(release): v1.1.1 (#668 )

Create FUNDING.yml
(docs): add a nice default theme (#667 )
2025-08-01 12:17:21 -05:00 · 2020-05-18 22:04:51 +08:00 · 2020-05-18 21:27:31 +08:00 · 2020-05-18 19:15:12 +08:00 · 2020-05-17 11:51:25 -04:00 · 2020-05-17 11:36:15 -04:00
57 changed files with 4755 additions and 1578 deletions
--- a/.dir-locals.el
+++ b/.dir-locals.el
@ -0,0 +1,4 @@
+;;; Directory Local Variables
+;;; For more information see (info "(emacs) Directory Variables")
+
+((emacs-lisp-mode . ((eval . (require 'org-roam-dev)))))
--- a/.github/FUNDING.yml
+++ b/.github/FUNDING.yml
@ -0,0 +1,12 @@
+# These are supported funding model platforms
+
+github: [jethrokuan, zaeph]
+patreon: # Replace with a single Patreon username
+open_collective: # Replace with a single Open Collective username
+ko_fi: # Replace with a single Ko-fi username
+tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel
+community_bridge: # Replace with a single Community Bridge project-name e.g., cloud-foundry
+liberapay: # Replace with a single Liberapay username
+issuehunt: # Replace with a single IssueHunt username
+otechie: # Replace with a single Otechie username
+custom: # Replace with up to 4 custom sponsorship URLs e.g., ['link1', 'link2']
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@ -1,14 +1,15 @@
 ---
 name: Bug Report
 about: Something's not working.
-title: ''
-labels: ''
-assignees: 'jethrokuan'
+title: ""
+labels: ""
+assignees: ""
 ---

 ### Description

 #### Steps to Reproduce
+
 <!--
 Example:

@ -18,13 +19,25 @@ Example:
 ...
 -->

+#### Backtrace
+<!--
+   Will help us track and understand issues faster.
+   How to provide a backtrace:
+   1. M-x toggle-debug-on-error
+   2. Trigger error. The debugger buffer should pop up.
+   3. Copy the contents of the debugger buffer and paste here
+-->

 #### Expected Results
+
 <!-- Example: File A is there -->

 #### Actual Results
+
 <!-- Example: File A is missing -->

-### Versions
- Emacs (`C-h v emacs-version`): vX.X.X
+### Environment
+
+<!-- Please M-x org-roam-diagnostics and paste results here -->
+
 - Org-roam commit: https://github.com/jethrokuan/org-roam/commit/commithashhere
--- a/.github/ISSUE_TEMPLATE/feature_request.md
+++ b/.github/ISSUE_TEMPLATE/feature_request.md
@ -1,9 +1,9 @@
 ---
 name: Feature Request
 about: Create a feature request to improve Org-roam
-title: ''
-labels: 'enhancement'
-assignees: 'jethrokuan'
+title: ""
+labels: "enhancement"
+assignees: ""
 ---

 ### Brief Abstract
@ -13,4 +13,5 @@ assignees: 'jethrokuan'
 ### Proposed Implementation (if any)

 ### Please check the following:
+
 - [ ] No similar feature requests
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@ -0,0 +1,31 @@
+# * docs.yml --- Build the documentation and publish to Github Pages
+
+name: "Docs"
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install deps
+      run: |
+        sudo apt-get install texinfo
+
+    - name: Build docs
+      continue-on-error: false
+      run: make html
+
+    - name: Deploy 🚀
+      uses: JamesIves/github-pages-deploy-action@releases/v3
+      with:
+        ACCESS_TOKEN: ${{ secrets.ACCESS_TOKEN }}
+        BRANCH: gh-pages # The branch the action should deploy to.
+        FOLDER: doc # The folder the action should deploy.
+        CLEAN: true
--- a/.github/workflows/stale.yml
+++ b/.github/workflows/stale.yml
@ -0,0 +1,19 @@
+name: Mark stale issues and pull requests
+
+on:
+  schedule:
+  - cron: "0 0 * * *"
+
+jobs:
+  stale:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/stale@v1
+      with:
+        repo-token: ${{ secrets.GITHUB_TOKEN }}
+        stale-issue-message: 'Stale issue message'
+        stale-pr-message: 'Stale pull request message'
+        stale-issue-label: 'no-issue-activity'
+        stale-pr-label: 'no-pr-activity'
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@ -29,7 +29,6 @@ on:
  push:
    branches:
      - master
-      - develop

 jobs:
  build:
@ -56,7 +55,7 @@ jobs:
    # as failures, so linting and testing are run as separate steps.

    - name: Lint
-      continue-on-error: true
+      continue-on-error: false
      run: ./makem.sh -vv --sandbox $SANDBOX_DIR lint

    - name: Test
--- a/.gitignore
+++ b/.gitignore
@ -1,2 +1,15 @@
 /.sandbox/
 **/*.elc
+/doc/dir
+/doc/*.info
+/doc/*.pdf
+/doc/*.epub
+/doc/META_INF/
+/doc/OEBPS/
+/doc/dir
+/doc/epub.xml
+/doc/org-roam/
+/doc/mimetype
+/doc/stats/
+/config.mk
+/doc/manual/
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@ -1,5 +1,45 @@
 # Changelog

+## 1.1.1 (18-05-2020)
+
+In this release, we added two new features:
+
+1. `org-roam-doctor`: a linting system that helps you discover possible problems with your Org-roam files. This is in the spirit of keeping notes in top quality.
+2. A tagging system: one can now use sub-directories, and the `#+ROAM_TAG` key add additional meta data to notes. For more information, see [here](https://org-roam.github.io/org-roam/manual/Tags.html#Tags).
+
+As usual, this release comes with a multitude of bug-fixes and refactorings.
+
+### Breaking Changes
+
+- [#523](https://github.com/org-roam/org-roam/pull/523) remove `org-roam-completion-fuzzy-match` in favor of using completion mechanism's configuration options directly
+- [#547](https://github.com/org-roam/org-roam/pull/547) Deprecate `org-roam-db--maybe-update`, in favour of `org-roam-db--update-maybe`
+- [#604](https://github.com/org-roam/org-roam/pull/604) Deprecate `org-roam-title-include-subdirs`, `org-roam-title-subdir-format` `org-roam-title-subdir-separator`, for a more general tagging system built on subdirectories
+
+### Bugfixes
+
+- [#509](https://github.com/org-roam/org-roam/pull/509) fix backup files being tracked in database
+- [#509](https://github.com/org-roam/org-roam/pull/509) fix external org files being tracked in database
+- [#537](https://github.com/org-roam/org-roam/pull/537) quote graphviz node and edge configuration options to allow multi-word configurations
+- [#545](https://github.com/org-roam/org-roam/pull/545) fix `org-roam--extract-links` to ensure that multiple citations (`cite:key1,key2`) are split correctly
+- [#547](https://github.com/org-roam/org-roam/pull/547) Fix unlinked citations
+- [#660](https://github.com/org-roam/org-roam/pull/660) fix rename-file advice not working for renaming to directories
+- [#660](https://github.com/org-roam/org-roam/pull/660) fix links breaking within file on file movement
+
+### Features
+
+- [#538](https://github.com/org-roam/org-roam/pull/538) Optionally use text in first headline as title
+- [#553](https://github.com/org-roam/org-roam/pull/553) Add prefix argument to `org-roam-db-build-cache` for forcing rebuilds
+- [#560](https://github.com/org-roam/org-roam/pull/560) Apply 'error face to distinguish broken links
+- [#570](https://github.com/org-roam/org-roam/pull/570) Add `org-roam-doctor` to diagnose org-roam files
+- [#625](https://github.com/org-roam/org-roam/pull/625) Add `org-roam-title-sources` to control how titles are retrieved within notes
+- [#604](https://github.com/org-roam/org-roam/pull/604) Add a tagging system. `org-roam-tag-sources` controls how tags are retrieved from notes
+
+### Internal Changes
+
+- [#547](https://github.com/org-roam/org-roam/pull/547) Added `type` column to the `refs` table
+- [#606](https://github.com/org-roam/org-roam/pull/606) Added `org-roam-dev.el` for developer coding standards
+- [#622](https://github.com/org-roam/org-roam/pull/622) Online documentation now points to the Org-based documentation
+
 ## 1.1.0 (21-04-2020)

 To the average user, this release is mainly a bugfix release with additional options to customize. However, the changes made to the source is significant. Most notably, in this release:
@ -8,31 +48,35 @@ To the average user, this release is mainly a bugfix release with additional opt
 2. [@kljohann](https://github.com/kljohann) did some fantastic work on graph generation: allowing building images for connected components within the graph up to a specified distance
 3. We also started supporting `org-ref` natively: cite links now show up in both the graph and the org-roam buffer.

-In the coming months, you can expect work on bigger projects (e.g. revamping the org-roam buffer). 
- 
+In the coming months, you can expect work on bigger projects (e.g. revamping the org-roam buffer).
+
 ### Breaking Changes
-* [#385](https://github.com/jethrokuan/org-roam/pull/385) Deprecate `org-roam-graph-node-shape` in favour of `org-roam-graph-node-extra-config`.
-* [#473](https://github.com/jethrokuan/org-roam/pull/473) Deprecate `org-roam-date-filename-format` and `org-roam-date-title-format`, in favour of `org-roam-dailies-capture-templates`.
+
+- [#385](https://github.com/org-roam/org-roam/pull/385) Deprecate `org-roam-graph-node-shape` in favour of `org-roam-graph-node-extra-config`.
+- [#473](https://github.com/org-roam/org-roam/pull/473) Deprecate `org-roam-date-filename-format` and `org-roam-date-title-format`, in favour of `org-roam-dailies-capture-templates`.

