-         ids)
-        t)
-    (error
-     (unless (listp ids)
-       (setq ids (list ids)))
-     (lwarn '(org-roam) :error
-            (format "Duplicate IDs in %s, one of:\n\n%s\n\nskipping..."
-                    (aref (car ids) 1)
-                    (string-join (mapcar (lambda (hl)
-                                           (aref hl 0)) ids) "\n")))
-     nil)))
-
-(defun org-roam-db--insert-tags (file tags)
-  "Insert TAGS for a FILE into the Org-roam cache."
-  (org-roam-db-query
-   [:insert :into tags
-    :values $v1]
-   (list (vector file tags))))
-
-(defun org-roam-db--insert-ref (file ref)
-  "Insert REF for FILE into the Org-roam cache.
-Returns t if successful, and nil otherwise.
-Insertions can fail if the key is already in the database."
-  (let ((key (cdr ref))
-        (type (car ref)))
-    (condition-case nil
-        (progn
-          (org-roam-db-query
-           [:insert :into refs :values $v1]
-           (list (vector key file type)))
-          t)
-      (error
-       (lwarn '(org-roam) :error
-              (format "Duplicate ref %s in:\n\nA: %s\nB: %s\n\nskipping..."
-                      key
-                      file
-                      (caar (org-roam-db-query
-                             [:select file :from refs
-                              :where (= ref $v1)]
-                             (vector key)))))
-       nil))))
+         (vector (point) source dest type properties))))))

 ;;;;; Fetching
 (defun org-roam-db--get-current-files ()
  "Return a hash-table of file to the hash of its file contents."
-  (let* ((current-files (org-roam-db-query [:select * :from files]))
-         (ht (make-hash-table :test #'equal)))
+  (let ((current-files (org-roam-db-query [:select [file hash] :from files]))
+        (ht (make-hash-table :test #'equal)))
    (dolist (row current-files)
      (puthash (car row) (cadr row) ht))
    ht))

-(defun org-roam-db--get-titles (file)
-  "Return the titles of FILE from the cache."
-  (caar (org-roam-db-query [:select [title] :from titles
-                            :where (= file $s1)
-                            :limit 1]
-                           file)))
-
-(defun org-roam-db--get-tags ()
-  "Return all distinct tags from the cache."
-  (let ((rows (org-roam-db-query [:select :distinct [tags] :from tags]))
-        acc)
-    (dolist (row rows)
-      (dolist (tag (car row))
-        (unless (member tag acc)
-          (push tag acc))))
-    acc))
-
-(defun org-roam-db--connected-component (file)
-  "Return all files reachable from/connected to FILE, including the file itself.
-If the file does not have any connections, nil is returned."
-  (let* ((query "WITH RECURSIVE
-                   links_of(file, link) AS
-                     (WITH filelinks AS (SELECT * FROM links WHERE NOT \"type\" = '\"cite\"'),
-                           citelinks AS (SELECT * FROM links
-                                                  JOIN refs ON links.\"to\" = refs.\"ref\"
-                                                            AND links.\"type\" = '\"cite\"')
-                      SELECT \"from\", \"to\" FROM filelinks UNION
-                      SELECT \"to\", \"from\" FROM filelinks UNION
-                      SELECT \"file\", \"from\" FROM citelinks UNION
-                      SELECT \"from\", \"file\" FROM citelinks),
-                   connected_component(file) AS
-                     (SELECT link FROM links_of WHERE file = $s1
-                      UNION
-                      SELECT link FROM links_of JOIN connected_component USING(file))
-                   SELECT * FROM connected_component;")
-         (files (mapcar 'car-safe (emacsql (org-roam-db) query file))))
-    files))
-
-(defun org-roam-db--links-with-max-distance (file max-distance)
-  "Return all files connected to FILE in at most MAX-DISTANCE steps.
-This includes the file itself. If the file does not have any
-connections, nil is returned."
-  (let* ((query "WITH RECURSIVE
-                   links_of(file, link) AS
-                     (WITH filelinks AS (SELECT * FROM links WHERE NOT \"type\" = '\"cite\"'),
-                           citelinks AS (SELECT * FROM links
-                                                  JOIN refs ON links.\"to\" = refs.\"ref\"
-                                                            AND links.\"type\" = '\"cite\"')
-                      SELECT \"from\", \"to\" FROM filelinks UNION
-                      SELECT \"to\", \"from\" FROM filelinks UNION
-                      SELECT \"file\", \"from\" FROM citelinks UNION
-                      SELECT \"from\", \"file\" FROM citelinks),
-                   -- Links are traversed in a breadth-first search.  In order to calculate the
-                   -- distance of nodes and to avoid following cyclic links, the visited nodes
-                   -- are tracked in 'trace'.
-                   connected_component(file, trace) AS
-                     (VALUES($s1, json_array($s1))
-                      UNION
-                      SELECT lo.link, json_insert(cc.trace, '$[' || json_array_length(cc.trace) || ']', lo.link) FROM
-                      connected_component AS cc JOIN links_of AS lo USING(file)
-                      WHERE (
-                        -- Avoid cycles by only visiting each file once.
-                        (SELECT count(*) FROM json_each(cc.trace) WHERE json_each.value == lo.link) == 0
-                        -- Note: BFS is cut off early here.
-                        AND json_array_length(cc.trace) < ($s2 + 1)))
-                   SELECT DISTINCT file, min(json_array_length(trace)) AS distance
-                   FROM connected_component GROUP BY file ORDER BY distance;")
-         ;; In principle the distance would be available in the second column.
-         (files (mapcar 'car-safe (emacsql (org-roam-db) query file max-distance))))
-    files))
-
 (defun org-roam-db--file-hash (&optional file-path)
  "Compute the hash of FILE-PATH, a file or current buffer."
  (if file-path
@ -387,167 +451,73 @@ connections, nil is returned."
     (secure-hash 'sha1 (current-buffer)))))

 ;;;;; Updating
-(defun org-roam-db--update-meta ()
-  "Update the metadata of the current buffer into the cache."
-  (let* ((file (or org-roam-file-name (buffer-file-name)))
-         (attr (file-attributes file))
-         (atime (file-attribute-access-time attr))
-         (mtime (file-attribute-modification-time attr))
-         (hash (org-roam-db--file-hash)))
-    (org-roam-db-query [:delete :from files
-                        :where (= file $s1)]
-                       file)
-    (org-roam-db--insert-meta file hash (list :atime atime :mtime mtime))))
-
-(defun org-roam-db--update-titles ()
-  "Update the title of the current buffer into the cache."
-  (let* ((file (or org-roam-file-name (buffer-file-name)))
-         (titles (or (org-roam--extract-titles)
-                     (list (org-roam--path-to-slug file)))))
-    (org-roam-db-query [:delete :from titles
-                        :where (= file $s1)]
-                       file)
-    (org-roam-db--insert-titles file titles)))
-
-(defun org-roam-db--update-tags ()
-  "Update the tags of the current buffer into the cache."
-  (let* ((file (or org-roam-file-name (buffer-file-name)))
-         (tags (org-roam--extract-tags file)))
-    (org-roam-db-query [:delete :from tags
-                        :where (= file $s1)]
-                       file)
-    (when tags
-      (org-roam-db--insert-tags file tags))))
-
-(defun org-roam-db--update-refs ()
-  "Update the ref of the current buffer into the cache."
-  (let ((file (or org-roam-file-name (buffer-file-name))))
-    (org-roam-db-query [:delete :from refs
-                        :where (= file $s1)]
-                       file)
-    (when-let ((ref (org-roam--extract-ref)))
-      (org-roam-db--insert-ref file ref))))
-
-(defun org-roam-db--update-links ()
-  "Update the file links of the current buffer in the cache."
-  (let ((file (or org-roam-file-name (buffer-file-name))))
-    (org-roam-db-query [:delete :from links
-                        :where (= from $s1)]
-                       file)
-    (when-let ((links (org-roam--extract-links)))
-      (org-roam-db--insert-links links))))
-
-(defun org-roam-db--update-ids ()
-  "Update the ids of the current buffer into the cache."
-  (let* ((file (or org-roam-file-name (buffer-file-name))))
-    (org-roam-db-query [:delete :from ids
-                        :where (= file $s1)]
-                       file)
-    (when-let ((ids (org-roam--extract-ids file)))
-      (org-roam-db--insert-ids ids))))
-
-(defun org-roam-db--update-file (&optional file-path)
-  "Update Org-roam cache for FILE-PATH.
-If the file does not exist anymore, remove it from the cache.
-If the file exists, update the cache with information."
-  (setq file-path (or file-path
-                      (buffer-file-name (buffer-base-buffer))))
-  (if (not (file-exists-p file-path))
-      (org-roam-db--clear-file file-path)
-    ;; save the file before performing a database update
-    (when-let ((buf (find-buffer-visiting file-path)))
-      (with-current-buffer buf
-        (save-buffer)))
-    (org-roam--with-temp-buffer file-path
-      (emacsql-with-transaction (org-roam-db)
-        (org-roam-db--update-meta)
-        (org-roam-db--update-tags)
-        (org-roam-db--update-titles)
-        (org-roam-db--update-refs)
-        (when org-roam-enable-headline-linking
-          (org-roam-db--update-ids))
-        (org-roam-db--update-links)))))
-
-(defun org-roam-db-build-cache (&optional force)
-  "Build the cache for `org-roam-directory'.
+;;;###autoload
+(defun org-roam-db-sync (&optional force)
+  "Synchronize the cache state with the current Org files on-disk.
 If FORCE, force a rebuild of the cache from scratch."
  (interactive "P")
  (when force (delete-file org-roam-db-location))
  (org-roam-db--close) ;; Force a reconnect
  (org-roam-db) ;; To initialize the database, no-op if already initialized
  (let* ((gc-cons-threshold org-roam-db-gc-threshold)
-	 (org-agenda-files nil)
+         (org-agenda-files nil)
         (org-roam-files (org-roam--list-all-files))
         (current-files (org-roam-db--get-current-files))
-         (file-count 0)
-         (id-count 0)
-         (link-count 0)
-         (tag-count 0)
-         (title-count 0)
-         (ref-count 0)
-         (deleted-count 0)
-         (processed-count 0))
+         (modified-files nil))
+    (dolist (file org-roam-files)
+      (let ((contents-hash (org-roam-db--file-hash file)))
+        (unless (string= (gethash file current-files)
+                         contents-hash)
+          (push file modified-files)))
+      (remhash file current-files))
    (emacsql-with-transaction (org-roam-db)
-      ;; Two-step building
-      ;; First step: Rebuild files and ids
-      (dolist (file org-roam-files)
-        (org-roam-message "Processed %s/%s files..." processed-count (length org-roam-files))
-        (let* ((attr (file-attributes file))
-               (atime (file-attribute-access-time attr))
-               (mtime (file-attribute-modification-time attr)))
-          (let ((contents-hash (org-roam-db--file-hash file)))
-            (unless (string= (gethash file current-files)
-                             contents-hash)
-              (condition-case nil
-                  (org-roam--with-temp-buffer file
-                    (org-roam-db--clear-file file)
-                    (org-roam-db-query
-                     [:insert :into files
-                      :values $v1]
-                     (vector file contents-hash (list :atime atime :mtime mtime)))
-                    (setq file-count (1+ file-count))
-                    (when org-roam-enable-headline-linking
-                      (when-let ((ids (org-roam--extract-ids file)))
-                        (when (org-roam-db--insert-ids ids)
-                          (setq id-count (+ id-count (length ids))))))
-                    (when-let (links (org-roam--extract-links file))
-                      (org-roam-db-query
-                       [:insert :into links
-                        :values $v1]
-                       links)
-                      (setq link-count (1+ link-count)))
-                    (when-let (tags (org-roam--extract-tags file))
-                      (org-roam-db-query
-                       [:insert :into tags
-                        :values $v1]
-                       (vector file tags))
-                      (setq tag-count (1+ tag-count)))
-                    (let ((titles (or (org-roam--extract-titles)
-                                      (list (org-roam--path-to-slug file)))))
-                      (org-roam-db--insert-titles file titles)
-                      (setq title-count (+ title-count (length titles))))
-                    (when-let* ((ref (org-roam--extract-ref)))
-                      (when (org-roam-db--insert-ref file ref)
-                        (setq ref-count (1+ ref-count)))))
-                (file-error
-                 (setq org-roam-files (remove file org-roam-files))
-                 (org-roam-db--clear-file file)
-                 (lwarn '(org-roam) :warning
-                        "Skipping unreadable file while building cache: %s" file))))
-            (remhash file current-files)
-            (setq processed-count (+ processed-count 1)))))
-      (dolist (file (hash-table-keys current-files))
-        ;; These files are no longer around, remove from cache...
-        (org-roam-db--clear-file file)
-        (setq deleted-count (1+ deleted-count))))
-    (org-roam-message "files: Δ%s, ids: Δ%s, links: Δ%s, tags: Δ%s, titles: Δ%s, refs: Δ%s, deleted: Δ%s"
-                      file-count
-                      id-count
-                      link-count
-                      tag-count
-                      title-count
-                      ref-count
-                      deleted-count)))
+      (if (fboundp 'dolist-with-progress-reporter)
+          (dolist-with-progress-reporter (file (hash-table-keys current-files))
+              "Clearing removed files..."
+            (org-roam-db-clear-file file))
+        (dolist (file (hash-table-keys current-files))
+          (org-roam-db-clear-file file)))
+      (if (fboundp 'dolist-with-progress-reporter)
+          (dolist-with-progress-reporter (file modified-files)
+              "Processing modified files..."
+            (org-roam-db-update-file file))
+        (dolist (file modified-files)
+          (org-roam-db-update-file file))))))
+
+(defun org-roam-db-update-file (&optional file-path)
+  "Update Org-roam cache for FILE-PATH.
+If the file does not exist anymore, remove it from the cache.
+If the file exists, update the cache with information."
+  (setq file-path (or file-path (buffer-file-name (buffer-base-buffer))))
+  (let ((content-hash (org-roam-db--file-hash file-path))
+        (db-hash (caar (org-roam-db-query [:select hash :from files
+                                           :where (= file $s1)] file-path))))
+    (unless (string= content-hash db-hash)
+      (org-roam-with-file file-path nil
+        (save-excursion
+          (org-set-regexps-and-options 'tags-only)
+          (org-roam-db-clear-file)
+          (org-roam-db-insert-file)
+          (org-roam-db-insert-file-node)
+          (org-roam-db-map-nodes
+           (list #'org-roam-db-insert-node-data
+                 #'org-roam-db-insert-aliases
+                 #'org-roam-db-insert-tags
+                 #'org-roam-db-insert-refs))
+          (org-roam-db-map-links
+           (list #'org-roam-db-insert-link)))))))
+
+(defun org-roam-db--update-on-save-h ()
+  "."
+  (add-hook 'after-save-hook #'org-roam-db-update-file nil t))
+
+(add-hook 'org-roam-find-file-hook #'org-roam-db--update-on-save-h)
+
+;; Diagnostic Interactives
+(defun org-roam-db-diagnose-node ()
+  "Print information about node at point."
+  (interactive)
+  (prin1 (org-roam-node-at-point)))

 (provide 'org-roam-db)

--- a/org-roam-dev.el
+++ b/org-roam-dev.el
@ -1,46 +0,0 @@
-;;; org-roam-dev.el --- Org-roam development code -mode -*- coding: utf-8; lexical-binding: t; -*-
-
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/org-roam/org-roam
-;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.2
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
-
-;; This file is NOT part of GNU Emacs.
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation; either version 3, or (at your option)
-;; any later version.
-;;
-;; This program is distributed in the hope that it will be useful,
-;; but WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;; GNU General Public License for more details.
-;;
-;; You should have received a copy of the GNU General Public License
-;; along with GNU Emacs; see the file COPYING.  If not, write to the
-;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
-;; Boston, MA 02110-1301, USA.
-
-;;; Commentary:
-;;
-;; This library provides code for org-roam developers.
-;; It is intended to be loaded before editing org-roam source files.
-;; It ensures consistent application of various developer settings.
-;;
-;;; Code:
-(require 'emacsql)
-
-;;;###autoload
-(define-minor-mode org-roam-dev-mode
-  "Minor mode for setting the dev environment of Org-roam."
-  :lighter " ORD"
-  (when org-roam-dev-mode
-    (emacsql-fix-vector-indentation)
-    (setq-local sentence-end-double-space nil)))
-
-(provide 'org-roam-dev)
-;;; org-roam-dev.el ends here
--- a/org-roam-doctor.el
+++ b/org-roam-doctor.el
@ -1,318 +0,0 @@
-;;; org-roam-doctor.el --- Linter for Org-roam files -*- coding: utf-8; lexical-binding: t; -*-
-;;
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
-;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.2
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
-
-;; This file is NOT part of GNU Emacs.
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation; either version 3, or (at your option)
-;; any later version.
-;;
-;; This program is distributed in the hope that it will be useful,
-;; but WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;; GNU General Public License for more details.
-;;
-;; You should have received a copy of the GNU General Public License
-;; along with GNU Emacs; see the file COPYING.  If not, write to the
-;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
-;; Boston, MA 02110-1301, USA.
-
-
-;;; Commentary:
-;;
-;; This library provides `org-roam-doctor', a utility for diagnosing and fixing
-;; Org-roam files. Running `org-roam-doctor' launches a list of checks defined
-;; by `org-roam-doctor--checkers'. Every checker is an instance of
-;; `org-roam-doctor-checker'.
-;;
-;; Each checker is given the Org parse tree (AST), and is expected to return a
-;; list of errors. The checker can also provide "actions" for auto-fixing errors
-;; (see `org-roam-doctor--remove-link' for an example).
-;;
-;; The UX experience is inspired by both org-lint and checkdoc, and their code
-;; is heavily referenced.
-;;
-;;; Code:
-;; Library Requires
-(require 'cl-lib)
-(require 'org)
-(require 'org-element)
-(require 's)
-(require 'dash)
-(require 'org-roam-macs)
-
-(declare-function org-roam-insert "org-roam")
-(declare-function org-roam--get-roam-buffers "org-roam")
-(declare-function org-roam--list-all-files "org-roam")
-(declare-function org-roam--org-roam-file-p "org-roam")
-(declare-function org-roam--str-to-list "org-roam")
-(declare-function org-roam-mode "org-roam")
-
-(defvar org-roam-verbose)
-(defvar org-roam-mode)
-
-(defcustom org-roam-doctor-inhibit-startup t
-  "Inhibit `org-mode' startup when processing files with `org-doctor'.
-When non-nil, images and LaTeX preview will not be generated,
-tables will not be aligned, and headlines will not respect
-startup visability. This significantly improves performance when
-processing multiple files"
-  :type 'boolean
-  :group 'org-roam)
-
-(cl-defstruct (org-roam-doctor-checker (:copier nil))
-  (name 'missing-checker-name)
-  (description "")
-  (actions nil))
-
-(defconst org-roam-doctor--checkers
-  (list
-   (make-org-roam-doctor-checker
-    :name 'org-roam-doctor-broken-links
-    :description "Fix broken links."
-    :actions '(("d" . ("Unlink" . org-roam-doctor--remove-link))
-               ("r" . ("Replace link" . org-roam-doctor--replace-link))
-               ("R" . ("Replace link (keep label)" . org-roam-doctor--replace-link-keep-label))))
-   (make-org-roam-doctor-checker
-    :name 'org-roam-doctor-check-roam-props
-    :description "Check #+roam_* properties.")
-   (make-org-roam-doctor-checker
-    :name 'org-roam-doctor-check-tags
-    :description "Check #+roam_tags.")
-   (make-org-roam-doctor-checker
-    :name 'org-roam-doctor-check-alias
-    :description "Check #+roam_alias.")))
-
-(defconst org-roam-doctor--supported-roam-properties
-  '("roam_tags" "roam_alias" "roam_key")
-  "List of supported Org-roam properties.")
-
-(defun org-roam-doctor-check-roam-props (ast)
-  "Checker for detecting invalid #+roam_* properties.
-AST is the org-element parse tree."
-  (let (reports)
-    (org-element-map ast 'keyword
-      (lambda (kw)
-        (let ((key (org-element-property :key kw)))
-          (when (and (string-prefix-p "ROAM_" key t)
-                     (not (member (downcase key) org-roam-doctor--supported-roam-properties)))
-            (push
-             `(,(org-element-property :begin kw)
-               ,(concat "Possible mispelled key: "
-                        (prin1-to-string key)
-                        "\nOrg-roam supports the following keys: "
-                        (s-join ", " org-roam-doctor--supported-roam-properties)))
-             reports)))))
-    reports))
-
-(defun org-roam-doctor-check-tags (ast)
-  "Checker for detecting invalid #+roam_tags.
-AST is the org-element parse tree."
-  (let (reports)
-    (org-element-map ast 'keyword
-      (lambda (kw)
-        (when (string-collate-equalp (org-element-property :key kw) "roam_tags" nil t)
-          (let ((tags (org-element-property :value kw)))
-            (condition-case nil
-                (org-roam--str-to-list tags)
-              (error
-               (push
-                `(,(org-element-property :begin kw)
-                  ,(concat "Unable to parse tags: "
-                           tags
-                           (when (s-contains? "," tags)
-                             "\nCheck that your tags are not comma-separated.")))
-                reports)))))))
-    reports))
-
-(defun org-roam-doctor-check-alias (ast)
-  "Checker for detecting invalid #+roam_alias.
-AST is the org-element parse tree."
-  (let (reports)
-    (org-element-map ast 'keyword
-      (lambda (kw)
-        (when (string-collate-equalp (org-element-property :key kw) "roam_alias" nil t)
-          (let ((aliases (org-element-property :value kw)))
-            (condition-case nil
-              (org-roam--str-to-list aliases)
-              (error
-               (push
-                `(,(org-element-property :begin kw)
-                  ,(concat "Unable to parse aliases: "
-                           aliases
-                           (when (s-contains? "," aliases)
-                             "\nCheck that your aliases are not comma-separated.")))
-                reports)))))))
-    reports))
-
-(defun org-roam-doctor-broken-links (ast)
-  "Checker for detecting broken links.
-AST is the org-element parse tree."
-  (let (reports)
-    (org-element-map ast 'link
-      (lambda (l)
-        (when (equal "file" (org-element-property :type l))
-          (let ((file (org-element-property :path l)))
-            (or (file-exists-p file)
-                (file-remote-p file)
-                (push
-                 `(,(org-element-property :begin l)
-                   ,(format (if (org-element-lineage l '(link))
-                                "Link to non-existent image file \"%s\"\
- in link description"
-                              "Link to non-existent local file \"%s\"")
-                            file))
-                 reports))))))
-    reports))
-
-(defun org-roam-doctor--check (buffer checkers)
-  "Check BUFFER for errors.
-CHECKERS is the list of checkers used."
-  (with-current-buffer buffer
-    (save-excursion
-      (goto-char (point-min))
-      (let* ((ast (org-element-parse-buffer))
-             (errors (sort (cl-mapcan
-                            (lambda (c)
-                              (mapcar
-                               (lambda (report)
-                                 (list (set-marker (make-marker) (car report))
-                                       (nth 1 report) c))
-                               (save-excursion
-                                 (funcall
-                                  (org-roam-doctor-checker-name c)
-                                  ast))))
-                            checkers)
-                           #'car-less-than-car)))
-        (dolist (e errors)
-          (pcase-let ((`(,m ,msg ,checker) e))
-            (switch-to-buffer buffer)
-            (goto-char m)
-            (org-reveal)
-            (undo-boundary)
-            (org-roam-doctor--resolve msg checker)
-            (set-marker m nil)))
-        errors))))
-
-;;; Actions
-(defun org-roam-doctor--recursive-edit ()
-  "Launch into a recursive edit."
-  (message "When you're done editing press C-M-c to continue.")
-  (recursive-edit))
-
-(defun org-roam-doctor--skip ()
-  "Skip the current error."
-  (org-roam-message "Skipping..."))
-
-(defun org-roam-doctor--replace-link ()
-  "Replace the current link with a new link."
-  (save-match-data
-    (unless (org-in-regexp org-link-bracket-re 1)
-      (user-error "No link at point"))
-    (let ((orig (buffer-string))
-          (p (point)))
-      (condition-case nil
-          (save-excursion
-            (replace-match "")
-            (org-roam-insert))
-        (quit (progn
-                (replace-buffer-contents orig)
-                (goto-char p)))))))
-
-(defun org-roam-doctor--replace-link-keep-label ()
-  "Replace the current link with a new link, keeping the current link's label."
-  (save-match-data
-    (unless (org-in-regexp org-link-bracket-re 1)
-      (user-error "No link at point"))
-    (let ((orig (buffer-string))
-          (p (point)))
-      (condition-case nil
-          (save-excursion
-            (let ((label (if (match-end 2)
-                             (match-string-no-properties 2)
-                           (org-link-unescape (match-string-no-properties 1)))))
-              (replace-match "")
-              (org-roam-insert nil nil label)))
-        (quit (progn
-                (replace-buffer-contents orig)
-                (goto-char p)))))))
-
-(defun org-roam-doctor--remove-link ()
-  "Unlink the text at point."
-  (unless (org-in-regexp org-link-bracket-re 1)
-    (user-error "No link at point"))
-  (save-excursion
-    (let ((label (if (match-end 2)
-                     (match-string-no-properties 2)
-                   (org-link-unescape (match-string-no-properties 1)))))
-      (delete-region (match-beginning 0) (match-end 0))
-      (insert label))))
-
-(defun org-roam-doctor--resolve (msg checker)
-  "Resolve an error.
-MSG is the error that was found, which is displayed in a help buffer.
-CHECKER is a org-roam-doctor checker instance."
-  (let ((actions (org-roam-doctor-checker-actions checker))
-        c)
-    (push '("e" . ("Edit" . org-roam-doctor--recursive-edit)) actions)
-    (push '("s" . ("Skip" . org-roam-doctor--skip)) actions)
-    (with-output-to-temp-buffer "*Org-roam-doctor Help*"
-      (mapc #'princ
-            (list "Error message:\n   " msg "\n\n"))
-      (dolist (action actions)
-        (princ (format "[%s]: %s\n"
-                       (car action)
-                       (cadr action))))
-      (princ "\n\n"))
-    (shrink-window-if-larger-than-buffer
-     (get-buffer-window "*Org-roam-doctor Help*"))
-    (message "Press key for command:")
-    (unwind-protect
-        (progn
-          (cl-loop
-           do (setq c (char-to-string (read-char-exclusive)))
-           until (assoc c actions)
-           do (message "Please enter a valid key for command:"))
-          (funcall (cddr (assoc c actions)))
-          (redisplay))
-      (when (get-buffer-window "*Org-roam-doctor Help*")
-        (delete-window (get-buffer-window "*Org-roam-doctor Help*"))
-        (kill-buffer "*Org-roam-doctor Help*")))))
-
-;;;###autoload
-(defun org-roam-doctor (&optional checkall)
-  "Perform a check on the current buffer to ensure cleanliness.
-If CHECKALL, run the check for all Org-roam files."
-  (interactive "P")
-  (unless org-roam-mode (org-roam-mode))
-  (let ((files (if checkall
-                  (org-roam--list-all-files)
-                (unless (org-roam--org-roam-file-p)
-                  (user-error "Not in an org-roam file"))
-                `(,(buffer-file-name)))))
-    (org-roam-doctor-start files org-roam-doctor--checkers)))
-
-(defun org-roam-doctor-start (files checkers)
-  "Lint FILES using CHECKERS."
-  (save-window-excursion
-    (let ((existing-buffers (org-roam--get-roam-buffers))
-          (org-inhibit-startup org-roam-doctor-inhibit-startup))
-      (dolist (f files)
-        (let ((buf (find-file-noselect f)))
-          (org-roam-doctor--check buf checkers)
-          (unless (memq buf existing-buffers)
-            (save-buffer buf)
-            (kill-buffer buf))))))
-  (org-roam-message "Linting completed."))
-
-(provide 'org-roam-doctor)
-
-;;; org-roam-doctor.el ends here
--- a/org-roam-faces.el
+++ b/org-roam-faces.el
@ -1,72 +0,0 @@
-;;; org-roam-faces.el --- Face definitions -*- coding: utf-8; lexical-binding: t; -*-
-
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/org-roam/org-roam
-;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.2
-;; Package-Requires: ((emacs "26.1"))
-
-;; This file is NOT part of GNU Emacs.
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation; either version 3, or (at your option)
-;; any later version.
-;;
-;; This program is distributed in the hope that it will be useful,
-;; but WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;; GNU General Public License for more details.
-;;
-;; You should have received a copy of the GNU General Public License
-;; along with GNU Emacs; see the file COPYING.  If not, write to the
-;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
-;; Boston, MA 02110-1301, USA.
-
-;;; Commentary:
-
-;; This file contains the face definitions for Org-roam.
-
-;;; Code:
-
-(defgroup org-roam-faces nil
-  "Faces used by Org-roam."
-  :group 'org-roam
-  :group 'faces)
-
-;;; Definitions
-(defface org-roam-link
-  '((t :inherit org-link))
-  "Face for Org-roam links."
-  :group 'org-roam-faces)
-
-(defface org-roam-tag
-  '((t :weight bold))
-  "Face for Org-roam tags in minibuffer commands."
-  :group 'org-roam-faces)
-
-(defface org-roam-link-current
-  '((t :inherit org-link))
-  "Face for Org-roam links pointing to the current buffer."
-  :group 'org-roam-faces)
-
-(defface org-roam-link-invalid
-  '((t :inherit (error org-link)))
-  "Face for Org-roam links that are not valid.
-This face is used for links without a destination."
-  :group 'org-roam-faces)
-
-(defface org-roam-link-shielded
-  '((t :inherit (warning org-link)))
-  "Face for Org-roam links that are shielded.
-This face is used on the region target by `org-roam-insertion'
-during an `org-roam-capture'."
-  :group 'org-roam-faces)
-
-;;; _
-
-(provide 'org-roam-faces)
-
-;;; org-roam-faces.el ends here
--- a/org-roam-graph.el
+++ b/org-roam-graph.el
@ -1,12 +1,12 @@
 ;;; org-roam-graph.el --- Graphing API -*- coding: utf-8; lexical-binding: t; -*-

-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>

 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.2
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))

 ;; This file is NOT part of GNU Emacs.