 ### New Features
-* [#350](https://github.com/jethrokuan/org-roam/pull/350) Add `org-roam-db-location` to customize location of org-roam database.
-* [#359](https://github.com/jethrokuan/org-roam/pull/359) Add `org-roam-verbose` to allow or silence printing of information.
-* [#374](https://github.com/jethrokuan/org-roam/pull/374) Add support for `org-ref` `cite:` links
-* [#380](https://github.com/jethrokuan/org-roam/pull/380) Allow `org-roam-buffer-position` to also be `top` or `bottom`
-* [#385](https://github.com/jethrokuan/org-roam/pull/385) Add `org-roam-graph-node-extra-config` to configure Graphviz nodes
-* [#398](https://github.com/jethrokuan/org-roam/pull/398), [#418](https://github.com/jethrokuan/org-roam/pull/418) Add graph building for connected components
-* [#435](https://github.com/jethrokuan/org-roam/pull/435) Add `org-roam-graph-edge-extra-config` to configure Graphviz edges
-* [#439](https://github.com/jethrokuan/org-roam/pull/439) Add support for `org-ref` citations to display as edges in graph. Add `org-roam-graph-edge-cites-extra-config` to configure these edges
-* [#465](https://github.com/jethrokuan/org-roam/pull/465) Add `org-roam-file-extensions` to allow detection of org files with different file extensions
-* [#488](https://github.com/jethrokuan/org-roam/pull/488) Allow a function for `org-roam-graph-viewer`
-* [#491](https://github.com/jethrokuan/org-roam/pull/491) Use TITLE as description when linking before first heading
+
+- [#350](https://github.com/org-roam/org-roam/pull/350) Add `org-roam-db-location` to customize location of org-roam database.
+- [#359](https://github.com/org-roam/org-roam/pull/359) Add `org-roam-verbose` to allow or silence printing of information.
+- [#374](https://github.com/org-roam/org-roam/pull/374) Add support for `org-ref` `cite:` links
+- [#380](https://github.com/org-roam/org-roam/pull/380) Allow `org-roam-buffer-position` to also be `top` or `bottom`
+- [#385](https://github.com/org-roam/org-roam/pull/385) Add `org-roam-graph-node-extra-config` to configure Graphviz nodes
+- [#398](https://github.com/org-roam/org-roam/pull/398), [#418](https://github.com/org-roam/org-roam/pull/418) Add graph building for connected components
+- [#435](https://github.com/org-roam/org-roam/pull/435) Add `org-roam-graph-edge-extra-config` to configure Graphviz edges
+- [#439](https://github.com/org-roam/org-roam/pull/439) Add support for `org-ref` citations to display as edges in graph. Add `org-roam-graph-edge-cites-extra-config` to configure these edges
+- [#465](https://github.com/org-roam/org-roam/pull/465) Add `org-roam-file-extensions` to allow detection of org files with different file extensions
+- [#488](https://github.com/org-roam/org-roam/pull/488) Allow a function for `org-roam-graph-viewer`
+- [#491](https://github.com/org-roam/org-roam/pull/491) Use TITLE as description when linking before first heading

 ### Bugfixes
-* [#470](https://github.com/jethrokuan/org-roam/pull/470) Add workaround for undocumented `file-truename` behaviour in `org-roam--org-roam-file-p`.
+
+- [#470](https://github.com/org-roam/org-roam/pull/470) Add workaround for undocumented `file-truename` behaviour in `org-roam--org-roam-file-p`.

 ### Internal Changes
-* [#363](https://github.com/jethrokuan/org-roam/pull/363), [#473](https://github.com/jethrokuan/org-roam/pull/473) Modularize org-roam features.
-* [#497](https://github.com/jethrokuan/org-roam/pull/497) Simplify `org-roam--list-files` implementation
+
+- [#363](https://github.com/org-roam/org-roam/pull/363), [#473](https://github.com/org-roam/org-roam/pull/473) Modularize org-roam features.
+- [#497](https://github.com/org-roam/org-roam/pull/497) Simplify `org-roam--list-files` implementation

 ## 1.0.0 (23-03-2020)

@ -40,16 +84,18 @@ Org-roam is now on MELPA! We have squashed most of the bugs, and Org-roam has
 been stable for the most part.

 ### New Features
-* [#269](https://github.com/jethrokuan/org-roam/pull/269) Add `org-roam-graphviz-extra-options`
-* [#257](https://github.com/jethrokuan/org-roam/pull/257) Add a company-backend `company-org-roam`
-* [#284](https://github.com/jethrokuan/org-roam/pull/284), [#289](https://github.com/jethrokuan/org-roam/pull/289) Configurable `org-roam-completion-system` with options `'default`, `'ido`, `'ivy` and `'helm`
-* [#289](https://github.com/jethrokuan/org-roam/pull/289) Add customizable `org-roam-fuzzy-match` to allow fuzzy-matching of candidates
-* [#290](https://github.com/jethrokuan/org-roam/pull/290) Add `org-roam-date-title-format` and `org-roam-date-filename-format` for customizing Org-roam's date files
-* [#296](https://github.com/jethrokuan/org-roam/pull/296) Allow multiple exclusion matchers in `org-roam-graph-exclude-matcher`
+
+- [#269](https://github.com/org-roam/org-roam/pull/269) Add `org-roam-graphviz-extra-options`
+- [#257](https://github.com/org-roam/org-roam/pull/257) Add a company-backend `company-org-roam`
+- [#284](https://github.com/org-roam/org-roam/pull/284), [#289](https://github.com/org-roam/org-roam/pull/289) Configurable `org-roam-completion-system` with options `'default`, `'ido`, `'ivy` and `'helm`
+- [#289](https://github.com/org-roam/org-roam/pull/289) Add customizable `org-roam-fuzzy-match` to allow fuzzy-matching of candidates
+- [#290](https://github.com/org-roam/org-roam/pull/290) Add `org-roam-date-title-format` and `org-roam-date-filename-format` for customizing Org-roam's date files
+- [#296](https://github.com/org-roam/org-roam/pull/296) Allow multiple exclusion matchers in `org-roam-graph-exclude-matcher`

 ### Bugfixes
-* [#293](https://github.com/jethrokuan/org-roam/pull/293) Fix capture templates not working as expected for `org-roam-find-file`
-* [#275](https://github.com/jethrokuan/org-roam/pull/275) Fix database rebuild when `org-roam-directory` is set locally
+
+- [#293](https://github.com/org-roam/org-roam/pull/293) Fix capture templates not working as expected for `org-roam-find-file`
+- [#275](https://github.com/org-roam/org-roam/pull/275) Fix database rebuild when `org-roam-directory` is set locally

 ## 1.0.0-rc1 (06-03-2020)

@ -59,82 +105,95 @@ backing storage has been changed to a SQLite database, and a
 templating system using `org-capture` is introduced.

 ### Breaking Changes
-* [#200](https://github.com/jethrokuan/org-roam/pull/200) Move Org-roam cache into a SQLite database.
-* [#203](https://github.com/jethrokuan/org-roam/pull/203) Roam protocol is deprecated, in favour of extending org-roam-protocol.
+
+- [#200](https://github.com/org-roam/org-roam/pull/200) Move Org-roam cache into a SQLite database.
+- [#203](https://github.com/org-roam/org-roam/pull/203) Roam protocol is deprecated, in favour of extending org-roam-protocol.

 ### New Features
-* [#182](https://github.com/jethrokuan/org-roam/pull/182) Support file name aliases via `#+ROAM_ALIAS`.
-* [#216](https://github.com/jethrokuan/org-roam/pull/216) Adds templating functionality by extending org-capture.
-* [#232](https://github.com/jethrokuan/org-roam/pull/232) Adds a prefix key to `org-roam-show-graph`, to generate graph without opening it.
-* [#233](https://github.com/jethrokuan/org-roam/pull/233) Adds `org-roam-graph-exclude-matcher`, which allows exclusion of nodes from graph.
-* [#247](https://github.com/jethrokuan/org-roam/pull/247) Add `org-roam-backlink` face, which allows customizing backlinks appearance
-* [#259](https://github.com/jethrokuan/org-roam/pull/259) Add optional initial-prompt to `org-roam-find-file`
+
+- [#182](https://github.com/org-roam/org-roam/pull/182) Support file name aliases via `#+ROAM_ALIAS`.
+- [#216](https://github.com/org-roam/org-roam/pull/216) Adds templating functionality by extending org-capture.
+- [#232](https://github.com/org-roam/org-roam/pull/232) Adds a prefix key to `org-roam-show-graph`, to generate graph without opening it.
+- [#233](https://github.com/org-roam/org-roam/pull/233) Adds `org-roam-graph-exclude-matcher`, which allows exclusion of nodes from graph.
+- [#247](https://github.com/org-roam/org-roam/pull/247) Add `org-roam-backlink` face, which allows customizing backlinks appearance
+- [#259](https://github.com/org-roam/org-roam/pull/259) Add optional initial-prompt to `org-roam-find-file`

 ### Bugfixes
-* [#207](https://github.com/jethrokuan/org-roam/pull/207), [#221](https://github.com/jethrokuan/org-roam/pull/221) small bugfixes to Org-roam graph generation
-* [#230](https://github.com/jethrokuan/org-roam/pull/230) remove nonspacing marks from filenames, to prevent cross-platform errors
+
+- [#207](https://github.com/org-roam/org-roam/pull/207), [#221](https://github.com/org-roam/org-roam/pull/221) small bugfixes to Org-roam graph generation
+- [#230](https://github.com/org-roam/org-roam/pull/230) remove nonspacing marks from filenames, to prevent cross-platform errors

 ### New Contributors
-* [@acowley][https://github.com/acowley]
-* [@teesloane][https://github.com/teesloane]
+
+- [@acowley][https://github.com/acowley]
+- [@teesloane][https://github.com/teesloane]

 ## 0.1.2 (2020-02-21)

 ### Breaking Changes
-* [#143](https://github.com/jethrokuan/org-roam/pull/143) `org-roam-mode` is now a global mode. The installation instructions have changed accordingly.
-* [#103](https://github.com/jethrokuan/org-roam/pull/103) Change `org-roam-file-format` to a function: `org-roam-file-name-function` to allow more flexible file name customizaton. Also changes `org-roam-use-timestamp-as-filename` to `org-roam-filename-noconfirm` to better describe what it does.
+
+- [#143](https://github.com/org-roam/org-roam/pull/143) `org-roam-mode` is now a global mode. The installation instructions have changed accordingly.
+- [#103](https://github.com/org-roam/org-roam/pull/103) Change `org-roam-file-format` to a function: `org-roam-file-name-function` to allow more flexible file name customizaton. Also changes `org-roam-use-timestamp-as-filename` to `org-roam-filename-noconfirm` to better describe what it does.

 ### New Features
-* [#145](https://github.com/jethrokuan/org-roam/pull/145) `org-roam-show-graph`: Fallback to Emacs SVG viewer
-* [#141](https://github.com/jethrokuan/org-roam/pull/141) add variable `org-roam-new-file-directory` for new Org-roam files
-* [#138](https://github.com/jethrokuan/org-roam/pull/138) add `org-roam-switch-to-buffer`
-* [#124](https://github.com/jethrokuan/org-roam/pull/124), [#141](https://github.com/jethrokuan/org-roam/pull/141) Maintain cache consistency on file rename and delete
-* [#87](https://github.com/jethrokuan/org-roam/pull/87), [#90](https://github.com/jethrokuan/org-roam/pull/90) Support encrypted Org files
-* [#110](https://github.com/jethrokuan/org-roam/pull/110) Add prefix to `org-roam-insert`, for inserting titles down-cased
-* [#99](https://github.com/jethrokuan/org-roam/pull/99) Add keybinding so that `<return>` or `mouse-1` in the backlinks buffer visits the source file of the backlink at point
+
+- [#145](https://github.com/org-roam/org-roam/pull/145) `org-roam-show-graph`: Fallback to Emacs SVG viewer
+- [#141](https://github.com/org-roam/org-roam/pull/141) add variable `org-roam-new-file-directory` for new Org-roam files
+- [#138](https://github.com/org-roam/org-roam/pull/138) add `org-roam-switch-to-buffer`
+- [#124](https://github.com/org-roam/org-roam/pull/124), [#141](https://github.com/org-roam/org-roam/pull/141) Maintain cache consistency on file rename and delete
+- [#87](https://github.com/org-roam/org-roam/pull/87), [#90](https://github.com/org-roam/org-roam/pull/90) Support encrypted Org files
+- [#110](https://github.com/org-roam/org-roam/pull/110) Add prefix to `org-roam-insert`, for inserting titles down-cased
+- [#99](https://github.com/org-roam/org-roam/pull/99) Add keybinding so that `<return>` or `mouse-1` in the backlinks buffer visits the source file of the backlink at point

 ### Changes

-* [#108](https://github.com/jethrokuan/org-roam/pull/108) Locally overwrite the link following behaviour in the org-roam-buffer to open files in the same window `org-roam` was called from
+- [#108](https://github.com/org-roam/org-roam/pull/108) Locally overwrite the link following behaviour in the org-roam-buffer to open files in the same window `org-roam` was called from

 ### Bugfixes
-* [#86](https://github.com/jethrokuan/org-roam/pull/86) Fix `org-roam--parse-content` incorrect `:to` computation for nested files
-* [#98](https://github.com/jethrokuan/org-roam/pull/98) Fix `org-roam--find-file` picking up temporary files
-* [#136](https://github.com/jethrokuan/org-roam/pull/136) Misc bugfixes
+
+- [#86](https://github.com/org-roam/org-roam/pull/86) Fix `org-roam--parse-content` incorrect `:to` computation for nested files
+- [#98](https://github.com/org-roam/org-roam/pull/98) Fix `org-roam--find-file` picking up temporary files
+- [#136](https://github.com/org-roam/org-roam/pull/136) Misc bugfixes

 ### Internal
-* [#122](https://github.com/jethrokuan/org-roam/pull/122), [#128](https://github.com/jethrokuan/org-roam/pull/128) Improve performance of post-command-hook
-* [#92](https://github.com/jethrokuan/org-roam/pull/92), [#105](https://github.com/jethrokuan/org-roam/pull/105) Add tests for core functionality
+
+- [#122](https://github.com/org-roam/org-roam/pull/122), [#128](https://github.com/org-roam/org-roam/pull/128) Improve performance of post-command-hook
+- [#92](https://github.com/org-roam/org-roam/pull/92), [#105](https://github.com/org-roam/org-roam/pull/105) Add tests for core functionality

 ### New Contributors
-* [@frigge](https://github.com/frigge)
-* [@juergenhoetzel](https://github.com/juergenhoetzel)
-* [@chip2n](https://github.com/chip2n)
-* [@l3kn](https://github.com/l3kn)
-* [@jdormit](https://github.com/jdormit)
-* [@herbertjones](https://github.com/herbertjones)
-* [@CeleritasCelery](https://github.com/CeleritasCelery)
-* [@daniel-koudouna](https://github.com/daniel-koudouna)
+
+- [@frigge](https://github.com/frigge)
+- [@juergenhoetzel](https://github.com/juergenhoetzel)
+- [@chip2n](https://github.com/chip2n)
+- [@l3kn](https://github.com/l3kn)
+- [@jdormit](https://github.com/jdormit)
+- [@herbertjones](https://github.com/herbertjones)
+- [@CeleritasCelery](https://github.com/CeleritasCelery)
+- [@daniel-koudouna](https://github.com/daniel-koudouna)

 ## 0.1.1 (2020-02-15)

 Mostly a documentation/cleanup release.

 ### New Features
-* [#62](https://github.com/jethrokuan/org-roam/pull/62) Add the options `org-roam-use-timestamps-as-filename` and `org-roam-file-format`, more in documentation.
+
+- [#62](https://github.com/org-roam/org-roam/pull/62) Add the options `org-roam-use-timestamps-as-filename` and `org-roam-file-format`, more in documentation.

 ### Breaking Changes
-* [#62](https://github.com/jethrokuan/org-roam/pull/62) The ID (file-name) workflow is no longer first-class, but a fallback when titles don't exist.
+
+- [#62](https://github.com/org-roam/org-roam/pull/62) The ID (file-name) workflow is no longer first-class, but a fallback when titles don't exist.

 ### Changes
-* [#66](https://github.com/jethrokuan/org-roam/pull/66), [#68](https://github.com/jethrokuan/org-roam/pull/68): Improved the quality of the package in preparation of submission to MELPA
-* [#73](https://github.com/jethrokuan/org-roam/pull/73): Added CI to the project via Github Issues (Thanks [@alphapapa](https://github.com/alphapapa/) for scripts and setup)
-* [#69](https://github.com/jethrokuan/org-roam/pull/69), [#72](https://github.com/jethrokuan/org-roam/pull/72), [#75](https://github.com/jethrokuan/org-roam/pull/75): Major cleanup and de-duplication of code
+
+- [#66](https://github.com/org-roam/org-roam/pull/66), [#68](https://github.com/org-roam/org-roam/pull/68): Improved the quality of the package in preparation of submission to MELPA
+- [#73](https://github.com/org-roam/org-roam/pull/73): Added CI to the project via Github Issues (Thanks [@alphapapa](https://github.com/alphapapa/) for scripts and setup)
+- [#69](https://github.com/org-roam/org-roam/pull/69), [#72](https://github.com/org-roam/org-roam/pull/72), [#75](https://github.com/org-roam/org-roam/pull/75): Major cleanup and de-duplication of code

 ### Bugfixes
-* [#67](https://github.com/jethrokuan/org-roam/pull/67): Fixed `org-roam--make-file` not creating files with extensions
-* [#71](https://github.com/jethrokuan/org-roam/pull/71), [#78](https://github.com/jethrokuan/org-roam/pull/78): Fixed `org-roam-insert` not inserting correct paths
-* [#82](https://github.com/jethrokuan/org-roam/pull/82): Fixed nested Org-roam files not being detected as part of Org-roam
+
+- [#67](https://github.com/org-roam/org-roam/pull/67): Fixed `org-roam--make-file` not creating files with extensions
+- [#71](https://github.com/org-roam/org-roam/pull/71), [#78](https://github.com/org-roam/org-roam/pull/78): Fixed `org-roam-insert` not inserting correct paths
+- [#82](https://github.com/org-roam/org-roam/pull/82): Fixed nested Org-roam files not being detected as part of Org-roam

 <!-- Local Variables: -->
 <!-- eval: (auto-fill-mode -1) -->
--- a/14
+++ b/14
@ -54,3 +54,17 @@ endif
 .DEFAULT: init
 init:
 	@./makem.sh $(DEBUG) $(VERBOSE) $(SANDBOX) $(INSTALL_DEPS) $(INSTALL_LINTERS)
+
+docs:
+	@$(MAKE) -C doc all
+
+html:
+	@$(MAKE) -C doc html-dir
+
+install: install-docs
+
+install-docs: docs
+	@$(MAKE) -C doc install-docs
+
+install-info: info
+	@$(MAKE) -C doc install-info
--- a/README.md
+++ b/README.md
@ -1,6 +1,5 @@
 [![License GPL 3][badge-license]](http://www.gnu.org/licenses/gpl-3.0.txt)
-[![Documentation Status](https://readthedocs.org/projects/org-roam/badge/?version=latest)](https://org-roam.readthedocs.io/en/latest/?badge=latest)
-[![GitHub Release](https://img.shields.io/github/v/release/jethrokuan/org-roam)](https://img.shields.io/github/v/release/jethrokuan/org-roam)
+[![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)

 ## Synopsis
@ -22,20 +21,20 @@ 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")

-As of February 2020, it is in a very early stage of development. 
-
 Important links:

 - **[Documentation][docs]**
- **[Org-roam Slack][slack]**
+- **[Discourse][discourse]**
+- **[Slack][slack]**

 ## A Preview

-Here's a screenshot of `org-roam`. The `org-roam` buffer shows
-backlinks for the active org buffer in the left window, 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.
+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)

@ -51,7 +50,7 @@ Here's a sample configuration with using `use-package`:

 ```emacs-lisp
 (use-package org-roam
-      :hook 
+      :hook
      (after-init . org-roam-mode)
      :custom
      (org-roam-directory "/path/to/org-files/")
@ -63,9 +62,15 @@ Here's a sample configuration with using `use-package`:
              (("C-c n i" . org-roam-insert))))
 ```

+`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.
+
 For more detailed installation and configuration instructions (including for
 Doom and Spacemacs users), please see [the
-documentation](https://org-roam.readthedocs.io/en/master/installation/).
+documentation][docs].