@ -31,16 +31,12 @@
 ;;
 ;;; Code:
 (require 'xml) ;xml-escape-string
-(require 's)   ;s-truncate, s-replace
-(require 'org-roam-macs)
+(eval-and-compile
+  (require 'org-roam-macs))
 (require 'org-roam-db)

 ;;;; Declarations
 (defvar org-roam-directory)
-(defvar org-roam-mode)
-(declare-function org-roam--org-roam-file-p  "org-roam")
-(declare-function org-roam--path-to-slug     "org-roam")
-(declare-function org-roam-mode              "org-roam")

 ;;;; Options
 (defcustom org-roam-graph-viewer (executable-find "firefox")
@ -60,6 +56,12 @@ It may be one of the following:
  :type 'string
  :group 'org-roam)

+(defcustom org-roam-graph-filetype "svg"
+  "File type to generate when producing graphs."
+  :type 'string
+  :group 'org-roam)
+
+
 (defcustom org-roam-graph-extra-config nil
  "Extra options passed to graphviz.
 Example:
@ -67,31 +69,34 @@ Example:
  :type '(alist)
  :group 'org-roam)

+(defcustom org-roam-graph-edge-extra-config nil
+  "Extra edge options passed to graphviz.
+Example:
+ '((\"dir\" . \"back\"))"
+  :type '(alist)
+  :group 'org-roam)
+
 (defcustom org-roam-graph-node-extra-config
-  '(("shape"      . "underline")
-    ("style"      . "rounded,filled")
-    ("fillcolor"  . "#EEEEEE")
-    ("color"      . "#C9C9C9")
-    ("fontcolor"  . "#111111"))
-  "Extra options for graphviz nodes.
-Example:
- '((\"color\" . \"skyblue\"))"
+  '(("id" . (("style"      . "bold,rounded,filled")
+             ("fillcolor"  . "#EEEEEE")
+             ("color"      . "#C9C9C9")
+             ("fontcolor"  . "#111111")))
+    ("http" . (("style"      . "rounded,filled")
+               ("fillcolor"  . "#EEEEEE")
+               ("color"      . "#C9C9C9")
+               ("fontcolor"  . "#0A97A6")))
+    ("https" . (("shape"      . "rounded,filled")
+                ("fillcolor"  . "#EEEEEE")
+                ("color"      . "#C9C9C9")
+                ("fontcolor"  . "#0A97A6"))))
+  "Extra options for graphviz nodes."
  :type '(alist)
  :group 'org-roam)

-(defcustom org-roam-graph-edge-extra-config
-  '(("color" . "#333333"))
-  "Extra options for graphviz edges.
-Example:
- '((\"dir\" . \"back\"))"
-  :type '(alist)
-  :group 'org-roam)
-
-(defcustom org-roam-graph-edge-cites-extra-config '(("color" . "red"))
-  "Extra options for graphviz edges for citation links.
-Example:
- '((\"dir\" . \"back\"))"
-  :type '(alist)
+(defcustom org-roam-graph-link-hidden-types
+  '("file")
+  "What sort of links to hide from the Org-roam graph."
+  :type '(repeat string)
  :group 'org-roam)

 (defcustom org-roam-graph-max-title-length 100
@ -112,45 +117,6 @@ All other values including nil will have no effect."
          (const :tag "no" nil))
  :group 'org-roam)

-(defcustom org-roam-graph-exclude-matcher nil
-  "Matcher for excluding nodes from the generated graph.
-Any nodes and links for file paths matching this string is
-excluded from the graph.
-
-If value is a string, the string is the only matcher.
-
-If value is a list, all file paths matching any of the strings
-are excluded."
-  :type '(choice
-          (string :tag "Matcher")
-          (list :tag "Matchers"))
-  :group 'org-roam)
-
-;;;; Functions
-(defun org-roam-graph--expand-matcher (col &optional negate where)
-  "Return the exclusion regexp from `org-roam-graph-exclude-matcher'.
-COL is the symbol to be matched against.  if NEGATE, add :not to sql query.
-set WHERE to true if WHERE query already exists."
-  (let ((matchers (pcase org-roam-graph-exclude-matcher
-                    ('nil nil)
-                    ((pred stringp) `(,(concat "%" org-roam-graph-exclude-matcher "%")))
-                    ((pred listp) (mapcar (lambda (m)
-                                            (concat "%" m "%"))
-                                          org-roam-graph-exclude-matcher))
-                    (_ (error "Invalid org-roam-graph-exclude-matcher"))))
-        res)
-    (dolist (match matchers)
-      (if where
-          (push :and res)
-        (push :where res)
-        (setq where t))
-      (push col res)
-      (when negate
-        (push :not res))
-      (push :like res)
-      (push match res))
-    (nreverse res)))
-
 (defun org-roam-graph--dot-option (option &optional wrap-key wrap-val)
  "Return dot string of form KEY=VAL for OPTION cons.
 If WRAP-KEY is non-nil it wraps the KEY.
@ -159,71 +125,104 @@ If WRAP-VAL is non-nil it wraps the VAL."
          "="
          wrap-val (cdr option) wrap-val))

-(defun org-roam-graph--dot (node-query)
-  "Build the graphviz dot string for NODE-QUERY.
-The Org-roam database titles table is read, to obtain the list of titles.
-The links table is then read to obtain all directed links, and formatted
-into a digraph."
-  (org-roam-db--ensure-built)
-  (org-roam--with-temp-buffer nil
-    (let* ((nodes (org-roam-db-query node-query))
-           (edges-query
-            `[:with selected :as [:select [file] :from ,node-query]
-              :select :distinct [to from] :from links
-              :where (and (in to selected) (in from selected))])
-           (edges-cites-query
-            `[:with selected :as [:select [file] :from ,node-query]
-              :select :distinct [file from]
-              :from links :inner :join refs :on (and (= links:to refs:ref)
-                                                     (= links:type "cite")
-                                                     (= refs:type "cite"))
-              :where (and (in file selected) (in from selected))])
-           (edges       (org-roam-db-query edges-query))
-           (edges-cites (org-roam-db-query edges-cites-query)))
+(defun org-roam-graph--connected-component (id distance)
+  "Return the edges for all nodes reachable from/connected to ID.
+DISTANCE is the maximum distance away from the root node."
+  (let* ((query
+          (if (= distance 0)
+              "
+WITH RECURSIVE
+  links_of(source, dest) AS
+  (SELECT source, dest FROM links UNION
+   SELECT dest, source FROM links),
+   connected_component(source) AS
+  (SELECT dest FROM links_of WHERE source = $s1 UNION
+   SELECT dest FROM links_of JOIN connected_component USING(source))
+SELECT source, dest, type FROM links WHERE source IN connected_component OR dest IN connected_component;"
+            "
+WITH RECURSIVE
+  links_of(source, dest) AS
+  (SELECT source, dest FROM links UNION
+   SELECT dest, source FROM links),
+  connected_component(source, trace) AS
+  (VALUES ($s1 , json_array($s1)) UNION
+   SELECT lo.dest, json_insert(cc.trace, '$[' || json_array_length(cc.trace) || ']', lo.dest) FROM
+   connected_component AS cc JOIN links_of AS lo USING(source)
+   WHERE (
+    -- Avoid cycles by only visiting each node once.
+    (SELECT count(*) FROM json_each(cc.trace) WHERE json_each.value == lo.dest) == 0
+    -- Note: BFS is cut off early here.
+    AND json_array_length(cc.trace) < $s2)),
+  nodes(source) as (SELECT DISTINCT source
+   FROM connected_component GROUP BY source ORDER BY min(json_array_length(trace)))
+SELECT source, dest, type FROM links WHERE source IN nodes OR dest IN nodes;")))
+    (org-roam-db-query query id distance)))
+
+(defun org-roam-graph--dot (&optional edges all-nodes)
+  "Build the graphviz given the EDGES of the graph.
+If ALL-NODES, include also nodes without edges."
+  (let ((org-roam-directory-temp org-roam-directory)
+        (nodes-table (org-roam--nodes-table))
+        (seen-nodes (list))
+        (edges (or edges (org-roam-db-query [:select :distinct [source dest type] :from links]))))
+    (with-temp-buffer
+      (setq-local org-roam-directory org-roam-directory-temp)
      (insert "digraph \"org-roam\" {\n")
      (dolist (option org-roam-graph-extra-config)
        (insert (org-roam-graph--dot-option option) ";\n"))
-      (dolist (attribute '("node" "edge"))
-        (insert (format " %s [%s];\n" attribute
-                        (mapconcat (lambda (var)
-                                     (org-roam-graph--dot-option var nil "\""))
-                                   (symbol-value
-                                    (intern (concat "org-roam-graph-" attribute "-extra-config")))
-                                   ","))))
-      (dolist (node nodes)
-        (let* ((file (xml-escape-string (car node)))
-               (title (or (cadr node)
-                          (org-roam--path-to-slug file)))
-               (shortened-title (pcase org-roam-graph-shorten-titles
-                                  (`truncate (s-truncate org-roam-graph-max-title-length title))
-                                  (`wrap (s-word-wrap org-roam-graph-max-title-length title))
-                                  (_ title)))
-               (shortened-title (org-roam-string-quote shortened-title))
-               (title (org-roam-string-quote title))
-               (node-properties
-                `(("label"   . ,shortened-title)
-                  ("URL"     . ,(concat "org-protocol://roam-file?file=" (url-hexify-string file)))
-                  ("tooltip" . ,(xml-escape-string title)))))
-          (insert
-           (format "  \"%s\" [%s];\n" file
-                   (mapconcat (lambda (n)
-                                (org-roam-graph--dot-option n nil "\""))
-                              node-properties ",")))))
-      (dolist (edge edges)
-        (insert (apply #'format `("  \"%s\" -> \"%s\";\n"
-                                  ,@(mapcar #'xml-escape-string edge)))))
-      (insert (format "  edge [%s];\n"
-                      (mapconcat #'org-roam-graph--dot-option
-                                 org-roam-graph-edge-cites-extra-config ",")))
-      (dolist (edge edges-cites)
-        (insert (apply #'format `("  \"%s\" -> \"%s\";\n"
-                                  ,@(mapcar #'xml-escape-string edge)))))
+      (insert (format " edge [%s];\n"
+                      (mapconcat (lambda (var)
+                                   (org-roam-graph--dot-option var nil "\""))
+                                 org-roam-graph-edge-extra-config
+                                 ",")))
+      (pcase-dolist (`(,source ,dest ,type) edges)
+        (unless (member type org-roam-graph-link-hidden-types)
+          (pcase-dolist (`(,node ,node-type) `((,source "id")
+                                               (,dest ,type)))
+            (unless (member node seen-nodes)
+              (insert (org-roam-graph--format-node
+                       (or (gethash node nodes-table) node) node-type))
+              (push node seen-nodes)))
+          (insert (format "  \"%s\" -> \"%s\";\n"
+                          (xml-escape-string source)
+                          (xml-escape-string dest)))))
+      (when all-nodes
+        (maphash (lambda (id node)
+                   (unless (member id seen-nodes)
+                     (insert (org-roam-graph--format-node node "id"))))
+                 nodes-table))
      (insert "}")
      (buffer-string))))

-(defun org-roam-graph--build (&optional node-query callback)
-  "Generate a graph showing the relations between nodes in NODE-QUERY.
-Execute CALLBACK when process exits successfully.
+(defun org-roam-graph--format-node (node type)
+  "Return a graphviz NODE with TYPE.
+Handles both Org-roam nodes, and string nodes (e.g. urls)."
+  (let (node-id node-properties)
+    (if (org-roam-node-p node)
+        (let* ((title (org-roam-quote-string (org-roam-node-title node)))
+               (shortened-title (org-roam-quote-string
+                                 (pcase org-roam-graph-shorten-titles
+                                   (`truncate (org-roam-truncate org-roam-graph-max-title-length title))
+                                   (`wrap (s-word-wrap org-roam-graph-max-title-length title))
+                                   (_ title)))))
+          (setq node-id (org-roam-node-id node)
+                node-properties `(("label"   . ,shortened-title)
+                                  ("URL"     . ,(concat "org-protocol://roam-node?node="
+                                                        (url-hexify-string (org-roam-node-id node))))
+                                  ("tooltip" . ,(xml-escape-string title)))))
+      (setq node-id node
+            node-properties (append `(("label" . ,(concat type ":" node)))
+                                    (when (member type (list "http" "https"))
+                                      `(("URL" . ,(xml-escape-string (concat type ":" node))))))))
+    (format "\"%s\" [%s];\n"
+            node-id
+            (mapconcat (lambda (n)
+                         (org-roam-graph--dot-option n nil "\""))
+                       (append (cdr (assoc type org-roam-graph-node-extra-config))
+                               node-properties) ","))))
+
+(defun org-roam-graph--build (graph &optional callback)
+  "Generate the GRAPH, and execute CALLBACK when process exits successfully.
 CALLBACK is passed the graph file as its sole argument."
  (unless (stringp org-roam-graph-executable)
    (user-error "`org-roam-graph-executable' is not a string"))
@ -231,18 +230,13 @@ CALLBACK is passed the graph file as its sole argument."
    (user-error (concat "Cannot find executable \"%s\" to generate the graph.  "
                        "Please adjust `org-roam-graph-executable'")
                org-roam-graph-executable))
-  (let* ((node-query (or node-query
-                         `[:select [file title] :from titles
-                           ,@(org-roam-graph--expand-matcher 'file t)
-                           :group :by file]))
-         (graph      (org-roam-graph--dot node-query))
-         (temp-dot   (make-temp-file "graph." nil ".dot" graph))
-         (temp-graph (make-temp-file "graph." nil ".svg")))
+  (let* ((temp-dot   (make-temp-file "graph." nil ".dot" graph))
+         (temp-graph (make-temp-file "graph." nil (concat "." org-roam-graph-filetype))))
    (org-roam-message "building graph")
    (make-process
     :name "*org-roam-graph--build-process*"
     :buffer "*org-roam-graph--build-process*"
-     :command `(,org-roam-graph-executable ,temp-dot "-Tsvg" "-o" ,temp-graph)
+     :command `(,org-roam-graph-executable ,temp-dot "-T" ,org-roam-graph-filetype "-o" ,temp-graph)
     :sentinel (when callback
                 (lambda (process _event)
                   (when (= 0 (process-exit-status process))
@ -261,47 +255,26 @@ CALLBACK is passed the graph file as its sole argument."
    ('nil (view-file file))
    (_ (signal 'wrong-type-argument `((functionp stringp null) ,org-roam-graph-viewer)))))