 ## Knowledge Bases using Org-roam

@ -90,5 +95,6 @@ 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://org-roam.readthedocs.io/
+[docs]: https://org-roam.github.io/org-roam/manual/
+[discourse]: https://org-roam.discourse.group/
 [slack]: https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg
--- a/default.mk
+++ b/default.mk
@ -0,0 +1,106 @@
+TOP := $(dir $(lastword $(MAKEFILE_LIST)))
+
+## User options ######################################################
+#
+# You can override these settings in "config.mk" or on the command
+# line.
+#
+# You might also want to set LOAD_PATH.  If you do, then it must
+# contain "-L .".
+#
+# If you don't do so, then the default is set in the "Load-Path"
+# section below.  The default assumes that all dependencies are
+# installed either at "../<DEPENDENCY>", or when using package.el
+# at "ELPA_DIR/<DEPENDENCY>-<HIGHEST-VERSION>".
+
+sharedir ?= $(HOME)/.local/share
+lispdir  ?= $(sharedir)/emacs/site-lisp/org-roam
+infodir  ?= $(sharedir)/info
+docdir   ?= $(sharedir)/doc/org-roam
+statsdir ?= $(TOP)/doc/stats
+
+CP       ?= install -p -m 644
+MKDIR    ?= install -p -m 755 -d
+RMDIR    ?= rm -rf
+TAR      ?= tar
+SED      ?= sed
+
+EMACSBIN ?= emacs
+BATCH     = $(EMACSBIN) -Q --batch $(LOAD_PATH)
+
+INSTALL_INFO     ?= $(shell command -v ginstall-info || printf install-info)
+MAKEINFO         ?= makeinfo
+MANUAL_HTML_ARGS ?= --css-ref /assets/page.css
+
+## Files #############################################################
+
+PKG       = org-roam
+PACKAGES  = org-roam
+
+TEXIPAGES = $(addsuffix .texi,$(PACKAGES))
+INFOPAGES = $(addsuffix .info,$(PACKAGES))
+HTMLFILES = $(addsuffix .html,$(PACKAGES))
+HTMLDIRS  = $(PACKAGES)
+PDFFILES  = $(addsuffix .pdf,$(PACKAGES))
+EPUBFILES = $(addsuffix .epub,$(PACKAGES))
+
+ELS = org-roam-buffer.el
+ELS += org-roam-capture.el
+ELS += org-roam-compat.el
+ELS += org-roam-completion.el
+ELS += org-roam-dailies.el
+ELS += org-roam-db.el
+ELS += org-roam.el
+ELS += org-roam-graph.el
+ELS += org-roam-macs.el
+ELS += org-roam-protocol.el
+ELCS = $(ELS:.el=.elc)
+ELMS = org-roam.el $(filter-out $(addsuffix .el,$(PACKAGES)),$(ELS))
+ELGS = org-roam-autoloads.el org-roam-version.el
+
+## Versions ##########################################################
+
+VERSION ?= $(shell test -e $(TOP).git && git describe --tags --abbrev=0 | cut -c2-)
+
+EMACS_VERSION = 26.1
+
+EMACSOLD := $(shell $(BATCH) --eval \
+  "(and (version< emacs-version \"$(EMACS_VERSION)\") (princ \"true\"))")
+ifeq "$(EMACSOLD)" "true"
+  $(error At least version $(EMACS_VERSION) of Emacs is required)
+endif
+
+## Load-Path #########################################################
+
+ifndef LOAD_PATH
+
+ELPA_DIR ?= $(HOME)/.emacs.d/elpa
+
+SYSTYPE := $(shell $(EMACSBIN) -Q --batch --eval "(princ system-type)")
+ifeq ($(SYSTYPE), windows-nt)
+  CYGPATH := $(shell cygpath --version 2>/dev/null)
+endif
+
+LOAD_PATH = -L $(TOP)
+
+# When making changes here, then don't forget to adjust "Makefile",
+# ".travis.yml", ".github/ISSUE_TEMPLATE/bug_report.md",
+# `magit-emacs-Q-command' and the "Installing from the Git Repository"
+# info node accordingly.  Also don't forget to "rgrep \b<pkg>\b".
+
+endif # ifndef LOAD_PATH
+
+ifndef ORG_LOAD_PATH
+ORG_LOAD_PATH  = $(LOAD_PATH)
+ORG_LOAD_PATH += -L $(TOP)../ox-texinfo-plus
+ORG_LOAD_PATH += -L $(TOP)../org-mode/contrib/lisp
+ORG_LOAD_PATH += -L $(TOP)../org-mode/lisp
+endif
+
+## Publish ###########################################################
+
+PUBLISH_TARGETS ?= html html-dir pdf epub
+
+DOCBOOK_XSL ?= /usr/share/xml/docbook/stylesheet/docbook-xsl/epub/docbook.xsl
+
+EPUBTRASH = epub.xml META-INF OEBPS
--- a/doc/.nojekyll
+++ b/doc/.nojekyll
--- a/doc/AUTHORS.md
+++ b/doc/AUTHORS.md
@ -0,0 +1,37 @@
+Authors
+=======
+
+The following people have contributed to Org-Roam.
+
+Names below are sorted alphabetically.
+
+Author
+------
+
+- Jethro Kuan <jethrokuan95@gmail.com>
+
+Maintainers
+----------
+
+- Jethro Kuan <jethrokuan95@gmail.com>
+- Leo Vivier <leo.vivier+dev@gmail.com>
+
+Contributors
+------------
+
+- Alexey Shmalko <rasen.dubi@gmail.com>
+- James Ravn <james@r-vn.org>
+- Jethro Kuan <jethrokuan95@gmail.com>
+- Johann Klähn <johann@jklaehn.de>
+- Josh English <josh@joshenglish.com>
+- Jürgen Hötzel <juergen@archlinux.org>
+- Langston Barrett <langston.barrett@gmail.com>
+- Leo Vivier <leo.vivier+dev@gmail.com>
+- Michael Glaesemann <grzm@seespotcode.net>
+- Michael Herold <github@michaeljherold.com>
+- Noboru <noboru.ota@gmail.com>
+- N V <44036031+progfolio@users.noreply.github.com>
+- Rafael Accácio Nogueira <raccacio@poli.ufrj.br>
+- Roland Coeurjoly <rolandcoeurjoly@gmail.com>
+- Sayan <dit7ya@users.noreply.github.com>
+- Tim Quelch <tim@quelch.name>
--- a/doc/Makefile
+++ b/doc/Makefile
@ -0,0 +1,130 @@
+-include ../config.mk
+include ../default.mk
+
+###################################################################
+MANUAL_HTML_ARGS = --css-ref assets/page.css
+
+.PHONY: texi install clean AUTHORS.md stats
+
+all: info
+
+## Build #############################################################
+
+info: $(INFOPAGES) dir
+html: $(HTMLFILES)
+pdf:  $(PDFFILES)
+epub: $(EPUBFILES)
+
+%.info: %.texi
+	@printf "Generating $@\n"
+	@$(MAKEINFO) --no-split $< -o $@
+
+dir: org-roam.info
+	@printf "Generating dir\n"
+	@echo $^ | xargs -n 1 $(INSTALL_INFO) --dir=$@
+
+%.html: %.texi
+	@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
+
+%.pdf: %.texi
+	@printf "Generating $@\n"
+	@texi2pdf --clean $< > /dev/null
+
+%.epub: %.texi
+	@printf "Generating $@\n"
+	@$(MAKEINFO) --docbook $< -o epub.xml
+	@xsltproc $(DOCBOOK_XSL) epub.xml 2> /dev/null
+	@echo "application/epub+zip" > mimetype
+	@zip -X --quiet --recurse-paths -0 $@ mimetype
+	@zip -X --quiet --recurse-paths -9 --no-dir-entries $@ META-INF OEBPS
+	@$(RMDIR) $(EPUBTRASH)
+
+## Install ###########################################################
+
+install: install-info install-docs
+
+install-docs: install-info
+	@$(MKDIR) $(DESTDIR)$(docdir)
+	$(CP) AUTHORS.md $(DESTDIR)$(docdir)
+
+install-info: info
+	@$(MKDIR) $(DESTDIR)$(infodir)
+	$(CP) $(INFOPAGES) $(DESTDIR)$(infodir)
+
+## Clean #############################################################
+
+clean:
+	@printf "Cleaning doc/*...\n"
+	@$(RMDIR) dir $(INFOPAGES) $(HTMLFILES) $(HTMLDIRS) $(PDFFILES)
+	@$(RMDIR) $(EPUBFILES) $(EPUBTRASH)
+
+## Release management ################################################
+
+ORG_ARGS  = --batch -Q $(ORG_LOAD_PATH)
+ORG_ARGS += -l ox-extra -l ox-texinfo+
+ORG_ARGS += --eval "(or (require 'org-man nil t) (require 'ol-man))"
+ORG_EVAL  = --eval "(ox-extras-activate '(ignore-headlines))"
+ORG_EVAL += --eval "(setq indent-tabs-mode nil)"
+ORG_EVAL += --eval "(setq org-src-preserve-indentation nil)"
+ORG_EVAL += --funcall org-texinfo-export-to-texinfo
+
+# This target first bumps version strings in the Org source.  The
+# necessary tools might be missing so other targets do not depend
+# on this target and it has to be run explicitly when appropriate.
+#
+#   AMEND=t make texi    Update manual to be amended to HEAD.
+#   VERSION=N make texi  Update manual for release.
+#
+texi:
+	@$(EMACSBIN) $(ORG_ARGS) $(PKG).org $(ORG_EVAL)
+	@printf "\n" >> $(PKG).texi
+	@rm -f $(PKG).texi~
+
+stats:
+	@printf "Generating statistics\n"
+	@gitstats -c style=/assets/stats.css -c max_authors=999 $(TOP) $(statsdir)
+
+authors: AUTHORS.md
+
+AUTHORS.md:
+	@printf "Generating AUTHORS.md..."
+	@test -e $(TOP).git \
+	&& (printf "$$AUTHORS_HEADER\n" > $@ \
+	&& git log --pretty=format:'- %aN <%aE>' | sort -u >> $@ \
+	&& printf "done\n" ; ) \
+	|| printf "FAILED (non-fatal)\n"
+
+# Templates ##########################################################
+
+define AUTHORS_HEADER
+Authors
+=======
+
+The following people have contributed to Org-Roam.
+
+Names below are sorted alphabetically.
+
+Author
+------
+
+- Jethro Kuan <jethrokuan95@gmail.com>
+
+Maintainers
+----------
+
+- Jethro Kuan <jethrokuan95@gmail.com>
+- Leo Vivier <leo.vivier+dev@gmail.com>
+
+Contributors
+------------
+
+endef
+export AUTHORS_HEADER
--- a/doc/anatomy.md
+++ b/doc/anatomy.md
@ -1,41 +0,0 @@
-The bulk of Org-roam's functionality is built on top of vanilla
-Org-mode. However, to support additional functionality, Org-roam adds
-several Org-roam-specific keywords. These functionality are not
-crucial to effective use of Org-roam.
-
-## File Aliases
-
-Suppose you want a note to be referred to by different names (e.g.
-"World War 2", "WWII"). You may specify such aliases using the
-`#+ROAM_ALIAS` attribute:
-
-```org
-#+TITLE: World War 2
-#+ROAM_ALIAS: "WWII" "World War II"
-```
-
-
-## File Refs
-
-Refs are unique identifiers for files. Each note can only have 1 ref.
-For example, a note for a website may contain a ref:
-
-```org
-#+TITLE: Google
-#+ROAM_KEY: https://www.google.com/
-```
-
-These keys come in useful for when taking website notes, using the
-`roam-ref` protocol (see [Roam Protocol](roam_protocol.md)).
-
-Alternatively, add a ref for notes for a specific paper, using its
-[org-ref](https://github.com/jkitchin/org-ref) citation key:
-
-```org
-#+TITLE: Neural Ordinary Differential Equations
-#+ROAM_KEY: cite:chen18_neural_ordin_differ_equat
-```
-
-The backlinks buffer will show any cites of this key: e.g.
-
-![org-ref-citelink](images/org-ref-citelink.png)
--- a/doc/assets/page.css
+++ b/doc/assets/page.css
@ -0,0 +1,442 @@
+/* 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);
+}
+
+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;
+}
+
+::selection {
+  /* Set background color for selected text */
+  background: var(--nc-ac-1);
+  color: var(--nc-ac-tx);
+}
+
+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 {
+  padding: 1rem 1.4rem;
+  max-width: 100%;
+  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;
+}
+
+img {
+  max-width: 100%;
+}
+
+/* Customizations */
+.menu-comment {
+  font-weight: bold;
+  border: 0;
+  margin: 0;
+  padding: 0;
+  font-size: 1.2rem;
+}
--- a/doc/comparison.md
+++ b/doc/comparison.md
@ -1,11 +0,0 @@
---
-title: "Comparing Org-roam With Other Packages"
-metaTitle: "Comparing Org-roam With Other Packages"
-metaDescription: "Comparing Org-roam With Other Packages"
---
-
-# Org-brain
-
-# Zetteldeft
-
-# Org-zettelkasten
--- a/doc/configuration.md
+++ b/doc/configuration.md
@ -1,142 +0,0 @@
-The number of configuration options is deliberately kept small, to
-keep the Org-roam codebase manageable. However, we attempt to
-accommodate as many usage styles as possible.
-
-All of Org-roam's customization options can be viewed via `M-x
-customize-group org-roam`.
-
-## Setting the Org-roam Directory
-
-Set `org-roam-directory` to the folder containing all your Org files:
-
-```emacs-lisp
-(setq org-roam-directory "/path/to/org/")
-```
-
-Every Org file, at any level of nesting, within `/path/to/org/` is
-considered part of the Org-roam ecosystem.
-
-### Having More Than One Org-roam Directory
-
-Emacs supports directory-local variables, allowing the value of
-`org-roam-directory` to be different in different directories. It does
-this by checking for a file named `.dir-locals.el`. 
-
-To add support for multiple directories, override the