-(defun org-roam-graph--build-connected-component (file &optional max-distance callback)
-  "Build a graph of nodes connected to FILE.
-If MAX-DISTANCE is non-nil, limit nodes to MAX-DISTANCE steps.
-CALLBACK is passed to `org-roam-graph--build'."
-  (let* ((file (expand-file-name file))
-         (files (or (if (and max-distance (>= max-distance 0))
-                        (org-roam-db--links-with-max-distance file max-distance)
-                      (org-roam-db--connected-component file))
-                    (list file)))
-         (query `[:select [file title]
-                  :from titles
-                  :where (in file [,@files])]))
-    (org-roam-graph--build query callback)))
-
 ;;;; Commands
 ;;;###autoload
-(defun org-roam-graph (&optional arg file node-query)
-  "Build and possibly display a graph for FILE from NODE-QUERY.
-If FILE is nil, default to current buffer's file name.
+(defun org-roam-graph (&optional arg node)
+  "Build and possibly display a graph for NODE.
 ARG may be any of the following values:
  - nil       show the graph.
-  - `\\[universal-argument]'     show the graph for FILE.
-  - `\\[universal-argument]' N   show the graph for FILE limiting nodes to N steps.
-  - `\\[universal-argument] \\[universal-argument]' build the graph.
-  - `\\[universal-argument]' -   build the graph for FILE.
-  - `\\[universal-argument]' -N  build the graph for FILE limiting nodes to N steps."
-  (interactive "P")
-  (unless org-roam-mode (org-roam-mode))
-  (let ((file (or file (buffer-file-name (buffer-base-buffer)))))
-    (unless (or (not arg) (equal arg '(16)))
-      (unless file
-        (user-error "Cannot build graph for nil file. Is current buffer visiting a file?"))
-      (unless (org-roam--org-roam-file-p file)
-        (user-error "\"%s\" is not an org-roam file" file)))
-    (pcase arg
-      ('nil            (org-roam-graph--build node-query #'org-roam-graph--open))
-      ('(4)            (org-roam-graph--build-connected-component file nil #'org-roam-graph--open))
-      ((pred integerp) (org-roam-graph--build-connected-component file (abs arg) (when (>= arg 0) #'org-roam-graph--open)))
-      ('(16)           (org-roam-graph--build node-query))
-      ('-              (org-roam-graph--build-connected-component file))
-      (_ (user-error "Unrecognized ARG: %s" arg)))))
+  - `\\[universal-argument]'     show the graph for NODE.
+  - `\\[universal-argument]' N   show the graph for NODE limiting nodes to N steps."
+  (interactive
+   (list current-prefix-arg
+         (and current-prefix-arg
+              (org-roam-node-at-point 'assert))))
+  (let ((graph (cl-typecase arg
+                 (null (org-roam-graph--dot nil 'all-nodes))
+                 (cons (org-roam-graph--dot (org-roam-graph--connected-component
+                                             (org-roam-node-id node) 0)))
+                 (integer (org-roam-graph--dot (org-roam-graph--connected-component
+                                                (org-roam-node-id node) (abs arg)))))))
+    (org-roam-graph--build graph #'org-roam-graph--open)))
+

 (provide 'org-roam-graph)

--- a/org-roam-link.el
+++ b/org-roam-link.el
@ -1,310 +0,0 @@
-;;; org-roam-link.el --- Custom links for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
-
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
-;;                  Alan Carroll
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/org-roam/org-roam
-;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.2
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
-
-;; This file is NOT part of GNU Emacs.
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation; either version 3, or (at your option)
-;; any later version.
-;;
-;; This program is distributed in the hope that it will be useful,
-;; but WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;; GNU General Public License for more details.
-;;
-;; You should have received a copy of the GNU General Public License
-;; along with GNU Emacs; see the file COPYING.  If not, write to the
-;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
-;; Boston, MA 02110-1301, USA.
-
-;;; Commentary:
-;;
-;; This adds the custom `roam:' link to Org-roam. `roam:' links allow linking to
-;; Org-roam files via their titles and headlines.
-;;
-;;; Code:
-;;;; Dependencies
-
-(require 'ol)
-(require 'org-roam-compat)
-
-(defvar org-roam-completion-ignore-case)
-(defvar org-roam-directory)
-(declare-function  org-roam--find-file                  "org-roam")
-(declare-function  org-roam-find-file                   "org-roam")
-(declare-function org-roam-format-link                  "org-roam")
-
-(defcustom org-roam-link-auto-replace t
-  "When non-nil, replace Org-roam's roam links with file or id links whenever possible."
-  :group 'org-roam
-  :type 'boolean)
-
-(defcustom org-roam-link-file-path-type 'relative
-  "How the path name in file links should be stored.
-Valid values are:
-
-relative  Relative to the current directory, i.e. the directory of the file
-          into which the link is being inserted.
-absolute  Absolute path, if possible with ~ for home directory.
-noabbrev  Absolute path, no abbreviation of home directory."
-  :group 'org-roam
-  :type '(choice
-          (const relative)
-          (const absolute)
-          (const noabbrev))
-  :safe #'symbolp)
-
-;;; the roam: link
-(org-link-set-parameters "roam"
-                         :follow #'org-roam-link-follow-link)
-
-(defun org-roam-link-follow-link (path)
-  "Navigates to location specified by PATH."
-  (pcase-let ((`(,link-type ,loc ,desc ,mkr) (org-roam-link--get-location path)))
-    (when (and org-roam-link-auto-replace loc desc)
-      (org-roam-link--replace-link link-type loc desc))
-    (pcase link-type
-          ("file"
-           (if loc
-               (org-roam--find-file loc)
-             (org-roam-find-file desc nil nil t)))
-          ("id"
-           (org-goto-marker-or-bmk mkr)))))
-
-;;; Retrieval Functions
-(defun org-roam-link--get-titles ()
-  "Return all titles within Org-roam."
-  (mapcar #'car (org-roam-db-query [:select [titles:title] :from titles])))
-
-(defun org-roam-link--get-headlines (&optional file with-marker use-stack)
-  "Return all outline headings for the current buffer.
-If FILE, return outline headings for passed FILE instead.
-If WITH-MARKER, return a cons cell of (headline . marker).
-If USE-STACK, include the parent paths as well."
-  (let* ((buf (or (and file
-                       (or (find-buffer-visiting file)
-                           (find-file-noselect file)))
-                  (current-buffer)))
-         (outline-level-fn outline-level)
-         (path-separator "/")
-         (stack-level 0)
-         stack cands name level marker)
-    (with-current-buffer buf
-      (save-excursion
-        (goto-char (point-min))
-        (while (re-search-forward org-complex-heading-regexp nil t)
-          (save-excursion
-            (setq name (substring-no-properties (or (match-string 4) "")))
-            (setq marker (point-marker))
-            (when use-stack
-              (goto-char (match-beginning 0))
-              (setq level (funcall outline-level-fn))
-              ;; Update stack.  The empty entry guards against incorrect
-              ;; headline hierarchies, e.g. a level 3 headline
-              ;; immediately following a level 1 entry.
-              (while (<= level stack-level)
-                (pop stack)
-                (cl-decf stack-level))
-              (while (> level stack-level)
-                (push name stack)
-                (cl-incf stack-level))
-              (setq name (mapconcat #'identity
-                                    (reverse stack)
-                                    path-separator)))
-            (push (if with-marker
-                      (cons name marker)
-                    name) cands)))))
-    (nreverse cands)))
-
-(defun org-roam-link--get-file-from-title (title &optional no-interactive)
-  "Return the file path corresponding to TITLE.
-When NO-INTERACTIVE, return nil if there are multiple options."
-  (let ((files (mapcar #'car (org-roam-db-query [:select [titles:file] :from titles
-                                                 :where (= titles:title $v1)]
-                                                (vector title)))))
-    (pcase files
-      ('nil nil)
-      (`(,file) file)
-      (_
-       (unless no-interactive
-         (completing-read "Select file: " files))))))
-
-(defun org-roam-link--get-id-from-headline (headline &optional file)
-  "Return (marker . id) correspondng to HEADLINE.
-If FILE, get headline from FILE instead.
-If there is no corresponding headline, return nil."
-  (save-excursion
-    (with-current-buffer (or (and file
-                                  (or (find-buffer-visiting file)
-                                      (find-file-noselect file)))
-                             (current-buffer))
-      (let ((headlines (org-roam-link--get-headlines file 'with-markers)))
-        (when-let ((marker (cdr (assoc-string headline headlines))))
-          (goto-char marker)
-          (cons marker
-                (when org-roam-link-auto-replace
-                  (org-id-get-create))))))))
-
-;;; Path-related functions
-(defun org-roam-link-get-path (path)
-  "Return the PATH of the link to use.
-Respect `org-link-file-path-type', see the variable documentation for details.
-If DIR is passed, use DIR as the default directory."
-  (pcase org-roam-link-file-path-type
-      ('absolute
-       (abbreviate-file-name (expand-file-name path)))
-      ('noabbrev
-       (expand-file-name path))
-      ('relative
-       (file-relative-name path))))
-
-(defun org-roam-link--split-path (path)
-  "Splits PATH into title and headline.
-Return a list of the form (type title has-headline-p headline star-idx).
-type is one of `title', `headline', `title+headline'.
-title is the title component of the path.
-headline is the headline component of the path.
-star-idx is the index of the asterisk, if any."
-  (save-match-data
-    (let* ((star-index (string-match-p "\\*" path))
-           (title (substring-no-properties path 0 star-index))
-           (headline (if star-index
-                         (substring-no-properties path (+ 1 star-index))
-                       ""))
-           (type (cond ((not star-index)
-                        'title)
-                       ((= 0 star-index)
-                        'headline)
-                       (t 'title+headline))))
-      (list type title headline star-index))))
-
-(defun org-roam-link--get-location (link)
-  "Return the location of Org-roam fuzzy LINK.
-The location is returned as a list containing (link-type loc desc marker).
-nil is returned if there is no matching location.
-
-link-type is either \"file\" or \"id\".
-loc is the target location: e.g. a file path, or an id.
-marker is a marker to the headline, if applicable."
-  (let (mkr link-type desc loc)
-    (pcase-let ((`(,type ,title ,headline _) (org-roam-link--split-path link)))
-      (pcase type
-        ('title+headline
-         (let ((file (org-roam-link--get-file-from-title title)))
-           (if (not file)
-               (org-roam-message "Cannot find matching file")
-             (setq mkr (org-roam-link--get-id-from-headline headline file))
-             (pcase mkr
-               (`(,marker . ,target-id)
-                (setq mkr marker
-                      loc target-id
-                      link-type "id"
-                      desc headline))
-               (_ (org-roam-message "cannot find matching id"))))))
-        ('title
-         (setq loc (org-roam-link--get-file-from-title title)
-               desc title
-               link-type "file"))
-        ('headline
-         (setq mkr (org-roam-link--get-id-from-headline headline))
-         (pcase mkr
-           (`(,marker . ,target-id)
-            (setq mkr marker
-                  loc target-id
-                  desc headline
-                  link-type "id"))
-           (_ (org-roam-message "Cannot find matching headline")))))
-      (list link-type loc desc mkr))))
-
-;;; Conversion Functions
-(defun org-roam-link--replace-link (link-type loc &optional desc)
-  "Replace link at point with a vanilla Org link.
-LINK-TYPE is the Org link type, typically \"file\" or \"id\".
-LOC is path for the Org link.
-DESC is the link description."
-  (save-excursion
-    (save-match-data
-      (unless (org-in-regexp org-link-bracket-re 1)
-        (user-error "No link at point"))
-      (replace-match "")
-      (insert (org-roam-format-link loc desc link-type)))))
-
-(defun org-roam-link-replace-all ()
-  "Replace all roam links in the current buffer."
-  (interactive)
-  (save-excursion
-    (goto-char (point-min))
-    (while (re-search-forward org-link-bracket-re nil t)
-      (let ((context (org-element-context)))
-          (pcase (org-element-lineage context '(link) t)
-            (`nil nil)
-            (link
-             (when (string-equal "roam" (org-element-property :type link))
-               (pcase-let ((`(,link-type ,loc ,desc _) (org-roam-link--get-location (org-element-property :path link))))
-                 (when (and link-type loc)
-                   (org-roam-link--replace-link link-type loc desc))))))))))
-
-(defun org-roam-link--replace-link-on-save ()
-  "Hook to replace all roam links on save."
-  (when org-roam-link-auto-replace
-    (org-roam-link-replace-all)))
-
-;;; Completion
-(defun org-roam-link-complete-at-point ()
-  "Do appropriate completion for the link at point."
-  (let ((end (point))
-        (start (point))
-        collection link-type headline-only-p)
-    (when (org-in-regexp org-link-bracket-re 1)
-      (setq start (match-beginning 1)
-            end (match-end 1))
-      (let ((context (org-element-context)))
-        (pcase (org-element-lineage context '(link) t)
-          (`nil nil)
-          (link
-           (setq link-type (org-element-property :type link))
-           (when (member link-type '("roam" "fuzzy"))
-             (when (string= link-type "roam") (setq start (+ start (length "roam:"))))
-             (pcase-let ((`(,type ,title _ ,star-idx)
-                          (org-roam-link--split-path (org-element-property :path link))))
-               (pcase type
-                 ('title+headline
-                  (when-let ((file (org-roam-link--get-file-from-title title t)))
-                    (setq collection (apply-partially #'org-roam-link--get-headlines file))
-                    (setq start (+ start star-idx 1))))
-                 ('title
-                  (setq collection #'org-roam-link--get-titles))
-                 ('headline
-                  (setq collection #'org-roam-link--get-headlines)
-                  (setq start (+ start star-idx 1))
-                  (setq headline-only-p t)))))))))
-    (when collection
-      (let ((prefix (buffer-substring-no-properties start end)))
-        (list start end
-              (if (functionp collection)
-                  (completion-table-case-fold
-                   (completion-table-dynamic
-                    (lambda (_)
-                      (cl-remove-if (apply-partially #'string= prefix)
-                                    (funcall collection))))
-                   (not org-roam-completion-ignore-case))
-                collection)
-              :exit-function
-              (lambda (str &rest _)
-                (delete-char (- 0 (length str)
-                                (if headline-only-p 1 0)))
-                (insert (concat (unless (string= link-type "roam") "roam:")
-                                (when headline-only-p "*")
-                                str))))))))
-
-(provide 'org-roam-link)
-;;; org-roam-link.el ends here
--- a/org-roam-macs.el
+++ b/org-roam-macs.el
@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.2
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))

 ;; This file is NOT part of GNU Emacs.