-`org-roam-directory` variable using directory-local variables. This is
-what `.dir-locals.el` may contain:
-
-```emacs-lisp
-((nil . ((org-roam-directory . "/path/to/here/"))))
-```
-
-All files within that directory will be treated as their own separate
-set of Org-roam files. Remember to run `org-roam-db-build-cache` from a
-file within that directory, at least once.
-
-## Org-roam Buffer
-
-The Org-roam buffer defaults to popping up from the right. You may
-choose to set it to pop up from the left with `(setq
-org-roam-buffer-position 'left)`.
-
-The Org-roam buffer name can also be renamed: e.g. `(setq
-org-roam-buffer "*my-buffer-name*")`.
-
-The Org-roam buffer width is adjustable via `org-roam-buffer-width`.
-The value of `org-roam-buffer-width` set as a percentage of the total
-frame width. For example:
-
-```emacs-lisp
-(setq org-roam-buffer-width 0.4)
-```
-
-Will result in the Org-roam buffer taking up 40% of the screen width.
-
-You can change backlinks appearance in the buffer by customizing
-`org-roam-backlink` face (`M-x customize-face org-roam-backlink`).
-
-## Org-roam Links
-
-By default, links are inserted with the title as the link description.
-This can make them hard to distinguish from external links. You may
-choose add special indicators for Org-roam links by tweaking
-`org-roam-link-title-format`, for example:
-
-```emacs-lisp
-(setq org-roam-link-title-format "R:%s")
-```
-
-If your version of Org is at least `9.2`, you may also choose to
-simply style the link differently, by customizing `org-roam-link` face
-(`M-x customize-face org-roam-link`).
-
-## Org-roam Files
-
-Org-roam files are created and prefilled using Org-roam's templating
-system. The templating system is customizable, and the system is
-described in detail in the [Org-roam Template](templating.md) page.
-
-### Encryption
-
-Encryption (via GPG) can be enabled for all new files by setting
-`org-roam-encrypt-files` to `t`. When enabled, new files are created
-with the `.org.gpg` extension and decryption are handled automatically
-by EasyPG. 
-
-Note that Emacs will prompt for a password for encrypted files during
-cache updates if it requires reading the encrypted file. To reduce the
-number of password prompts, you may wish to cache the password.
-
-## Org-roam Graph Viewer
-
-Org-roam generates an SVG image using
-[Graphviz](https://graphviz.org/). To setup graph navigation, see the
-[Graph Setup](graph_setup.md) page.
-
-Org-roam tries its best to locate the Graphviz executable from your
-`PATH`, but if it fails to do so, you may set it manually:
-
-```
-(setq org-roam-graph-executable "/path/to/dot")
-```
-
-You may also choose to use `neato` in place of `dot`, which generates a more compact graph layout.
-
-```
-(setq org-roam-graph-executable "/path/to/neato")
-(setq org-roam-graph-extra-config '(("overlap" . "false")))
-```
-
-Org-roam also attempts to use Firefox (located on `PATH`) to view the
-SVG, you may choose to set it to any compatible program:
-
-```
-(setq org-roam-graph-viewer "/path/to/image-viewer")
-```
-
-### Excluding Nodes and Edges
-One may want to exclude certain files to declutter the graph. You can do so by setting `org-roam-graph-exclude-matcher`.
-
-```
-(setq org-roam-graph-exclude-matcher '("private" "dailies"))
-```
-
-This setting excludes all files whose path contain "private" or "dailies".
-
-## Org-roam Completion System
-
-Org-roam offers completion when choosing note titles etc.
-The completion system is configurable. The default setting,
-
-```
-(setq org-roam-completion-system 'default)
-```
-
-uses Emacs' standard `completing-read`. If you prefer [Helm](https://emacs-helm.github.io/helm/), use
-
-```
-(setq org-roam-completion-system 'helm)
-```
-
-Other options included `'ido`, and `'ivy'`.
--- a/doc/ecosystem.md
+++ b/doc/ecosystem.md
@ -1,134 +0,0 @@
-A number of packages work well combined with Org-Roam:
-
-## Deft
-
-[Deft][deft] provides a nice interface for browsing and filtering
-org-roam notes.
-
-```emacs-lisp
-(use-package deft
-  :after org
-  :bind
-  ("C-c n d" . deft)
-  :custom
-  (deft-recursive t)
-  (deft-use-filter-string-for-filename t)
-  (deft-default-extension "org")
-  (deft-directory "/path/to/org-roam-files/"))
-```
-
-If the title of the Org file is not the first line, you might not get
-nice titles. You may choose to patch this to use `org-roam`'s
-functionality. Here I'm using [el-patch](https://github.com/raxod502/el-patch):
-
-```emacs-lisp
-(use-package el-patch
-  :straight (:host github
-                   :repo "raxod502/el-patch"
-                   :branch "develop"))
-
-(eval-when-compile
-  (require 'el-patch))
-
-(use-package deft
-  ;; same as above...
-  :config/el-patch
-  (defun deft-parse-title (file contents)
-    "Parse the given FILE and CONTENTS and determine the title.
-If `deft-use-filename-as-title' is nil, the title is taken to
-be the first non-empty line of the FILE.  Else the base name of the FILE is
-used as title."
-    (el-patch-swap (if deft-use-filename-as-title
-                       (deft-base-filename file)
-                     (let ((begin (string-match "^.+$" contents)))
-                       (if begin
-                           (funcall deft-parse-title-function
-                                    (substring contents begin (match-end 0))))))
-                   (org-roam--get-title-or-slug file))))
-```
-
-The Deft interface can slow down quickly when the number of files get
-huge. [Notdeft][notdeft] is a fork of Deft that uses an external
-search engine and indexer.
-
-## Org-journal
-
-[Org-journal](https://github.com/bastibe/org-journal) is a more powerful
-alternative to the simple function `org-roam-dailies-today`. It provides better
-journaling capabilities, and a nice calendar interface to see all dated entries.
-
-```emacs-lisp
-(use-package org-journal
-  :bind
-  ("C-c n j" . org-journal-new-entry)
-  :custom
-  (org-journal-date-prefix "#+TITLE: ")
-  (org-journal-file-format "%Y-%m-%d.org")
-  (org-journal-dir "/path/to/org-roam-files/")
-  (org-journal-date-format "%A, %d %B %Y"))
-```
-
-## Note-taking Add-ons
-
-These are some plugins that make note-taking in Org-mode more
-enjoyable.
-
-### Org-download
-
-[Org-download][org-download] lets you screenshot and yank images from
-the web into your notes:
-
-![org-download](images/org-download.gif)
-
-```emacs-lisp
-(use-package org-download
-  :after org
-  :bind
-  (:map org-mode-map
-        (("s-Y" . org-download-screenshot)
-         ("s-y" . org-download-yank))))
-```
-
-### mathpix.el
-
-[mathpix.el][mathpix-el] uses [Mathpix's](https://mathpix.com/) API to convert clips into
-latex equations:
-
-![mathpix](images/mathpix.gif)
-
-```emacs-lisp
-(use-package mathpix.el
-  :straight (:host github :repo "jethrokuan/mathpix.el")
-  :custom ((mathpix-app-id "app-id")
-           (mathpix-app-key "app-key"))
-  :bind
-  ("C-x m" . mathpix-screenshot))
-```
-
-### Org-noter / Interleave
-
-[Org-noter][org-noter] and [Interleave][interleave] are both projects
-that allow synchronised annotation of documents (PDF, EPUB etc.)
-within Org-mode.
-
-### Org-ref
-
-[Org-ref][org-ref] does citation and bibliography management in
-Org-mode, and a great tool for scientific notes.
-
-### Spaced Repetition
-
-[Org-fc][org-fc] is a spaced repetition system that scales well with a
-large number of files. Other alternatives include
-[org-drill][org-drill], and [pamparam][pamparam].
-
-[deft]: https://jblevins.org/projects/deft/
-[notdeft]: https://github.com/hasu/notdeft
-[org-download]: https://github.com/abo-abo/org-download
-[mathpix-el]: https://github.com/jethrokuan/mathpix.el
-[org-noter]: https://github.com/weirdNox/org-noter
-[interleave]: https://github.com/rudolfochrist/interleave
-[org-ref]: https://github.com/jkitchin/org-ref
-[org-fc]: https://github.com/l3kn/org-fc/
-[org-drill]: https://orgmode.org/worg/org-contrib/org-drill.html
-[pamparam]: https://github.com/abo-abo/pamparam
--- a/doc/htmlxref.cnf
+++ b/doc/htmlxref.cnf
@ -0,0 +1,15 @@
+# https://www.gnu.org/software/texinfo/manual/texinfo/html_node/HTML-Xref-Configuration.html
+
+EMACS = https://www.gnu.org/software/emacs/manual
+
+auth		mono	${EMACS}/html_mono/auth.html
+auth		node	${EMACS}/html_node/auth/
+
+ediff		mono	${EMACS}/html_mono/ediff.html
+ediff		node	${EMACS}/html_node/ediff/
+
+elisp		mono	${EMACS}/html_mono/elisp.html
+elisp		node	${EMACS}/html_node/elisp/
+
+emacs		mono	${EMACS}/html_mono/emacs.html
+emacs		node	${EMACS}/html_node/emacs/
--- a/doc/images/org-roam-bibtex.gif
+++ b/doc/images/org-roam-bibtex.gif
--- a/doc/index.html
+++ b/doc/index.html
@ -0,0 +1,3 @@
+<html>
+  <h1>--> <a href="manual/index.html">MANUAL HERE</a> <--</h1>
+</html>
--- a/doc/index.md
+++ b/doc/index.md
@ -1,62 +0,0 @@
-![org-roam][org-roam-intro-image]
-
-## What is Org-roam?
-
-Org-roam is a [Roam][roamresearch] replica built around the
-all-powerful [Org-mode][org].
-
-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.
-
-To understand more about Roam, a collection of links are available in
-[the appendix](notetaking_workflow.md).
-
-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.
-
-## Why use Org-roam?
-
-##### Private and Secure
-
-Edit your personal wiki completely offline, entirely in your control.
-Encrypt your notes with GPG.
-
-##### Longevity
-
-Unlike web solutions like Roam research, the notes are first and
-foremost plain Org-mode files -- Org-roam simply builds up an
-auxilliary database to give the personal wiki superpowers. Having your
-notes in plain-text is crucial for the longevity of your wiki. Never
-have to worry about proprietary web solutions being taken down. Edit
-your plain-text notes in notepad if all other editors cease to exist.
-
-##### Free and Open-source
-
-Org-roam is free and open-source, which means that if you feel unhappy
-with any part of Org-roam, you may choose to extend Org-roam, or open
-a PR.
-
-##### Leverage the Org-mode Ecosystem
-
-Over the years, Emacs and Org-mode has developed into a mature system
-for plain-text organization. Building upon Org-mode already puts
-Org-roam light-years ahead of many other solutions.
-
-Emacs is also a fantastic interface for editing text, and we can
-inherit many of the powerful text-navigation and editing packages
-available to Emacs.
-
-There are several packages that are similar to Org-roam, see the
-[Comparison](comparison.md) page for a detailed comparison.
-
-## Project Status
-
-As of March 2020, most of the core functionality and interfaces have
-stabilized, and a stable release is near.
-
-[org-roam-intro-image]: images/org-roam-intro.png
-[roamresearch]: https://www.roamresearch.com/
-[org]: https://orgmode.org/
--- a/doc/installation.md
+++ b/doc/installation.md
@ -1,195 +0,0 @@
-## Basic Install and Configuration
-
-Org-roam is now available on MELPA, so you can install it via the following
-command:
-
-```
-M-x package-install RET org-roam RET
-```
-
-Alternatively, you may use package managers such as [straight][straight] or
-[quelpa][quelpa] to install the package.
-
-The recommended method of configuration is to use [use-package][use-package].
-
-```emacs-lisp
-(use-package org-roam
-      :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 b" . org-roam-switch-to-buffer)
-               ("C-c n g" . org-roam-graph))
-              :map org-mode-map
-              (("C-c n i" . org-roam-insert))))
-```
-
-Or without `use-package`:
-
-```emacs-lisp
-(require 'org-roam)
-(define-key org-roam-mode-map (kbd "C-c n l") #'org-roam)
-(define-key org-roam-mode-map (kbd "C-c n f") #'org-roam-find-file)
-(define-key org-roam-mode-map (kbd "C-c n b") #'org-roam-switch-to-buffer)
-(define-key org-roam-mode-map (kbd "C-c n g") #'org-roam-graph)
-(define-key org-mode-map (kbd "C-c n i") #'org-roam-insert)
-(org-roam-mode +1)
-```
-
-The [Configuration](configuration.md) page details some of the common
-configuration options available.
-
-### Completion
-
-Link auto-completion is offered via
-[company-org-roam](https://github.com/jethrokuan/company-org-roam/), refer to
-the documentation there for further details.
-
-## Spacemacs
-
-If you are using Spacemacs, install org-roam by creating a simple layer that
-wraps Org-roam. Paste the following into a new file
-`~/.emacs.d/private/org-roam/packages.el`.
-
-```emacs-lisp
-(defconst org-roam-packages
-  '(org-roam))
-
-(defun org-roam/init-org-roam ()
-  (use-package org-roam
-    :hook
-    (after-init . org-roam-mode)
-    :custom
-    (org-roam-directory "/path/to/org-files/")
-    :init
-    (progn
-      (spacemacs/declare-prefix "ar" "org-roam")
-      (spacemacs/set-leader-keys
-       "arl" 'org-roam
-       "art" 'org-roam-dailies-today
-       "arf" 'org-roam-find-file
-       "arg" 'org-roam-graph)
-
-      (spacemacs/declare-prefix-for-mode 'org-mode "mr" "org-roam")
-      (spacemacs/set-leader-keys-for-major-mode 'org-mode
-                                                "rl" 'org-roam
-                                                "rt" 'org-roam-dailies-today
-                                                "rb" 'org-roam-switch-to-buffer
-                                                "rf" 'org-roam-find-file
-                                                "ri" 'org-roam-insert
-                                                "rg" 'org-roam-graph))))
-```
-
-Next, append `org-roam` to the `dotspacemacs-configuration-layers`
-list in your `.spacemacs` configuration file. Reload (`SPC f e R`) or
-restart Emacs to load `org-roam`. It's functions are available under
-the prefix `SPC a r` and `, r` when visiting an org-mode buffer.
-
-If you also have the ranger layer installed, the prefix 'ar' conflict
-with that of the ranger layer. You might want to change it to 'aor'
-(also change the 'ar' to 'aor' in the other key-binding declarations)
-
-## Doom Emacs
-
-[Doom Emacs][doom] has a `+roam` flag on its `org` module for easy
-installation and configuration. Simply add the flag to the `org` section
-of your `~/.doom.d/init.el` and run `~/.emacs.d/bin/doom sync`.
-
-[use-package]: https://github.com/jwiegley/use-package
-[straight]: https://github.com/raxod502/straight.el
-[quelpa]: https://github.com/quelpa/quelpa
-[doom]: https://github.com/hlissner/doom-emacs
-[doom-getting-started]: https://github.com/hlissner/doom-emacs/blob/develop/docs/getting_started.org#configuring-packages
-
-## Windows
-
-On Windows, if you follow the installation instructions above, you will likely get the error message: **"No EmacSQL SQLite binary available, aborting"**, and `org-roam` won't start properly.
-
-You need to do some additional steps to get `org-roam` to work.
-
-Essentially, you will need to have a binary file for `emacsql-sqlite` so that your Emacs can work with `sqlite` database -- `org-roam` uses it to track backlinks. The following options have been reported to work by Windows users in the community.
-
-Option 1. **Windows Subsystem for Linux (WSL)**
-: This option lets you use Linux on your Windows machine. It's Linux, so you don't need to do anything specific for Windows.
-
-Option 2. **mingw-x64**
-: Use mingw-x64. You would spend a bit of time to download it, and get familiar with how it works. You should be able to use Linux tools within your Windows [more contribution welcome].
-
-Option 3. **scoop**
-: Use [scoop](https://scoop.sh/) to install a couple of software tools (make and gcc) and manually compile a binary (`.exe`) file yourself. Find a short step-by-step guide below.
-
-Option 4. **emacsql-sqlite3**
-: Use another Emacs package called [`emacsql-sqlite3`](https://github.com/cireu/emacsql-sqlite3). You can download an [official binary](https://sqlite.org/download.html) for `sqlite3`. `emacsql-sqlite3` lets you use it. For this option to work, you need to adjust the `org-roam` source code, and get your modified version to work in your Emacs environment. Find a suggestion below.
-
-### scoop
-**Step 1.** In PowerShell, install `scoop` ([instruction here](https://scoop.sh/)).
-
-```powershell
-iwr -useb get.scoop.sh | iex
-```
-
-**Step 2.** In PowerShell, install `make` and `gcc` via scoop
-
-```powershell
-scoop install make gcc
-```
-
-**Step 3.** In Emacs, install the `emacsql-sqlite` package for your Emacs if it is not done yet.
-
-**Step 4.** In PowerShell, move to the directory where `emacsql.c` is stored.
-
-With MELPA, it is likely to be under your ELPA folder:
-
-```
-~\AppData\Roaming\.emacs.d\elpa\emacsql-sqlite-20190727.1710\sqlite
-```
-
-With Doom Emacs, it should be under your `.emacs\.local`:
-
-```
-~\.emacs.d\.local\straight\build\emacsql-sqlite\sqlite
-```
-
-Check the files via `dir` command. You should see these files:
-
-```powershell
-Mode                LastWriteTime         Length Name
----                -------------         ------ ----
-a----       22/03/2020  12:10 PM           5170 emacsql.c
-a----       22/03/2020  12:10 PM            439 Makefile
-a----       22/03/2020  12:10 PM        7516138 sqlite3.c
-a----       22/03/2020  12:10 PM         526684 sqlite3.h
-```
-
-**Step 5.** Compile the `.exe` file with `make`
-
-```powershell
-make emacsql-sqlite CC=gcc LDLIBS=
-```
-
-You will see the process triggered with lots of text automatically scrolling down; it may take a couple of minutes for compilation to finish.
-
-Once compilation is done, check that `emacsql-sqlite.exe` has been added to the directory.
-
-**Step 6.** Relaunch Emacs, use `org-roam`
-
-When you start `org-roam` (e.g. via `org-roam-mode`), now you should no longer see the "No EmacSQL SQLite binary available, aborting" error. You are good to go.
-
-
-### emacsql-sqlite3
-
-1. In Emacs, install the `emacsql-sqlite3` package
-
-2. Using your text editor, etc. modify `org-roam-db.el`:
-
-    1. Replace `(require 'emacsql-sqlite)` with `(require 'emacsql-sqlite3)`
-
-    2. Comment/deactivate the complete `(defconst org-roam-db--sqlite-available-p ... )`
-
-    3. In `(defun org-roam-db ...`, replace `emacsql-sqlite`
-with `emacsql-sqlite3`
-
-3. If you compile `.el` files, ensure to replace `org-roam-db.elc` with the new source you modified.
--- a/doc/notetaking_workflow.md
+++ b/doc/notetaking_workflow.md
@ -1,24 +0,0 @@
-## Recommended Books
- [How to Take Smart Notes][1]
-
-## Articles
- [How to Take Smart Notes in Org-mode - Jethro Kuan][7]
- [The Zettelkasten Method - LessWrong 2.0][3]
- [Building a second brain in Roam][4]
- [Roam: Why I Love It and How I Use It][5]
- [Adam Keesling's Twitter Thread][6]
-
-## Threads
- [Ask HN: How to Take Good Notes][8]
-
-## What to Do With Your Notes
- [How to Use Roam to Outline a New Article in Under 20 Minutes][2]
-
-[1]: https://www.goodreads.com/book/show/34507927-how-to-take-smart-notes?ac=1&from_search=true&qid=6L8iEE1FIA&rank=1
-[2]: https://www.youtube.com/watch?v=RvWic15iXjk
-[3]: https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettelkasten-method-1
-[4]: https://reddit.com/r/RoamResearch/comments/eho7de/building_a_second_brain_in_roamand_why_you_might
-[5]: https://www.nateliason.com/blog/roam
-[6]: https://twitter.com/adam_keesling/status/1196864424725774336?s=20
-[7]: https://blog.jethro.dev/posts/how_to_take_smart_notes_org/
-[8]: https://news.ycombinator.com/item?id=22473209
--- a/doc/org-roam.org
+++ b/doc/org-roam.org
@ -0,0 +1,974 @@
+#+TITLE: Org-roam User Manual
+:PREAMBLE:
+#+AUTHOR: Jethro Kuan
+#+EMAIL: jethrokuan95@gmail.com
+#+DATE: 2020-2020
+#+LANGUAGE: en
+
+#+TEXINFO_DIR_CATEGORY: Emacs
+#+TEXINFO_DIR_TITLE: Org-roam: (org-roam).
+#+TEXINFO_DIR_DESC: Rudimentary Roam Replica for Emacs.
+#+SUBTITLE: for version 1.1.1
+
+#+OPTIONS: H:4 num:3 toc:2 creator:t
+#+PROPERTY: header-args :eval never
+#+TEXINFO: @noindent
+
+This manual is for Org-roam version 1.1.1.
+
+#+BEGIN_QUOTE
+Copyright (C) 2020-2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+You can redistribute this document 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 document 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.
+#+END_QUOTE
+
+:END:
+
+* Introduction
+
+Org-roam is a [[https://roamresearch.com/][Roam Research]] replica built around the
+all-powerful [[https://orgmode.org/][Org-mode]].
+
+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.
+
+To understand more about Roam, a collection of links are available in
+[[*Note-taking Workflows][Note-taking Workflows]].
+
+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.
+
+Org-roam provides several benefits over other tooling:
+
+- Privacy and Security :: Edit your personal wiki completely offline, entirely in your control. Encrypt your notes with GPG.
+- Longevity of Plain Text :: Unlike web solutions like Roam research, the notes are first and foremost plain Org-mode files -- Org-roam simply builds up an auxilliary database to give the personal wiki superpowers. Having your notes in plain-text is crucial for the longevity of your wiki. Never have to worry about proprietary web solutions being taken down. Edit your plain-text notes in notepad if all other editors cease to exist
+- Free and Open Source :: Org-roam is free and open-source, which means that if you feel unhappy with any part of Org-roam, you may choose to extend Org-roam, or open a PR.
+- Leverages the Org-mode ecosystem :: Over the years, Emacs and Org-mode has developed into a mature system for plain-text organization. Building upon Org-mode already puts Org-roam light-years ahead of many other solutions.
+- Built on Emacs :: Emacs is also a fantastic interface for editing text, and we can inherit many of the powerful text-navigation and editing packages available to Emacs.
+* Installation
+** _ :ignore:
+Org-roam can be installed using Emacs' package manager or manually from its development repository.
+
+** Installing from MELPA
+
+Org-roam is available from Melpa and Melpa-Stable. If you haven't used Emacs' package manager before, you may familiarize yourself with it by reading the documentation in the Emacs manual, see info:emacs#Packages. Then, add one of the archives to =package-archives=:
+
+- To use Melpa:
+
+#+BEGIN_SRC emacs-lisp
+  (require 'package)
+  (add-to-list 'package-archives
+               '("melpa" . "http://melpa.org/packages/") t)
+#+END_SRC
+
+- To use Melpa-Stable:
+
+#+BEGIN_SRC emacs-lisp
+  (require 'package)
+  (add-to-list 'package-archives
+               '("melpa-stable" . "http://stable.melpa.org/packages/") t)