@ -27,75 +27,64 @@

 ;;; Commentary:
 ;;
-;; This library implements macros and utility functions used throughout
-;; org-roam.
-;;
+;; This library implements macros used throughout org-roam.
 ;;
 ;;; Code:
-;;;; Library Requires
-(require 'dash)
+(defmacro org-roam-plist-map! (fn plist)
+  "Map FN over PLIST, modifying it in-place."
+  (declare (indent 1))
+  (let ((plist-var (make-symbol "plist"))
+        (k (make-symbol "k"))
+        (v (make-symbol "v")))
+    `(let ((,plist-var (copy-sequence ,plist)))
+       (while ,plist-var
+         (setq ,k (pop ,plist-var))
+         (setq ,v (pop ,plist-var))
+         (setq ,plist (plist-put ,plist ,k (funcall ,fn ,k ,v)))))))

-(defvar org-roam-verbose)
+(defmacro org-roam-with-file (file keep-buf-p &rest body)
+  "Execute BODY within FILE.
+If FILE is nil, execute BODY in the current buffer.
+Kills the buffer if KEEP-BUF-P is nil, and FILE is not yet visited."
+  (declare (indent 2) (debug t))
+  `(let* (new-buf
+          (auto-mode-alist nil)
+          (buf (or (and (not ,file)
+                        (current-buffer)) ;If FILE is nil, use current buffer
+                   (find-buffer-visiting ,file) ; If FILE is already visited, find buffer
+                   (progn
+                     (setq new-buf t)
+                     (find-file-noselect ,file)))) ; Else, visit FILE and return buffer
+          res)
+     (with-current-buffer buf
+       (unless (equal major-mode 'org-mode)
+         (delay-mode-hooks
+           (let ((org-inhibit-startup t)
+                 (org-agenda-files nil))
+             (org-mode))))
+       (setq res (progn ,@body))
+       (unless (and new-buf (not ,keep-buf-p))
+         (save-buffer)))
+     (if (and new-buf (not ,keep-buf-p))
+       (when (find-buffer-visiting ,file)
+         (kill-buffer (find-buffer-visiting ,file))))
+     res))

-;;;; Utility Functions
-(defun org-roam--list-interleave (lst separator)
-  "Interleaves elements in LST with SEPARATOR."
-  (when lst
-    (let ((new-lst (list (pop lst))))
-      (dolist (it lst)
-        (nconc new-lst (list separator it)))
-      new-lst)))
-
-(defmacro org-roam--with-temp-buffer (file &rest body)
+(defmacro org-roam-with-temp-buffer (file &rest body)
  "Execute BODY within a temp buffer.
 Like `with-temp-buffer', but propagates `org-roam-directory'.
-If FILE, set `org-roam-temp-file-name' to file and insert its contents."
+If FILE, set `default-directory' to FILE's directory and insert its contents."
  (declare (indent 1) (debug t))
  (let ((current-org-roam-directory (make-symbol "current-org-roam-directory")))
    `(let ((,current-org-roam-directory org-roam-directory))
       (with-temp-buffer
-         (let ((org-roam-directory ,current-org-roam-directory)
-               (org-mode-hook nil)
-               (org-inhibit-startup t))
-           (org-mode)
+         (let ((org-roam-directory ,current-org-roam-directory))
+           (delay-mode-hooks (org-mode))
           (when ,file
             (insert-file-contents ,file)
-             (setq-local org-roam-file-name ,file))
+             (setq-local default-directory (file-name-directory ,file)))
           ,@body)))))

-(defun org-roam-message (format-string &rest args)
-  "Pass FORMAT-STRING and ARGS to `message' when `org-roam-verbose' is t."
-  (when org-roam-verbose
-    (apply #'message `(,(concat "(org-roam) " format-string) ,@args))))
-
-(defun org-roam-string-quote (str)
-  "Quote STR."
-  (->> str
-       (s-replace "\\" "\\\\")
-       (s-replace "\"" "\\\"")))
-
-;;; Shielding regions
-(defun org-roam-shield-region (beg end)
-  "Shield REGION against modifications.
-REGION must be a cons-cell containing the marker to the region
-beginning and maximum values."
-  (when (and beg end)
-    (add-text-properties beg end
-                           '(font-lock-face org-roam-link-shielded
-                                            read-only t)
-                           (marker-buffer beg))
-    (cons beg end)))
-
-(defun org-roam-unshield-region (beg end)
-  "Unshield the shielded REGION."
-  (when (and beg end)
-    (let ((inhibit-read-only t))
-      (remove-text-properties beg end
-                              '(font-lock-face org-roam-link-shielded
-                                               read-only t)
-                              (marker-buffer beg)))
-    (cons beg end)))
-
 (provide 'org-roam-macs)

 ;;; org-roam-macs.el ends here
--- a/org-roam-migrate.el
+++ b/org-roam-migrate.el
@ -0,0 +1,192 @@
+;;; org-roam-migrate.el --- Migration utilities from v1 to v2 -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;;  To ease transition from v1 to v2, we provide various migration utilities.
+;;  This library helps convert v1 notes to v2, and informs the user.
+;;
+;;; Code:
+;;;; Dependencies
+;;;;
+;;; v1 breaking warning
+(require 'org-roam-db)
+
+(defvar org-roam-v2-ack nil)
+
+(unless org-roam-v2-ack
+  (lwarn 'org-roam :error "
+------------------------------------
+WARNING: You're now on Org-roam v2!
+------------------------------------
+
+You may have arrived here from a package upgrade. Please read the
+wiki entry at
+https://github.com/org-roam/org-roam/wiki/Hitchhiker's-Rough-Guide-to-Org-roam-V2
+for an overview of the major changes.
+
+Notes taken in v1 are incompatible with v1, but you can upgrade
+them to the v2 format via a simple command. To migrate your
+notes, run:
+
+  M-x org-roam-migrate-wizard
+
+If you wish to stay on v1, v1 is unfortunately not distributed on
+MELPA. See org-roam/org-roam-v1 on GitHub on how to install v1.
+
+If you've gone through the migration steps (if necessary), and
+know what you're doing set `org-roam-v2-ack' to `t' to disable
+this warning. You can do so by adding:
+
+(setq org-roam-v2-ack t)
+
+To your init file.
+
+"))
+
+;;;###autoload
+(defun org-roam-migrate-wizard ()
+  "Migrate all notes from to be compatible with Org-roam v2.
+1. Convert all notes from v1 format to v2.
+2. Rebuild the cache.
+3. Replace all file links with ID links."
+  (interactive)
+  (when (yes-or-no-p "Org-roam will now convert all your notes from v1 to v2.
+This will take a while. Are you sure you want to do this?")
+    ;; Back up notes
+    (let ((backup-dir (expand-file-name "org-roam.bak"
+                                        (file-name-directory (directory-file-name org-roam-directory)))))
+      (message "Backing up files to %s" backup-dir)
+      (copy-directory org-roam-directory backup-dir))
+
+    ;; Convert v1 to v2
+    (dolist (f (org-roam--list-all-files))
+      (org-roam-with-file f nil
+        (org-roam-migrate-v1-to-v2)))
+    ;; Rebuild cache
+    (org-roam-db-sync 'force)
+
+    ;;Replace all file links with ID links
+    (dolist (f (org-roam--list-all-files))
+      (org-roam-with-file f nil
+        (org-roam-migrate-replace-file-links-with-id)
+        (save-buffer)))))
+
+(defun org-roam-migrate-v1-to-v2 ()
+  "Convert the current buffer to v2 format."
+  ;; Create file level ID
+  (org-with-point-at 1
+    (org-id-get-create))
+  ;; Replace roam_key into properties drawer roam_ref
+  (when-let* ((refs (mapcan #'split-string-and-unquote
+                            (cdar (org-collect-keywords '("roam_key"))))))
+    (let ((case-fold-search t))
+      (org-with-point-at 1
+        (dolist (ref refs)
+          (org-roam-ref-add ref))
+        (while (re-search-forward "^#\\+roam_key:" (point-max) t)
+          (beginning-of-line)
+          (kill-line 1)))))
+
+  ;; Replace roam_alias into properties drawer roam_aliases
+  (when-let* ((aliases (mapcan #'split-string-and-unquote
+                               (cdar (org-collect-keywords '("roam_alias"))))))
+    (let ((case-fold-search t))
+      (org-with-point-at 1
+        (dolist (alias aliases)
+          (org-roam-alias-add alias))
+        (while (re-search-forward "^#\\+roam_alias:" (point-max) t)
+          (beginning-of-line)
+          (kill-line 1)))))
+
+  ;; Replace #+roam_tags into #+filetags
+  (org-with-point-at 1
+    (let* ((roam-tags (org-roam-migrate-get-prop-list "ROAM_TAGS"))
+           (file-tags (org-roam-migrate-get-prop-list "FILETAGS"))
+           (tags (append roam-tags file-tags))
+           (tags (seq-map (lambda (tag)
+                            (replace-regexp-in-string
+                             "[^[:alnum:]_@#%]"
+                             "_"
+                             tag)) tags))
+           (tags (seq-uniq tags)))
+      (when tags
+        (org-roam-migrate-prop-set "filetags" (string-join tags " "))))
+    (let ((case-fold-search t))
+      (org-with-point-at 1
+        (while (re-search-forward "^#\\+roam_tags:" (point-max) t)
+          (beginning-of-line)
+          (kill-line 1)))))
+  (save-buffer))
+
+(defun org-roam-migrate-get-prop-list (keyword)
+  "Return prop list for KEYWORD."
+  (let ((re (format "^#\\+%s:[ \t]*\\([^\n]+\\)" (upcase keyword)))
+        lst)
+    (goto-char (point-min))
+    (while (re-search-forward re 2048 t)
+      (setq lst (append lst (split-string-and-unquote
+                             (buffer-substring-no-properties
+                              (match-beginning 1) (match-end 1))))))
+    lst))
+
+(defun org-roam-migrate-prop-set (name value)
+  "Set a file property called NAME to VALUE in buffer file.
+If the property is already set, replace its value."
+  (setq name (downcase name))
+  (org-with-point-at 1
+    (let ((case-fold-search t))
+      (if (re-search-forward (concat "^#\\+" name ":\\(.*\\)")
+                             (point-max) t)
+          (replace-match (concat "#+" name ": " value) 'fixedcase)
+        (while (and (not (eobp))
+                    (looking-at "^[#:]"))
+          (if (save-excursion (end-of-line) (eobp))
+              (progn
+                (end-of-line)
+                (insert "\n"))
+            (forward-line)
+            (beginning-of-line)))
+        (insert "#+" name ": " value "\n")))))
+
+(defun org-roam-migrate-replace-file-links-with-id ()
+  "Replace all file: links with ID links in current buffer."
+  (org-with-point-at 1
+    (while (re-search-forward org-link-bracket-re nil t)
+      (let* ((mdata (match-data))
+             (path (match-string 1))
+             (desc (match-string 2)))
+        (when (string-prefix-p "file:" path)
+          (setq path (expand-file-name (substring path 5)))
+          (when-let ((node-id (caar (org-roam-db-query [:select [id] :from nodes
+                                                        :where (= file $s1)
+                                                        :and (= level 0)] path))))
+            (set-match-data mdata)
+            (replace-match (org-link-make-string (concat "id:" node-id) desc))))))))
+
+(provide 'org-roam-migrate)
+;;; org-roam-migrate.el ends here
--- a/org-roam-mode.el
+++ b/org-roam-mode.el
@ -0,0 +1,468 @@
+;;; org-roam-mode.el --- create and refresh Org-roam buffers -*- lexical-binding: t -*-
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library implements the abstract major-mode `org-roam-mode', from which
+;; almost all other Org-roam major-modes derive.
+;;
+;;; Code:
+(require 'magit-section)
+
+(require 'org-roam-utils)
+
+(defvar org-roam-directory)
+(defvar org-roam-find-file-hook)
+
+(declare-function org-roam-node-at-point "org-roam")
+
+;;; Faces
+(defface org-roam-header-line
+  `((((class color) (background light))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :foreground "DarkGoldenrod4"
+     :weight bold)
+    (((class color) (background  dark))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :foreground "LightGoldenrod2"
+     :weight bold))
+  "Face for the `header-line' in some Org-roam modes."
+  :group 'org-roam-faces)
+
+(defface org-roam-title
+  '((t :weight bold))
+  "Face for Org-roam titles."
+  :group 'org-roam-faces)
+
+(defface org-roam-olp
+  '((((class color) (background light)) :foreground "grey60")
+    (((class color) (background  dark)) :foreground "grey40"))
+  "Face for the OLP of the node."
+  :group 'org-roam-faces)
+
+(defface org-roam-preview-heading
+  `((((class color) (background light))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :background "grey80"
+     :foreground "grey30")
+    (((class color) (background dark))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :background "grey25"
+     :foreground "grey70"))
+  "Face for preview headings."
+  :group 'org-roam-faces)
+
+(defface org-roam-preview-heading-highlight
+  `((((class color) (background light))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :background "grey75"
+     :foreground "grey30")
+    (((class color) (background dark))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :background "grey35"
+     :foreground "grey70"))
+  "Face for current preview headings."
+  :group 'org-roam-faces)
+
+(defface org-roam-preview-heading-selection
+  `((((class color) (background light))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :inherit org-roam-preview-heading-highlight
+     :foreground "salmon4")
+    (((class color) (background dark))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :inherit org-roam-preview-heading-highlight
+     :foreground "LightSalmon3"))
+  "Face for selected preview headings."
+  :group 'org-roam-faces)
+
+(defface org-roam-preview-region
+  `((t :inherit bold
+       ,@(and (>= emacs-major-version 27)
+              (list :extend (ignore-errors (face-attribute 'region :extend))))))
+  "Face used by `org-roam-highlight-preview-region-using-face'.
+
+This face is overlaid over text that uses other hunk faces,
+and those normally set the foreground and background colors.
+The `:foreground' and especially the `:background' properties
+should be avoided here.  Setting the latter would cause the
+loss of information.  Good properties to set here are `:weight'
+and `:slant'."
+  :group 'org-roam-faces)
+
+(defface org-roam-dim
+  '((((class color) (background light)) :foreground "grey60")
+    (((class color) (background  dark)) :foreground "grey40"))
+  "Face for the dimmer part of the widgets."
+  :group 'org-roam-faces)
+
+;;; Variables
+(defvar org-roam-current-node nil
+  "The current node at point.")
+
+(defvar org-roam-current-directory nil
+  "The `org-roam-directory' value for the current node.")
+
+(defcustom org-roam-mode-section-functions (list #'org-roam-backlinks-section
+                                                 #'org-roam-reflinks-section)
+  "Functions which insert sections of the `org-roam-buffer'.
+Each function is called with one argument, which is the current org-roam node at point."
+  :group 'org-roam
+  :type 'hook)
+
+;;; The mode
+(defvar org-roam-mode-map
+  (let ((map (make-sparse-keymap)))
+    (set-keymap-parent map magit-section-mode-map)
+    (define-key map [C-return]  'org-roam-visit-thing)
+    (define-key map (kbd "C-m") 'org-roam-visit-thing)
+    (define-key map [remap revert-buffer] 'org-roam-buffer-render)
+    map)
+  "Parent keymap for all keymaps of modes derived from `org-roam-mode'.")
+
+(define-derived-mode org-roam-mode magit-section-mode "Org-roam"
+  "Major mode for Org-roam's buffer."
+  :group 'org-roam
+  (face-remap-add-relative 'header-line 'org-roam-header-line))
+
+;;; Key functions
+(defun org-roam-visit-thing ()
+  "This is a placeholder command.
+Where applicable, section-specific keymaps bind another command
+which visits the thing at point."
+  (interactive)
+  (user-error "There is no thing at point that could be visited"))
+
+(defun org-roam-buffer-render ()
+  "Render the current node at point."
+  (interactive)
+  (when (derived-mode-p 'org-roam-mode)
+    (let ((inhibit-read-only t))
+      (erase-buffer)
+      (setq-local default-directory org-roam-current-directory)
+      (setq-local org-roam-directory org-roam-current-directory)
+      (org-roam-set-header-line-format (org-roam-node-title org-roam-current-node))
+      (magit-insert-section (org-roam)
+        (magit-insert-heading)
+        (run-hook-with-args 'org-roam-mode-section-functions org-roam-current-node)))))
+
+(defun org-roam-buffer ()
+  "Launch an Org-roam buffer for the current node at point."
+  (interactive)
+  (if-let ((node (org-roam-node-at-point))
+           (source-org-roam-directory org-roam-directory))
+      (progn
+        (let ((buffer (get-buffer-create
+                       (concat "org-roam: "
+                               (file-relative-name (buffer-file-name) org-roam-directory)))))
+          (with-current-buffer buffer
+            (org-roam-mode)
+            (setq-local org-roam-current-node node)
+            (setq-local org-roam-current-directory source-org-roam-directory)
+            (org-roam-buffer-render))
+          (switch-to-buffer-other-window buffer)))
+    (user-error "No node at point")))
+
+;;; Persistent buffer
+(defvar org-roam-buffer "*org-roam*"
+  "The persistent Org-roam buffer name.")
+
+(defun org-roam-buffer--post-command-h ()
+  "Reconstructs the Org-roam buffer.
+This needs to be quick or infrequent, because this is run at
+`post-command-hook'.  If REDISPLAY, force an update of
+the Org-roam buffer."
+  (when (get-buffer-window org-roam-buffer)
+    (when-let ((node (org-roam-node-at-point)))
+      (unless (equal node org-roam-current-node)
+        (setq org-roam-current-node node)
+        (setq org-roam-current-directory org-roam-directory)
+        (org-roam-buffer-persistent-redisplay)))))
+
+(define-inline org-roam-buffer--visibility ()
+  "Return whether the current visibility state of the org-roam buffer.
+Valid states are 'visible, 'exists and 'none."
+  (declare (side-effect-free t))
+  (inline-quote
+   (cond
+    ((get-buffer-window org-roam-buffer) 'visible)
+    ((get-buffer org-roam-buffer) 'exists)
+    (t 'none))))
+
+(defun org-roam-buffer-toggle ()
+  "Toggle display of the Org-roam buffer."
+  (interactive)
+  (pcase (org-roam-buffer--visibility)
+    ('visible
+     (progn
+       (delete-window (get-buffer-window org-roam-buffer))
+       (remove-hook 'post-command-hook #'org-roam-buffer--post-command-h)))
+    ((or 'exists 'none)
+     (progn
+       (setq org-roam-current-node (org-roam-node-at-point)
+             org-roam-current-directory org-roam-directory)
+       (display-buffer (get-buffer-create org-roam-buffer))
+       (org-roam-buffer-persistent-redisplay)))))
+
+(defun org-roam-buffer-persistent-redisplay ()
+  "Recompute contents of the persistent Org-roam buffer.
+Has no effect when `org-roam-current-node' is nil."
+  (when org-roam-current-node
+    (with-current-buffer (get-buffer-create org-roam-buffer)
+      (let ((inhibit-read-only t))
+        (erase-buffer)
+        (org-roam-mode)
+        (setq-local default-directory org-roam-current-directory)
+        (setq-local org-roam-directory org-roam-current-directory)
+        (org-roam-set-header-line-format (org-roam-node-title org-roam-current-node))
+        (magit-insert-section (org-roam)
+          (magit-insert-heading)
+          (dolist (fn org-roam-mode-section-functions)
+            (funcall fn org-roam-current-node)))))))
+
+(defun org-roam-buffer--redisplay ()
+  "."
+  (add-hook 'post-command-hook #'org-roam-buffer--post-command-h nil t))
+
+(add-hook 'org-roam-find-file-hook #'org-roam-buffer--redisplay)
+
+;;; Sections
+;;;; Backlinks
+(cl-defstruct (org-roam-backlink (:constructor org-roam-backlink-create)
+                                 (:copier nil))
+  source-node target-node
+  point properties)
+
+(cl-defmethod org-roam-populate ((backlink org-roam-backlink))
+  "Populate BACKLINK from database."
+  (setf (org-roam-backlink-source-node backlink)
+        (org-roam-populate (org-roam-backlink-source-node backlink))
+        (org-roam-backlink-target-node backlink)
+        (org-roam-populate (org-roam-backlink-target-node backlink)))
+  backlink)
+
+(defun org-roam-backlinks-get (node)
+  "Return the backlinks for NODE."
+  (let ((backlinks (org-roam-db-query
+                    [:select [source dest pos properties]
+                     :from links
+                     :where (= dest $s1)
+                     :and (= type "id")]
+                    (org-roam-node-id node))))
+    (cl-loop for backlink in backlinks
+             collect (pcase-let ((`(,source-id ,dest-id ,pos ,properties) backlink))
+                       (org-roam-populate
+                        (org-roam-backlink-create
+                         :source-node (org-roam-node-create :id source-id)
+                         :target-node (org-roam-node-create :id dest-id)
+                         :point pos
+                         :properties properties))))))
+
+(defun org-roam-backlinks-sort (a b)
+  "Default sorting function for backlinks A and B.
+Sorts by title."
+  (string< (org-roam-node-title (org-roam-backlink-source-node a))
+           (org-roam-node-title (org-roam-backlink-source-node b))))
+
+(defun org-roam-backlinks-section (node)
+  "The backlinks section for NODE."
+  (when-let ((backlinks (seq-sort #'org-roam-backlinks-sort (org-roam-backlinks-get node))))
+    (magit-insert-section (org-roam-backlinks)
+      (magit-insert-heading "Backlinks:")
+      (dolist (backlink backlinks)
+        (org-roam-node-insert-section
+         :source-node (org-roam-backlink-source-node backlink)
+         :point (org-roam-backlink-point backlink)
+         :properties (org-roam-backlink-properties backlink)))
+      (insert ?\n))))
+
+;;;; Reflinks
+(cl-defstruct (org-roam-reflink (:constructor org-roam-reflink-create)
+                                (:copier nil))
+  source-node ref
+  point properties)
+
+(cl-defmethod org-roam-populate ((reflink org-roam-reflink))
+  "Populate REFLINK from database."
+  (setf (org-roam-reflink-source-node reflink)
+        (org-roam-populate (org-roam-reflink-source-node reflink)))
+  reflink)
+
+(defun org-roam-reflinks-get (node)
+  "Return the reflinks for NODE."
+  (let ((refs (org-roam-db-query [:select [ref] :from refs
+                                  :where (= node-id $s1)]
+                                 (org-roam-node-id node)))
+        links)
+    (pcase-dolist (`(,ref) refs)
+      (pcase-dolist (`(,source-id ,pos ,properties) (org-roam-db-query
+                                                     [:select [source pos properties]
+                                                      :from links
+                                                      :where (= dest $s1)]
+                                                     ref))
+        (push (org-roam-populate
+               (org-roam-reflink-create
+                :source-node (org-roam-node-create :id source-id)
+                :ref ref
+                :point pos
+                :properties properties)) links)))
+    links))
+
+(defun org-roam-reflinks-sort (a b)
+  "Default sorting function for reflinks A and B.
+Sorts by title."
+  (string< (org-roam-node-title (org-roam-reflink-source-node a))
+           (org-roam-node-title (org-roam-reflink-source-node b))))
+
+(defun org-roam-reflinks-section (node)
+  "The reflinks section for NODE."
+  (when (org-roam-node-refs node)
+    (let* ((reflinks (seq-sort #'org-roam-reflinks-sort (org-roam-reflinks-get node))))
+      (magit-insert-section (org-roam-reflinks)
+        (magit-insert-heading "Reflinks:")
+        (dolist (reflink reflinks)
+          (org-roam-node-insert-section
+           :source-node (org-roam-reflink-source-node reflink)
+           :point (org-roam-reflink-point reflink)
+           :properties (org-roam-reflink-properties reflink)))
+        (insert ?\n)))))
+
+;;;; Unlinked references
+(defvar org-roam-grep-map
+  (let ((map (make-sparse-keymap)))
+    (set-keymap-parent map org-roam-mode-map)
+    (define-key map [remap org-roam-visit-thing] 'org-roam-file-visit)
+    map)
+  "Keymap for Org-roam grep result sections.")
+
+(defclass org-roam-grep-section (magit-section)
+  ((keymap :initform 'org-roam-grep-map)
+   (file :initform nil)
+   (row :initform nil)
+   (col :initform nil)))
+
+(defun org-roam-file-at-point (&optional assert)
+  "Return the file at point.
+If ASSERT, throw an error."
+  (if-let ((file (magit-section-case
+                   (org-roam-node-section (org-roam-node-file (oref it node)))
+                   (org-roam-grep-section (oref it file))
+                   (org-roam-preview-section (oref it file)))))
+      file
+    (when assert
+      (user-error "No file at point"))))
+
+(defun org-roam-file-visit (file &optional other-window row col)
+  "Visits FILE.
+With a prefix argument OTHER-WINDOW, display the buffer in
+another window instead.
+If ROW, move to the row, and if COL move to the COL."
+  (interactive (list (org-roam-file-at-point t)
+                     current-prefix-arg
+                     (oref (magit-current-section) row)
+                     (oref (magit-current-section) col)))
+  (let ((buf (find-file-noselect file)))
+    (with-current-buffer buf
+      (widen)
+      (goto-char (point-min))
+      (when row
+        (forward-line (1- row)))
+      (when col
+        (forward-char (1- col))))
+    (funcall (if other-window
+                 #'switch-to-buffer-other-window
+               #'pop-to-buffer-same-window) buf)))
+
+(defvar org-roam-unlinked-references-result-re
+  (rx (group (one-or-more anything))
+      ":"
+      (group (one-or-more digit))
+      ":"
+      (group (one-or-more digit))
+      ":"
+      (group (zero-or-more anything)))
+  "Regex for the return result of a ripgrep query.")
+
+(defun org-roam-unlinked-references-preview-line (file row)
+  "Return the preview line from FILE.
+This is the ROW within FILE."
+  (with-temp-buffer
+    (insert-file-contents-literally file)
+    (forward-line (1- row))
+    (buffer-substring-no-properties
+     (save-excursion
+       (beginning-of-line)
+       (point))
+     (save-excursion
+       (end-of-line)
+       (point)))))
+
+(defun org-roam-unlinked-references-section (node)
+  "The unlinked references section for NODE.
+References from FILE are excluded."
+  (when (and (executable-find "rg")
+             (not (string-match "PCRE2 is not available"
+                                (shell-command-to-string "rg --pcre2-version"))))
+    (let* ((titles (cons (org-roam-node-title node)
+                         (org-roam-node-aliases node)))
+           (rg-command (concat "rg -o --vimgrep -P -i "
+                               (mapconcat (lambda (glob) (concat "-g " glob))
+                                          (org-roam--list-files-search-globs org-roam-file-extensions)
+                                          " ")
+                               (format " '\\[([^[]]++|(?R))*\\]%s' "
+                                       (mapconcat (lambda (title)
+                                                    (format "|(\\b%s\\b)" (shell-quote-argument title)))
+                                                  titles ""))
+                               org-roam-directory))
+           (results (split-string (shell-command-to-string rg-command) "\n"))
+           f row col match)
+      (magit-insert-section (unlinked-references)
+        (magit-insert-heading "Unlinked References:")
+        (dolist (line results)
+          (save-match-data
+            (when (string-match org-roam-unlinked-references-result-re line)
+              (setq f (match-string 1 line)
+                    row (string-to-number (match-string 2 line))
+                    col (string-to-number (match-string 3 line))
+                    match (match-string 4 line))
+              (when (and match
+                         (not (f-equal-p (org-roam-node-file node) f))
+                         (member (downcase match) (mapcar #'downcase titles)))
+                (magit-insert-section section (org-roam-grep-section)
+                  (oset section file f)
+                  (oset section row row)
+                  (oset section col col)
+                  (insert (propertize (format "%s:%s:%s"
+                                              (truncate-string-to-width (file-name-base f) 15 nil nil "...")
+                                              row col) 'font-lock-face 'org-roam-dim)
+                          " "
+                          (org-roam-fontify-like-in-org-mode
+                           (org-roam-unlinked-references-preview-line f row))
+                          "\n"))))))
+        (insert ?\n)))))
+
+(provide 'org-roam-mode)
+;;; org-roam-mode.el ends here
--- a/org-roam-overlay.el
+++ b/org-roam-overlay.el
@ -0,0 +1,98 @@
+;;; org-roam-overlay.el --- Link overlay for Org-roam nodes -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library is an attempt at injecting Roam functionality into Org-mode.
+;; This is achieved primarily through building caches for forward links,
+;; backward links, and file titles.
+;;
+;;
+;;; Code:
+;;;; Dependencies
+
+(defface org-roam-overlay
+  '((((class color) (background light))
+     :background "grey90" :box (:line-width -1 :color "black"))
+    (((class color) (background dark))
+     :background "grey10" :box (:line-width -1 :color "white")))
+  "Face for the Org-roam overlay."
+  :group 'org-roam-faces)
+
+(defun org-roam-overlay--make (l r &rest props)
+  "Make an overlay from L to R with PROPS."
+  (let ((o (make-overlay l (or r l))))
+    (overlay-put o 'category 'org-roam)
+    (while props (overlay-put o (pop props) (pop props)))
+    o))
+
+(defun org-roam-overlay-make-link-overlay (link)
+  "Create overlay for LINK."
+  (save-excursion
+    (save-match-data
+      (let* ((type (org-element-property :type link))
+             (id (org-element-property :path link))
+             (pos (org-element-property :end link))
+             (desc-p (org-element-property :contents-begin link))
+             node)
+        (when (and (string-equal type "id")
+                   (setq node (org-roam-node-from-id id))
+                   (not desc-p))
+          (org-roam-overlay--make
+           pos pos
+           'after-string (format "%s "
+                                 (propertize (org-roam-node-title node)
+                                             'face 'org-roam-overlay))))))))
+
+(defun org-roam-overlay-enable ()
+  "Enable Org-roam overlays."
+  (org-roam-db-map-links
+   (list #'org-roam-overlay-make-link-overlay)))
+
+(defun org-roam-overlay-disable ()
+  "Disable Org-roam overlays."
+  (remove-overlays nil nil 'category 'org-roam))
+
+(defun org-roam-overlay-redisplay ()
+  "Redisplay Org-roam overlays."
+  (org-roam-overlay-disable)
+  (org-roam-overlay-enable))
+
+(define-minor-mode org-roam-overlay-mode
+  "Overlays for Org-roam ID links.
+Org-roam overlay mode is a minor mode.  When enabled,
+overlay displaying the node's title is displayed."
+  :lighter " org-roam-overlay"
+  (if org-roam-overlay-mode
+      (progn
+        (org-roam-overlay-enable)
+        (add-hook 'after-save-hook #'org-roam-overlay-redisplay nil t))
+    (org-roam-overlay-disable)
+    (remove-hook 'after-save-hook #'org-roam-overlay-redisplay t)))
+
+(provide 'org-roam-overlay)
+;;; org-roam-overlay.el ends here
--- a/org-roam-protocol.el
+++ b/org-roam-protocol.el
@ -4,8 +4,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.2
-;; Package-Requires: ((emacs "26.1") (org "9.3"))
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))

 ;; This file is NOT part of GNU Emacs.

@ -31,14 +31,21 @@
 ;;
 ;; We define 2 protocols:
 ;;
-;; 1. "roam-file": This protocol simply opens the file given by the FILE key
+;; 1. "roam-node": This protocol simply opens the node given by the node ID
 ;; 2. "roam-ref": This protocol creates or opens a note with the given REF
 ;;
 ;;; Code:
 (require 'org-protocol)
 (require 'org-roam)
+(eval-when-compile
+  (require 'org-roam-macs))
 (require 'ol) ;; for org-link-decode

+(defcustom org-roam-protocol-store-links nil
+  "Whether to store links when capturing websites with `org-roam-protocol'."
+  :type 'boolean
+  :group 'org-roam)
+
 ;;;; Functions
 (defun org-roam-protocol-open-ref (info)
  "Process an org-protocol://roam-ref?ref= style url with INFO.
@ -46,28 +53,37 @@
 It opens or creates a note with the given ref.

  javascript:location.href = \\='org-protocol://roam-ref?template=r&ref=\\='+ \\
-        encodeURIComponent(location.href) + \\='&title=\\=' \\
+        encodeURIComponent(location.href) + \\='&title=\\=' + \\
        encodeURIComponent(document.title) + \\='&body=\\=' + \\
        encodeURIComponent(window.getSelection())"
-  (when-let* ((alist (org-roam--plist-to-alist info))
-              (decoded-alist (mapcar (lambda (k.v)
-                                       (let ((key (car k.v))
-                                             (val (cdr k.v)))
-                                         (cons key (org-link-decode val)))) alist)))
-    (unless (assoc 'ref decoded-alist)
-      (error "No ref key provided"))
-    (when-let ((title (cdr (assoc 'title decoded-alist))))
-      (push (cons 'slug (funcall org-roam-title-to-slug-function title)) decoded-alist))
-    (let* ((org-roam-capture-templates org-roam-capture-ref-templates)
-           (org-roam-capture--context 'ref)
-           (org-roam-capture--info decoded-alist)
-           (template (cdr (assoc 'template decoded-alist))))
-      (raise-frame)
-      (org-roam-capture--capture nil template)
-      (org-roam-message "Item captured.")))
+  (unless (plist-get info :ref)
+    (user-error "No ref key provided"))
+  (org-roam-plist-map! (lambda (k v)
+                         (org-link-decode
+                          (if (equal k :ref)
+                              (org-protocol-sanitize-uri v)
+                            v))) info)
+  (when org-roam-protocol-store-links
+    (push (list (plist-get info :ref)
+                (plist-get info :title)) org-stored-links))
+  (org-link-store-props :type (and (string-match org-link-plain-re
+                                                 (plist-get info :ref))
+                                   (match-string 1 (plist-get info :ref)))
+                        :link (plist-get info :ref)
+                        :annotation (org-link-make-string (plist-get info :ref)
+                                                          (or (plist-get info :title)
+                                                              (plist-get info :ref)))
+                        :initial (or (plist-get info :body) ""))
+  (raise-frame)
+  (org-roam-capture-
+   :keys (plist-get info :template)
+   :node (org-roam-node-create :title (plist-get info :title))
+   :info (list :ref (plist-get info :ref)
+               :body (plist-get info :body))
+   :templates org-roam-capture-ref-templates)
  nil)

-(defun org-roam-protocol-open-file (info)
+(defun org-roam-protocol-open-node (info)
  "This handler simply opens the file with emacsclient.