+#+END_SRC
+
+Once you have added your preferred archive, you need to update the
+local package list using:
+
+#+BEGIN_EXAMPLE
+  M-x package-refresh-contents RET
+#+END_EXAMPLE
+
+Once you have done that, you can install Org-roam and its dependencies
+using:
+
+#+BEGIN_EXAMPLE
+  M-x package-install RET org-roam RET
+#+END_EXAMPLE
+
+Now see [[*Post-Installation Tasks][Post-Installation Tasks]].
+
+** TODO Installing from the Git Repository
+
+** TODO Post-Installation Tasks
+
+* Getting Started
+
+This short tutorial describes the essential commands used in Org-roam, to help
+you get started.
+
+First, it is important to understand how Org-roam was designed. Org-roam was
+built to support a workflow that was not possible with vanilla Org-mode. This
+flow is modelled after the [[https://zettelkasten.de/][Zettelkasten Method]], and many of [[https://roamresearch.com][Roam Research's]]
+workflows. Org-roam does not magically make note-taking better -- this often
+requires a radical change in your current note-taking workflow. To understand
+more about the methods and madness, see [[*Note-taking Workflows][Note-taking Workflows]].
+
+To begin using Org-roam, one should set the =org-roam-directory= to the directory
+containing your notes. For this tutorial, create an empty directory, and set the
+=org-roam-directory=:
+
+#+BEGIN_SRC emacs-lisp
+(make-directory "~/org-roam")
+(setq org-roam-directory "~/org-roam")
+#+END_SRC
+
+We encourage using a flat hierarchy for storing notes, but some prefer using
+folders for storing specific kinds of notes (e.g. websites, papers). This is
+fine; Org-roam searches recursively within =org-roam-directory= for any notes.
+Instead of relying on the file hierarchy for any form of categorization, we
+solely rely on links between files to establish connections between notes.
+
+Next, we need to enable the global minor mode =org-roam-mode=. This sets up Emacs
+with several hooks, builds a cache and keeps it consistent. We recommend
+starting =org-roam-mode= on startup:
+
+#+BEGIN_SRC emacs-lisp
+(add-hook 'after-init-hook 'org-roam-mode)
+#+END_SRC
+
+To build the cache manually, one can run =M-x org-roam-db-build-cache=. The cache
+is a sqlite database named =org-roam.db=, which defaults to residing in the root
+=org-roam-directory=. Cache builds may take a while the first time, but is often
+instantaneous in subsequent runs.
+
+Let us now create our first note. Call =M-x org-roam-find-file=. This shows a list
+of titles for notes that reside in =org-roam-directory=. It should show nothing
+right now, since there are no notes in the directory. Entering the title of the
+note you wish to create, and pressing =RET= should begin the note creation
+process. This process uses =org-capture='s templating system, and can be freely
+customized (see [[*The Templating System][The Templating System]]). Using the default template, pressing =C-c
+C-c= finishes the note capture. Running =M-x org-roam-find-file= again should show
+the note you have created, and selecting that entry will bring you to that note.
+
+The crux of Org-roam is making it easy to create notes, and link them together.
+To link notes together, we call =M-x org-roam-insert=. This brings up a prompt
+with a list of title for existing notes. Selecting an existing entry will create
+and insert a link to the current file. Entering a non-existent title will create
+a new note with that title. Good usage of Org-roam requires liberally linking
+files: this facilitates building up a dense knowledge graph of inter-connected
+notes.
+
+Org-roam provides an interface to view backlinks. It shows backlinks for the
+currently active Org-roam note, along with some surrounding context. To toggle
+the visibility of this buffer, call =M-x org-roam=.
+
+For a visual representation of the notes and their connections, Org-roam also
+provides graphing capabilities, using Graphviz. It generates graphs with notes
+as nodes, and links between them as edges. The generated graph can be used to
+navigate to the files, but this requires some additional setup (see [[*Roam Protocol][Roam
+Protocol]]).
+
+* Anatomy of an Org-roam File
+
+The bulk of Org-roam's functionality is built on top of vanilla
+Org-mode. However, to support additional functionality, Org-roam adds
+several Org-roam-specific keywords. These functionality are not crucial
+to effective use of Org-roam.
+
+** Titles
+
+To easily find a note, a title needs to be prescribed to a note. A note can have
+many titles: this allows a note to be referred to by different names, which is
+especially useful for topics or concepts with acronyms. For example, for a note
+like "World War 2", it may be desirable to also refer to it using the acronym
+"WWII".
+
+Org-roam calls =org-roam--extract-titles= to extract titles. It uses the
+variable =org-roam-title-sources=, to control how the titles are extracted. The
+title extraction methods supported are:
+
+1. ='title=: This extracts the title using the file =#+TITLE= property
+2. ='headline=: This extracts the title from the first headline in the Org file
+3. ='alias=: This extracts a list of titles using the =#ROAM_ALIAS= property.
+   The aliases are space-delimited, and can be multi-worded using quotes
+
+Take for example the following org file:
+
+#+BEGIN_SRC org
+  #+TITLE: World War 2
+  #+ROAM_ALIAS: "WWII" "World War II"
+
+  * Headline
+#+END_SRC
+
+| Method      | Titles                   |
+|-------------+--------------------------|
+| ='title=    | '("World War 2")         |
+| ='headline= | '("Headline")            |
+| ='alias=    | '("WWII" "World War II") |
+
+One can freely control which extraction methods to use by customizing
+=org-roam-title-sources=: see the doc-string for the variable for more
+information. If all methods of title extraction return no results, the file-name
+is used in place of the titles for completions.
+
+If you wish to add your own title extraction method, you may push a symbol
+='foo= into =org-roam-title-sources=, and define a
+=org-roam--extract-titles-foo= which accepts no arguments. See
+=org-roam--extract-titles-title= for an example.
+
+** Tags
+
+Tags are used as meta-data for files: they facilitate interactions with notes
+where titles are insufficient. For example, tags allow for categorization of
+notes: differentiating between bibliographical and structure notes during interactive commands.
+
+Org-roam calls =org-roam--extract-tags= to extract tags from files. It uses the
+variable =org-roam-tag-sources=, to control how tags are extracted. The tag
+extraction methods supported are:
+
+1. ='prop=: This extracts tags from the =#+ROAM_TAGS= property. Tags are space delimited, and can be multi-word using double quotes.
+2. ='all-directories=: All sub-directories relative to =org-roam-directory= are
+   extracted as tags. That is, if a file is located at relative path
+   =foo/bar/file.org=, the file will have tags =foo= and =bar=.
+3. ='last-directory=: Extracts the last directory relative to
+   =org-roam-directory= as the tag. That is, if a file is located at relative
+   path =foo/bar/file.org=, the file will have tag =bar=.
+
+By default, only the ='prop= extraction method is enabled. To enable the other
+extraction methods, you may modify =org-roam-tag-sources=:
+
+#+BEGIN_SRC emacs-lisp
+(setq org-roam-tag-sources '(prop last-directory))
+#+END_SRC
+
+If you wish to add your own tag extraction method, you may push a symbol ='foo=
+into =org-roam-tag-sources=, and define a =org-roam--extract-tags-foo= which
+accepts the absolute file path as its argument. See
+=org-roam--extract-tags-prop= for an example.
+
+** File Refs
+
+Refs are unique identifiers for files. Each note can only have 1 ref.
+For example, a note for a website may contain a ref:
+
+#+BEGIN_SRC org
+  #+TITLE: Google
+  #+ROAM_KEY: https://www.google.com/
+#+END_SRC
+
+These keys come in useful for when taking website notes, using the
+=roam-ref= protocol (see [[*Roam Protocol][Roam Protocol]]).
+
+Alternatively, add a ref for notes for a specific paper, using its
+[[https://github.com/jkitchin/org-ref][org-ref]] citation key:
+
+#+BEGIN_SRC org
+  #+TITLE: Neural Ordinary Differential Equations
+  #+ROAM_KEY: cite:chen18_neural_ordin_differ_equat
+#+END_SRC
+
+The backlinks buffer will show any cites of this key: e.g.
+
+#+CAPTION: org-ref-citelink
+[[file:images/org-ref-citelink.png]]
+* The Templating System
+
+Rather than creating blank files on =org-roam-insert= and =org-roam-find-file=, it
+may be desirable to prefill the file with templated content. This may include:
+
+- Time of creation
+- File it was created from
+- Clipboard content
+- Any other data you may want to input manually
+
+This requires a complex template insertion system. Fortunately, Org ships with a
+powerful one: =org-capture=. However, org-capture was not designed for such use.
+Org-roam abuses =org-capture=, extending its syntax. To first understand how
+org-roam's templating system works, it may be useful to look into basic usage of
+=org-capture=.
+
+Org-roam's templates can be customized by modifying the variable
+=org-roam-capture-templates=.
+
+** Template Walkthrough
+
+To demonstrate the additions made to org-capture templates. Here, we walkthrough
+the default template, reproduced below.
+
+#+BEGIN_SRC emacs-lisp
+  ("d" "default" plain (function org-roam--capture-get-point)
+       "%?"
+       :file-name "%<%Y%m%d%H%M%S>-${slug}"
+       :head "#+TITLE: ${title}\n"
+       :unnarrowed t)
+#+END_SRC
+
+1. The template has short key ="d"=. If you have only one template,
+   org-roam automatically chooses this template for you.
+2. The template is given a description of ="default"=.
+3. =plain= text is inserted. Other options include Org headings via
+   =entry=.
+4. =(function org-roam--capture-get-point)= should not be changed.
+5. ="%?"= is the template inserted on each call to =org-roam-capture--capture=.
+   This template means don't insert any content, but place the cursor
+   here.
+6. =:file-name= is the file-name template for a new note, if it doesn't
+   yet exist. This creates a file at path that looks like
+   =/path/to/org-roam-directory/20200213032037-foo.org=.
+7. =:head= contains the initial template to be inserted (once only), at
+   the beginning of the file. Here, the title global attribute is
+   inserted.
+8. =:unnarrowed t= tells org-capture to show the contents for the whole
+   file, rather than narrowing to just the entry.
+
+Other options you may want to learn about include =:immediate-finish=.
+
+** Org-roam Template Expansion
+
+Org-roam's template definitions also extend org-capture's template syntax, to
+allow prefilling of strings. We have seen a glimpse of this in [[*Template Walkthrough][Template
+Walkthrough]].
+
+In org-roam templates, the =${var}= syntax allows for the expansion of
+variables, stored in =org-roam-capture--info=. For example, during
+=org-roam-insert=, the user is prompted for a title. Upon entering a
+non-existent title, the =title= key in =org-roam-capture--info= is set to the
+provided title. =${title}= is then expanded into the provided title during the