 INFO is an alist containing additional information passed by the protocol URL.
@ -75,15 +91,15 @@ It should contain the FILE key, pointing to the path of the file to open.

  Example protocol string:

-org-protocol://roam-file?file=/path/to/file.org"
-  (when-let ((file (plist-get info :file)))
+org-protocol://roam-node?node=uuid"
+  (when-let ((node (plist-get info :node)))
    (raise-frame)
-    (org-roam--find-file file))
+    (org-roam-node-visit (org-roam-populate (org-roam-node-create :id node))))
  nil)

 (push '("org-roam-ref"  :protocol "roam-ref"   :function org-roam-protocol-open-ref)
      org-protocol-protocol-alist)
-(push '("org-roam-file"  :protocol "roam-file"   :function org-roam-protocol-open-file)
+(push '("org-roam-node"  :protocol "roam-node"   :function org-roam-protocol-open-node)
      org-protocol-protocol-alist)

 (provide 'org-roam-protocol)
--- a/org-roam-utils.el
+++ b/org-roam-utils.el
@ -0,0 +1,296 @@
+;;; org-roam-utils.el --- Utilities for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library implements utility functions used throughout
+;; Org-roam.
+;;
+;;
+;;; Code:
+;;;; Library Requires
+(require 'dash)
+
+(eval-when-compile
+  (require 'org-roam-macs)
+  (require 'org-macs))
+
+(defvar org-roam-verbose)
+
+;; This is necessary to ensure all dependents on this module see
+;; `org-mode-hook' and `org-inhibit-startup' as dynamic variables,
+;; regardless of whether Org is loaded before their compilation.
+(require 'org)
+
+;;;; String Utilities
+(defun org-roam-truncate (len s &optional ellipsis)
+  "If S is longer than LEN, cut it down and add ELLIPSIS to the end.
+
+The resulting string, including ellipsis, will be LEN characters
+long.
+
+When not specified, ELLIPSIS defaults to ‘...’."
+  (declare (pure t) (side-effect-free t))
+  (unless ellipsis
+    (setq ellipsis "..."))
+  (if (> (length s) len)
+      (format "%s%s" (substring s 0 (- len (length ellipsis))) ellipsis)
+    s))
+
+(defun org-roam-replace (old new s)
+  "Replace OLD with NEW in S."
+  (declare (pure t) (side-effect-free t))
+  (replace-regexp-in-string (regexp-quote old) new s t t))
+
+(defun org-roam-quote-string (s)
+  "Quotes string S."
+  (->> s
+    (org-roam-replace "\\" "\\\\")
+    (org-roam-replace "\"" "\\\"")))
+
+;;;; Utility Functions
+(defun org-roam--list-interleave (lst separator)
+  "Interleaves elements in LST with SEPARATOR."
+  (when lst
+    (let ((new-lst (list (pop lst))))
+      (dolist (it lst)
+        (nconc new-lst (list separator it)))
+      new-lst)))
+
+(defun org-roam-up-heading-or-point-min ()
+  "Fixed version of Org's `org-up-heading-or-point-min'."
+  (ignore-errors (org-back-to-heading t))
+  (let ((p (point)))
+    (if (< 1 (funcall outline-level))
+        (progn
+          (org-up-heading-safe)
+          (when (= (point) p)
+            (goto-char (point-min))))
+      (unless (bobp) (goto-char (point-min))))))
+
+(defun org-roam-message (format-string &rest args)
+  "Pass FORMAT-STRING and ARGS to `message' when `org-roam-verbose' is t."
+  (when org-roam-verbose
+    (apply #'message `(,(concat "(org-roam) " format-string) ,@args))))
+
+(defvar org-ref-buffer-hacked)
+
+(defun org-roam-fontify-like-in-org-mode (s)
+  "Fontify string S like in Org mode.
+Like `org-fontify-like-in-org-mode', but supports `org-ref'."
+  ;; NOTE: pretend that the temporary buffer created by `org-fontify-like-in-org-mode' to
+  ;; fontify a `cite:' reference has been hacked by org-ref, whatever that means;
+  ;;
+  ;; `org-ref-cite-link-face-fn', which is used to supply a face for `cite:' links, calls
+  ;; `hack-dir-local-variables' rationalizing that `bibtex-completion' would throw some warnings
+  ;; otherwise.  This doesn't seem to be the case and calling this function just before
+  ;; `org-font-lock-ensure' (alias of `font-lock-ensure') actually instead of fixing the alleged
+  ;; warnings messes the things so badly that `font-lock-ensure' crashes with error and doesn't let
+  ;; org-roam to proceed further. I don't know what's happening there exactly but disabling this hackery
+  ;; fixes the crashing.  Fortunately, org-ref provides the `org-ref-buffer-hacked' switch, which we use
+  ;; here to make it believe that the buffer was hacked.
+  ;;
+  ;; This is a workaround for `cite:' links and does not have any effect on other ref types.
+  ;;
+  ;; `org-ref-buffer-hacked' is a buffer-local variable, therefore we inline
+  ;; `org-fontify-like-in-org-mode' here
+  (with-temp-buffer
+    (insert s)
+    (let ((org-ref-buffer-hacked t))
+      (org-mode)
+      (org-font-lock-ensure)
+      (buffer-string))))
+
+(defun org-roam-set-header-line-format (string)
+  "Set the header-line using STRING.
+If the `face' property of any part of STRING is already set, then
+that takes precedence. Also pad the left side of STRING so that
+it aligns with the text area."
+  (setq-local header-line-format
+              (concat (propertize " " 'display '(space :align-to 0))
+                      string)))
+
+;;; Keywords
+(defun org-roam--get-keyword (name &optional bound)
+  "Return keyword property NAME in current buffer.
+If BOUND, scan up to BOUND bytes of the buffer."
+  (save-excursion
+    (let ((re (format "^#\\+%s:[ \t]*\\([^\n]+\\)" (upcase name))))
+      (goto-char (point-min))
+      (when (re-search-forward re bound t)
+        (buffer-substring-no-properties (match-beginning 1) (match-end 1))))))
+
+(defun org-roam-get-keyword (name &optional file bound)
+  "Return keyword property NAME from an org FILE.
+FILE defaults to current file.
+Only scans up to BOUND bytes of the document."
+  (unless bound
+    (setq bound 1024))
+  (if file
+      (with-temp-buffer
+        (insert-file-contents-literally file nil 0 bound)
+        (org-roam--get-keyword name))
+    (org-roam--get-keyword name bound)))
+
+;;; Shielding regions
+(defface org-roam-shielded
+  '((t :inherit (warning)))
+  "Face for regions that are shielded (marked as read-only).
+This face is used on the region target by org-roam-insertion
+during an `org-roam-capture'."
+  :group 'org-roam-faces)
+
+(defun org-roam-shield-region (beg end)
+  "Shield region against modifications.
+BEG and END are markers for the beginning and end regions.
+REGION must be a cons-cell containing the marker to the region
+beginning and maximum values."
+  (add-text-properties beg end
+                       '(font-lock-face org-roam-shielded
+                                        read-only t)
+                       (marker-buffer beg)))
+
+(defun org-roam-unshield-region (beg end)
+  "Unshield the shielded REGION.
+BEG and END are markers for the beginning and end regions."
+  (let ((inhibit-read-only t))
+    (remove-text-properties beg end
+                            '(font-lock-face org-roam-shielded
+                                             read-only t)
+                            (marker-buffer beg))))
+
+;;; Formatting
+(defun org-roam-format (template replacer)
+  "Format TEMPLATE with the function REPLACER.
+REPLACER takes an argument of the format variable and optionally
+an extra argument which is the EXTRA value from the call to
+`org-roam-format'.
+Adapted from `s-format'."
+  (let ((saved-match-data (match-data)))
+    (unwind-protect
+        (replace-regexp-in-string
+         "\\${\\([^}]+\\)}"
+         (lambda (md)
+           (let ((var (match-string 1 md))
+                 (replacer-match-data (match-data)))
+             (unwind-protect
+                 (let ((v (progn
+                            (set-match-data saved-match-data)
+                            (funcall replacer var))))
+                   (if v (format "%s" v) (signal 'org-roam-format-resolve md)))
+               (set-match-data replacer-match-data)))) template
+         ;; Need literal to make sure it works
+         t t)
+      (set-match-data saved-match-data))))
+
+(defvar org-roam--cached-display-format nil)
+
+(defun org-roam--process-display-format (format)
+  "Pre-calculate minimal widths needed by the FORMAT string."
+  (or org-roam--cached-display-format
+      (setq org-roam--cached-display-format
+            (let* ((fields-width 0)
+                   (string-width
+                    (string-width
+                     (org-roam-format
+                      format
+                      (lambda (field)
+                        (setq fields-width
+                              (+ fields-width
+                                 (string-to-number
+                                  (or (cadr (split-string field ":"))
+                                      "")))))))))
+              (cons format (+ fields-width string-width))))))
+
+;;; for org-roam-demote-entire-buffer in org-roam-refile.el
+(defun org-roam--file-keyword-get (keyword)
+  "Pull a KEYWORD setting from the top of the file.
+
+Keyword must be specified in ALL CAPS."
+  (cadr (assoc keyword
+               (org-collect-keywords (list keyword)))))
+
+(defun org-roam--file-keyword-kill (keyword)
+  "Erase KEYWORD setting line from the top of the file."
+  (let ((case-fold-search t))
+    (org-with-point-at 1
+      (when (re-search-forward (concat "^#\\+" keyword ":") nil t)
+        (beginning-of-line)
+        (delete-region (point) (line-end-position))
+        (delete-char 1)))))
+
+(defun org-roam--kill-empty-buffer ()
+  "If the source buffer has been emptied, kill it.
+
+If the buffer is associated with a file, delete the file.
+
+If the buffer is associated with an in-process capture operation, abort the operation."
+  (when (eq (buffer-size) 0)
+    (if (buffer-file-name)
+        (delete-file (buffer-file-name)))
+    (set-buffer-modified-p nil)
+    (when (and org-capture-mode
+               (buffer-base-buffer (current-buffer)))
+      (org-capture-kill))
+    (kill-buffer (current-buffer))))
+
+;;; Diagnostics
+;;;###autoload
+(defun org-roam-version (&optional message)
+  "Return `org-roam' version.
+Interactively, or when MESSAGE is non-nil, show in the echo area."
+  (interactive)
+  (let* ((version
+          (with-temp-buffer
+            (insert-file-contents-literally (locate-library "org-roam.el"))
+            (goto-char (point-min))
+            (save-match-data
+              (if (re-search-forward "\\(?:;; Version: \\([^z-a]*?$\\)\\)" nil nil)
+                  (substring-no-properties (match-string 1))
+                "N/A")))))
+    (if (or message (called-interactively-p 'interactive))
+        (message "%s" version)
+      version)))
+
+;;;###autoload
+(defun org-roam-diagnostics ()
+  "Collect and print info for `org-roam' issues."
+  (interactive)
+  (with-current-buffer (switch-to-buffer-other-window (get-buffer-create "*org-roam diagnostics*"))
+    (erase-buffer)
+    (insert (propertize "Copy info below this line into issue:\n" 'face '(:weight bold)))
+    (insert (format "- Emacs: %s\n" (emacs-version)))
+    (insert (format "- Framework: %s\n"
+                    (condition-case _
+                        (completing-read "I'm using the following Emacs framework:"
+                                         '("Doom" "Spacemacs" "N/A" "I don't know"))
+                      (quit "N/A"))))
+    (insert (format "- Org: %s\n" (org-version nil 'full)))
+    (insert (format "- Org-roam: %s" (org-roam-version)))))
+
+(provide 'org-roam-utils)
+;;; org-roam-utils.el ends here
--- a/org-roam.el
+++ b/org-roam.el
--- a/tests/roam-files/alias.org
+++ b/tests/roam-files/alias.org
@ -1,2 +0,0 @@
-#+roam_alias: "a1" "a 2"
-#+title: t1
--- a/tests/roam-files/bar.org
+++ b/tests/roam-files/bar.org
@ -1,3 +1,6 @@
+:PROPERTIES:
+:ID:       440795d0-70c1-4165-993d-aebd5eef7a24
+:END:
 #+title: Bar

-This is file bar. Bar links to [[file:nested/bar.org][Nested Bar]].
+[[id:884b2341-b7fe-434d-848c-5282c0727861][Foo]]
--- a/tests/roam-files/base.org
+++ b/tests/roam-files/base.org
@ -1 +0,0 @@
-#+title: Base
--- a/tests/roam-files/foo.org
+++ b/tests/roam-files/foo.org
@ -1,8 +1,4 @@
+:PROPERTIES:
+:ID:       884b2341-b7fe-434d-848c-5282c0727861
+:END:
 #+title: Foo
-
-This is the foo file. It contains a link to [[file:bar.org][Bar]].
-
-To make the tests more robust, here are some arbitrary links:
-
- [[https:google.com][Google]]
- [[mailto:foo@john.com][mail to foo]]
--- a/tests/roam-files/headlines/headline.org
+++ b/tests/roam-files/headlines/headline.org
@ -1,14 +0,0 @@
-#+TITLE: Headline
-
-* Headline 1
-:PROPERTIES:
-:ID:       e84d0630-efad-4017-9059-5ef917908823
-:END:
-
-* No headline here
-Oops.
-
-* Headline 2
-:PROPERTIES:
-:ID:       801b58eb-97e2-435f-a33e-ff59a2f0c213
-:END:
--- a/tests/roam-files/nested/bar.org
+++ b/tests/roam-files/nested/bar.org
@ -1,3 +0,0 @@
-#+title: Nested Bar
-
-This file is nested, 1 level deeper. It links to both [[file:../foo.org][Foo]] and [[file:foo.org][Nested Foo]].
--- a/tests/roam-files/nested/deeply/deeply_nested_file.org
+++ b/tests/roam-files/nested/deeply/deeply_nested_file.org
@ -1 +0,0 @@
-#+title: Deeply Nested File
--- a/tests/roam-files/nested/foo.org
+++ b/tests/roam-files/nested/foo.org
@ -1,3 +0,0 @@
-#+title: Nested Foo
-
-This file has no links.
--- a/tests/roam-files/no-title.org
+++ b/tests/roam-files/no-title.org
@ -1,5 +0,0 @@
-no title in this file :O
-
-links to itself, with no title: [[file:no-title.org][no-title]]
-
-* Headline title
--- a/tests/roam-files/tags/no_tag.org
+++ b/tests/roam-files/tags/no_tag.org
@ -1,3 +0,0 @@
-#+title: Tagless File
-
-This file has no tags, and should not yield any tags on extracting via ~#+roam_tags~.
--- a/tests/roam-files/tags/tag.org
+++ b/tests/roam-files/tags/tag.org
@ -1,4 +0,0 @@
-#+roam_tags: "t1" "t2 with space" t3
-#+title: Tags
-
-This file is used to test functionality for =(org-roam--extract-tags)=
--- a/tests/roam-files/titles/aliases.org
+++ b/tests/roam-files/titles/aliases.org
@ -1 +0,0 @@
-#+roam_alias: "roam" "alias"
--- a/tests/roam-files/titles/combination.org
+++ b/tests/roam-files/titles/combination.org
@ -1,4 +0,0 @@
-#+title: TITLE PROP
-#+roam_alias: "roam" "alias"
-
-* Headline
--- a/tests/roam-files/titles/headline.org
+++ b/tests/roam-files/titles/headline.org
@ -1 +0,0 @@
-* Headline
--- a/tests/roam-files/titles/title.org
+++ b/tests/roam-files/titles/title.org
@ -1 +0,0 @@
-#+title: Title
--- a/tests/roam-files/unlinked.org
+++ b/tests/roam-files/unlinked.org
@ -1,3 +0,0 @@
-#+title: Unlinked
-
-Nothing links here :(
--- a/tests/roam-files/web_ref.org
+++ b/tests/roam-files/web_ref.org
@ -1 +0,0 @@
-#+roam_key: https://google.com/
--- a/tests/test-org-roam-perf.el
+++ b/tests/test-org-roam-perf.el
@ -1,53 +0,0 @@
-;;; test-org-roam-perf.el --- Performance Tests for Org-roam -*- lexical-binding: t; -*-
-
-;; Copyright (C) 2020 Jethro Kuan
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; Package-Requires: ((buttercup))
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation, either version 3 of the License, or
-;; (at your option) any later version.
-
-;; This program is distributed in the hope that it will be useful,
-;; but WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;; GNU General Public License for more details.
-
-;; You should have received a copy of the GNU General Public License
-;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
-
-;;; Commentary:
-;;; Code:
-
-(require 'buttercup)
-(require 'org-roam)
-
-(defconst test-org-roam-perf-zip-url "https://github.com/org-roam/test-org-files/archive/master.zip"
-  "Path to zip for test org-roam files.")
-
-(defun test-org-roam-perf--abs-path (file-path)
-  "Get absolute FILE-PATH from `org-roam-directory'."
-  (expand-file-name file-path org-roam-directory))
-
-(defun test-org-roam-perf--init ()
-  "."
-  (let* ((temp-loc (expand-file-name (make-temp-name "test-org-files-") temporary-file-directory))
-         (zip-file-loc (concat temp-loc ".zip"))
-         (_ (url-copy-file test-org-roam-perf-zip-url zip-file-loc))
-         (_ (shell-command (format "mkdir -p %s && unzip -j -qq %s -d %s" temp-loc zip-file-loc temp-loc))))
-    (setq org-roam-directory temp-loc)))
-
-(describe "Cache Build"
-  (it "cache build from scratch time to be acceptable"
-    (test-org-roam-perf--init)
-    (pcase (benchmark-run 1 (org-roam-db-build-cache t))
-      (`(,time ,gcs ,time-in-gc)
-       (message "Elapsed time: %fs (%fs in %d GCs)" time time-in-gc gcs)
-       (expect time :to-be-less-than 90))))
-  (it "builds quickly without change"
-    (pcase (benchmark-run 1 (org-roam-db-build-cache))
-      (`(,time ,gcs ,time-in-gc)
-       (message "Elapsed time: %fs (%fs in %d GCs)" time time-in-gc gcs)
-       (expect time :to-be-less-than 5)))))
--- a/tests/test-org-roam.el
+++ b/tests/test-org-roam.el
@ -23,326 +23,31 @@

 (require 'buttercup)
 (require 'org-roam)
-(require 'dash)

-(defun test-org-roam--abs-path (file-path)
-  "Get absolute FILE-PATH from `org-roam-directory'."
-  (expand-file-name file-path org-roam-directory))
-
-(defun test-org-roam--find-file (path)
-  "PATH."
-  (let ((path (test-org-roam--abs-path path)))
-    (make-directory (file-name-directory path) t)
-    (find-file path)))
-
-(defvar test-org-roam-directory (expand-file-name "tests/roam-files")
-  "Directory containing org-roam test org files.")
-
-(defun test-org-roam--init ()
-  "."
-  (let ((original-dir test-org-roam-directory)
-        (new-dir (expand-file-name (make-temp-name "org-roam") temporary-file-directory)))
-    (copy-directory original-dir new-dir)
-    (setq org-roam-directory new-dir)
-    (org-roam-mode +1)
-    (sleep-for 2)))
-
-(defun test-org-roam--teardown ()
-  (org-roam-mode -1)
-  (delete-file org-roam-db-location)
-  (org-roam-db--close))
-
-(describe "org-roam--str-to-list"
-  (it "nil"
-    (expect (org-roam--str-to-list nil)
-            :to-be
-            nil))
-  (it "\"multi word\" prop 123"
-    (expect (org-roam--str-to-list "\"multi word\" prop 123")
-            :to-equal
-            '("multi word" "prop" "123")))
-  (it "prop \"multi word\" 123"
-    (expect (org-roam--str-to-list "\"multi word\" prop 123")
-            :to-equal
-            '("multi word" "prop" "123")))
-  (it "errors on bad input"
-    (expect (org-roam--str-to-list 1)
-            :to-throw)
-    (expect (org-roam--str-to-list "\"hello")
-            :to-throw)))
-
-(describe "Title extraction"
-  :var (org-roam-title-sources)
+(describe "org-roam-db-sync"
  (before-all
-    (test-org-roam--init))
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory))
+    (org-roam-setup))

  (after-all
-    (test-org-roam--teardown))
+    (org-roam-teardown)
+    (delete-file org-roam-db-location))

-  (cl-flet
-      ((test (fn file)
-             (let ((buf (find-file-noselect
-                         (test-org-roam--abs-path file))))
-               (with-current-buffer buf
-                 (funcall fn)))))
-    (it "extracts title from title property"
-      (expect (test #'org-roam--extract-titles-title
-                    "titles/title.org")
-              :to-equal
-              '("Title"))
-      (expect (test #'org-roam--extract-titles-title
-                    "titles/aliases.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-titles-title
-                    "titles/headline.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-titles-title
-                    "titles/combination.org")
-              :to-equal
-              '("TITLE PROP")))
-
-    (it "extracts alias"
-      (expect (test #'org-roam--extract-titles-alias
-                    "titles/title.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-titles-alias
-                    "titles/aliases.org")
-              :to-equal
-              '("roam" "alias"))
-      (expect (test #'org-roam--extract-titles-alias
-                    "titles/headline.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-titles-alias
-                    "titles/combination.org")
-              :to-equal
-              '("roam" "alias")))
-
-    (it "extracts headlines"
-      (expect (test #'org-roam--extract-titles-alias
-                    "titles/title.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-titles-headline
-                    "titles/aliases.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-titles-headline
-                    "titles/headline.org")
-              :to-equal
-              '("Headline"))
-      (expect (test #'org-roam--extract-titles-headline
-                    "titles/combination.org")
-              :to-equal
-              '("Headline")))
-
-    (describe "uses org-roam-title-sources correctly"
-      (it "'((title headline) alias)"
-        (expect (let ((org-roam-title-sources '((title headline) alias)))
-                  (test #'org-roam--extract-titles
-                        "titles/combination.org"))
-                :to-equal
-                '("TITLE PROP" "roam" "alias")))
-      (it "'((headline title) alias)"
-        (expect (let ((org-roam-title-sources '((headline title) alias)))
-                  (test #'org-roam--extract-titles
-                        "titles/combination.org"))
-                :to-equal
-                '("Headline" "roam" "alias")))
-      (it "'(headline alias title)"
-        (expect (let ((org-roam-title-sources '(headline alias title)))
-                  (test #'org-roam--extract-titles
-                        "titles/combination.org"))
-                :to-equal
-                '("Headline" "roam" "alias" "TITLE PROP"))))))
-
-(describe "Tag extraction"
-  :var (org-roam-tag-sources)
-  (before-all
-    (test-org-roam--init))
-
-  (after-all
-    (test-org-roam--teardown))
-
-  (cl-flet
-      ((test (fn file)
-             (let* ((fname (test-org-roam--abs-path file))
-                    (buf (find-file-noselect fname)))
-               (with-current-buffer buf
-                 (funcall fn fname)))))
-    (it "extracts from prop"
-      (expect (test #'org-roam--extract-tags-prop
-                    "tags/tag.org")
-              :to-equal
-              '("t1" "t2 with space" "t3"))
-      (expect (test #'org-roam--extract-tags-prop
-                    "tags/no_tag.org")
-              :to-equal
-              nil))
-
-    (it "extracts from all directories"
-      (expect (test #'org-roam--extract-tags-all-directories
-                    "base.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-tags-all-directories
-                    "tags/tag.org")
-              :to-equal
-              '("tags"))
-      (expect (test #'org-roam--extract-tags-all-directories
-                    "nested/deeply/deeply_nested_file.org")
-              :to-equal
-              '("nested" "deeply")))
-
-    (it "extracts from last directory"
-      (expect (test #'org-roam--extract-tags-last-directory
-                    "base.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-tags-last-directory
-                    "tags/tag.org")
-              :to-equal
-              '("tags"))
-      (expect (test #'org-roam--extract-tags-last-directory
-                    "nested/deeply/deeply_nested_file.org")
-              :to-equal
-              '("deeply")))
-
-    (it "extracts from first directory"
-      (expect (test #'org-roam--extract-tags-first-directory
-                    "base.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-tags-first-directory
-                    "tags/tag.org")
-              :to-equal
-              '("tags"))
-      (expect (test #'org-roam--extract-tags-first-directory
-                    "nested/deeply/deeply_nested_file.org")
-              :to-equal
-              '("nested")))
-
-    (describe "uses org-roam-tag-sources correctly"
-      (it "'(prop)"
-        (expect (let ((org-roam-tag-sources '(prop)))
-                  (test #'org-roam--extract-tags
-                        "tags/tag.org"))
-                :to-equal
-                '("t1" "t2 with space" "t3")))
-      (it "'(prop all-directories)"
-        (expect (let ((org-roam-tag-sources '(prop all-directories)))
-                  (test #'org-roam--extract-tags
-                        "tags/tag.org"))
-                :to-equal
-                '("t1" "t2 with space" "t3" "tags"))))))
-
-(describe "ID extraction"
-  (before-all
-    (test-org-roam--init))
-
-  (after-all
-    (test-org-roam--teardown))
-
-  (cl-flet
-      ((test (fn file)
-             (let* ((fname (test-org-roam--abs-path file))
-                    (buf (find-file-noselect fname)))
-               (with-current-buffer buf
-                 (funcall fn fname)))))
-    (it "extracts ids"
-      (expect (test #'org-roam--extract-ids
-                    "headlines/headline.org")
-              :to-have-same-items-as
-              `(["e84d0630-efad-4017-9059-5ef917908823" ,(test-org-roam--abs-path "headlines/headline.org") 1]
-                ["801b58eb-97e2-435f-a33e-ff59a2f0c213" ,(test-org-roam--abs-path "headlines/headline.org") 1])))))
-
-(describe "Test roam links"
-  (it ""
-    (expect (org-roam-link--split-path "")
+  (it "has the correct number of files"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from files]))
            :to-equal
-            '(title "" "" nil)))
-  (it "title"
-    (expect (org-roam-link--split-path "title")
+            2))
+
+  (it "has the correct number of nodes"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from nodes]))
            :to-equal
-            '(title "title" "" nil)))
-  (it "title*"
-    (expect (org-roam-link--split-path "title*")
+            2))
+
+  (it "has the correct number of links"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links]))
            :to-equal
-            '(title+headline "title" "" 5)))
-  (it "title*headline"
-    (expect (org-roam-link--split-path "title*headline")
-            :to-equal
-            '(title+headline "title" "headline" 5)))
-  (it "*headline"
-    (expect (org-roam-link--split-path "*headline")
-            :to-equal
-            '(headline "" "headline" 0))))
-
-;;; Tests
-(xdescribe "org-roam-db-build-cache"
-  (before-each
-    (test-org-roam--init))
-
-  (after-each
-    (test-org-roam--teardown))
-
-  (it "initializes correctly"
-    ;; Cache
-    (expect (caar (org-roam-db-query [:select (funcall count) :from files])) :to-be 8)
-    (expect (caar (org-roam-db-query [:select (funcall count) :from links])) :to-be 5)
-    (expect (caar (org-roam-db-query [:select (funcall count) :from titles])) :to-be 8)
-    (expect (caar (org-roam-db-query [:select (funcall count) :from titles
-                                      :where titles :is-null])) :to-be 1)
-    (expect (caar (org-roam-db-query [:select (funcall count) :from refs])) :to-be 1)
-
-    ;; Links
-    (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= from $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 1)
-    (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= from $s1)]
-                                     (test-org-roam--abs-path "nested/bar.org"))) :to-be 2)
-
-    ;; Links -- File-to
-    (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= to $s1)]
-                                     (test-org-roam--abs-path "nested/foo.org"))) :to-be 1)
-    (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= to $s1)]
-                                     (test-org-roam--abs-path "nested/bar.org"))) :to-be 1)
-    (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= to $s1)]
-                                     (test-org-roam--abs-path "unlinked.org"))) :to-be 0)
-    ;; TODO Test titles
-    (expect (org-roam-db-query [:select * :from titles])
-            :to-have-same-items-as
-            (list (list (test-org-roam--abs-path "alias.org")
-                        (list "t1" "a1" "a 2"))
-                  (list (test-org-roam--abs-path "bar.org")
-                        (list "Bar"))
-                  (list (test-org-roam--abs-path "foo.org")
-                        (list "Foo"))
-                  (list (test-org-roam--abs-path "nested/bar.org")
-                        (list "Nested Bar"))
-                  (list (test-org-roam--abs-path "nested/foo.org")
-                        (list "Nested Foo"))
-                  (list (test-org-roam--abs-path "no-title.org")
-                        (list "Headline title"))
-                  (list (test-org-roam--abs-path "web_ref.org") nil)
-                  (list (test-org-roam--abs-path "unlinked.org")
-                        (list "Unlinked"))))
-
-    (expect (org-roam-db-query [:select * :from refs])
-            :to-have-same-items-as
-            (list (list "https://google.com/" (test-org-roam--abs-path "web_ref.org") "website")))
-
-    ;; Expect rebuilds to be really quick (nothing changed)
-    (expect (org-roam-db-build-cache)
-            :to-equal
-            (list :files 0 :links 0 :tags 0 :titles 0 :refs 0 :deleted 0))))
+            1)))

 (provide 'test-org-roam)