+org-capture process. Any variables that do not contain strings, are prompted for
+values using =completing-read=.
+
+After doing this expansion, the org-capture's template expansion system
+is used to fill up the rest of the template. You may read up more on
+this on [[https://orgmode.org/manual/Template-expansion.html#Template-expansion][org-capture's documentation page]].
+
+To illustrate this dual expansion process, take for example the template string:
+="%<%Y%m%d%H%M%S>-${title}"=, with the title ="Foo"=. The template is first
+expanded into =%<%Y%m%d%H%M%S>-Foo=. Then org-capture expands =%<%Y%m%d%H%M%S>=
+with timestamp: e.g. =20200213032037-Foo=.
+
+All of the flexibility afforded by Emacs and Org-mode are available. For
+example, if you want to encode a UTC timestamp in the filename, you can take
+advantage of org-mode's =%(EXP)= template expansion to call =format-time-string=
+directly to provide its third argument to specify UTC.
+
+#+BEGIN_SRC emacs-lisp
+  ("d" "default" plain (function org-roam--capture-get-point)
+       "%?"
+       :file-name "%(format-time-string \"%Y-%m-%d--%H-%M-%SZ--${slug}\" (current-time) t)"
+       :head "#+TITLE: ${title}\n"
+       :unnarrowed t)
+#+END_SRC
+
+* Concepts and Configuration
+The number of configuration options is deliberately kept small, to keep
+the Org-roam codebase manageable. However, we attempt to accommodate as
+many usage styles as possible.
+
+All of Org-roam's customization options can be viewed via
+=M-x customize-group org-roam=.
+
+** Directories and Files
+
+This section concerns the placement and creation of files.
+
+- Variable: org-roam-directory
+
+  This is the default path to Org-roam files. All Org files, at any level of
+  nesting, are considered part of the Org-roam.
+
+- Variable: org-roam-db-location
+
+  Location of the Org-roam database. If this is non-nil, the Org-roam sqlite
+  database is saved here.
+
+  It is the user’s responsibility to set this correctly, especially when used
+  with multiple Org-roam instances.
+
+** The Org-roam Buffer
+
+The Org-roam buffer displays backlinks for the currently active Org-roam note.
+
+- User Option: org-roam-buffer
+
+  The name of the org-roam buffer. Defaults to =*org-roam*=.
+
+- User Option: org-roam-buffer-position
+
+  The position of the Org-roam buffer side window. Valid values are ='left=,
+  ='right=, ='top=, ='bottom=.
+
+- User Option: org-roam-buffer-width
+
+  Width of =org-roam-buffer=. Has an effect only if =org-roam-buffer-position= is
+  ='left= or ='right=.
+
+- User Option: org-roam-buffer-height
+
+  Height of =org-roam-buffer=. Has an effect only if =org-roam-buffer-position= is
+  ='top= or ='bottom=.
+
+- User Option: org-roam-buffer-no-delete-other-windows
+
+  The =no-delete-window= parameter for the org-roam buffer. Setting it to ='t= prevents the window from being deleted when calling =delete-other-windows=.
+
+** Org-roam Links
+
+Org-roam links are regular =file:= links in Org-mode. By default, links are
+inserted with the title as the link description with =org-roam-insert=.
+
+- User Option: org-roam-link-title-format
+
+  To distinguish between org-roam links and regular links, one may choose to use
+  special indicators for Org-roam links. Defaults to ="%s"=.
+
+  If your version of Org is at least =9.2=, consider styling the link differently,
+  by customizing the =org-roam-link=, and =org-roam-link-current= faces.
+
+** Org-roam Files
+
+Org-roam files are created and prefilled using Org-roam's templating
+system. The templating system is customizable (see [[*The Templating System][The Templating System]]).
+
+* Navigating Around
+
+** Index File
+
+As your collection grows, you might want to create an index where you keep links
+to your main files.
+
+In Org-roam, you can define the path to your index file by setting
+=org-roam-index-file=.
+
+- Variable: org-roam-index-file
+
+  Path to the Org-roam index file.
+
+  The path can be a string or a function. If it is a string, it should be the
+  path (absolute or relative to =org-roam-directory=) to the index file. If it
+  is is a function, the function should return the path to the index file.
+  Otherwise, the index is assumed to be a note in =org-roam-index= whose
+  title is ="Index"=.
+
+- Function: org-roam-find-index
+
+  Opens the Index file in the current =org-roam-directory=.
+
+* Encryption
+
+One may wish to keep private, encrypted files. Org-roam supports encryption (via
+GPG), which can be enabled for all new files by setting =org-roam-encrypt-files=
+to =t=. When enabled, new files are created with the =.org.gpg= extension and
+decryption are handled automatically by EasyPG.
+
+Note that Emacs will prompt for a password for encrypted files during
+cache updates if it requires reading the encrypted file. To reduce the
+number of password prompts, you may wish to cache the password.
+
+- Variable: org-roam-encrypt-files
+
+  Whether to encrypt new files.  If true, create files with .org.gpg extension.
+
+* Graphing
+
+Org-roam provides graphing capabilities to explore interconnections between
+notes. This is done by performing SQL queries and generating images using
+[[https://graphviz.org/][Graphviz]]. The graph can also be navigated: see [[*Roam Protocol][Roam Protocol]].
+
+The entry point to graph creation is =org-roam-graph=.
+
+- Function: 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.
+  ARG may be any of the following values:
+
+  - =nil=       show the graph.
+  - =C-u=       show the graph for FILE.
+  - =C-u N=     show the graph for FILE limiting nodes to N steps.
+  - =C-u C-u=   build the graph.
+  - =C-u -=     build the graph for FILE.
+  - =C-u -N=    build the graph for FILE limiting nodes to N steps.
+
+- User Option: org-roam-graph-executable
+
+  Path to the graphing executable (in this case, Graphviz). Set this if Org-roam is unable to find the Graphviz executable on your system.
+
+  You may also choose to use =neato= in place of =dot=, which generates a more
+  compact graph layout.
+
+- User Option: org-roam-graph-viewer
+
+  Org-roam defaults to using Firefox (located on PATH) to view the SVG, but you may choose to set it to:
+
+  1. A string, which is a path to the program used
+  2. a function accepting a single argument: the graph file path.
+
+  =nil= uses =view-file= to view the graph.
+
+** Graph Options
+
+Graphviz provides many options for customizing the graph output, and Org-roam supports some of them. See https://graphviz.gitlab.io/_pages/doc/info/attrs.html for customizable options.
+
+- User Option: org-roam-graph-extra-config
+
+  Extra options passed to graphviz for the digraph (The "G" attributes).
+  Example: ='=(("rankdir" . "LR"))=
+
+- User Option: org-roam-graph-node-extra-config
+
+  Extra options for nodes in the graphviz output (The "N" attributes).
+  Example: ='(("color" . "skyblue"))=
+
+- User Option: org-roam-graph-edge-extra-config
+
+  Extra options for edges in the graphviz output (The "E" attributes).
+  Example: ='(("dir" . "back"))=
+
+- User Option: org-roam-graph-edge-cites-extra-config
+
+  Extra options for citation edges in the graphviz output.
+  Example: ='(("color" . "red"))=
+
+** Excluding Nodes and Edges
+
+One may want to exclude certain files to declutter the graph.
+
+- User Option: org-roam-graph-exclude-matcher
+
+  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.
+
+#+BEGIN_EXAMPLE
+    (setq org-roam-graph-exclude-matcher '("private" "dailies"))
+#+END_EXAMPLE
+
+This setting excludes all files whose path contain "private" or "dailies".
+
+* Org-roam Completion System
+
+Org-roam offers completion when choosing note titles etc. The completion
+system is configurable. The default setting,
+
+#+BEGIN_SRC emacs-lisp
+  (setq org-roam-completion-system 'default)
+#+END_SRC
+
+uses Emacs' standard =completing-read=. If you prefer
+[[https://emacs-helm.github.io/helm/][Helm]], use
+
+#+BEGIN_SRC emacs-lisp
+  (setq org-roam-completion-system 'helm)
+#+END_SRC
+
+Other options include ='ido=, and ='ivy=.
+
+* Roam Protocol
+** _ :ignore:
+Org-roam extending =org-protocol= with 2 protocols: the =roam-file=
+and =roam-ref= protocol.
+
+** Installation
+
+To enable Org-roam's protocol extensions, you have to add the following to your init file:
+
+#+BEGIN_SRC emacs-lisp
+(require 'org-roam-protocol)
+#+END_SRC
+
+The instructions for setting up =org-protocol== are reproduced below.
+
+We will also need to create a desktop application for =emacsclient=. The
+instructions for various platforms are shown below.
+
+For Linux users, create a desktop application in =~/.local/share/applications/org-protocol.desktop=:
+
+#+begin_example
+[Desktop Entry]
+Name=Org-Protocol
+Exec=emacsclient %u
+Icon=emacs-icon
+Type=Application
+Terminal=false
+MimeType=x-scheme-handler/org-protocol
+#+end_example
+
+Associate =org-protocol://= links with the desktop application by
+running in your shell:
+
+#+BEGIN_SRC bash
+xdg-mime default org-protocol.desktop x-scheme-handler/org-protocol
+#+END_SRC
+
+To disable the "confirm" prompt in Chrome, you can also make Chrome
+show a checkbox to tick, so that the =Org-Protocol Client= app will be used
+without confirmation. To do this, run in a shell:
+
+#+BEGIN_SRC bash
+sudo mkdir -p /etc/opt/chrome/policies/managed/
+sudo tee /etc/opt/chrome/policies/managed/external_protocol_dialog.json >/dev/null <<'EOF'
+{
+  "ExternalProtocolDialogShowAlwaysOpenCheckbox": true
+}
+EOF
+sudo chmod 644 /etc/opt/chrome/policies/managed/external_protocol_dialog.json
+#+END_SRC
+
+and then restart Chrome (for example, by navigating to <chrome://restart>) to
+make the new policy take effect.
+
+See [[https://www.chromium.org/administrators/linux-quick-start][here]] for more info on the =/etc/opt/chrome/policies/managed= directory and
+[[https://cloud.google.com/docs/chrome-enterprise/policies/?policy=ExternalProtocolDialogShowAlwaysOpenCheckbox][here]] for information on the =ExternalProtocolDialogShowAlwaysOpenCheckbox= policy.
+
+For MacOS, one solution is to use [[https://github.com/sveinbjornt/Platypus][Platypus]]. Here are the instructions for
+setting up with Platypus and Chrome:
+
+1. Install and launch Platypus (with [[https://brew.sh/][Homebrew]]):
+
+#+BEGIN_SRC bash
+brew cask install platypus
+#+END_SRC
+
+2. Create a script =launch_emacs.sh=:
+
+#+BEGIN_SRC bash
+#!/usr/bin/env bash
+/usr/local/bin/emacsclient --no-wait $1
+#+END_SRC
+
+3. Create a Platypus app with the following settings:
+
+#+begin_example
+| Setting                        | Value                     |
+|--------------------------------+---------------------------|
+| App Name                       | "OrgProtocol"             |
+| Script Type                    | "env" · "/usr/bin/env"    |
+| Script Path                    | "path/to/launch-emacs.sh" |
+| Interface                      | None                      |
+| Accept dropped items           | true                      |
+| Remain running after execution | false                     |
+#+end_example
+
+
+Inside =Settings=:
+
+#+begin_example
+| Setting                        | Value          |
+|--------------------------------+----------------|
+| Accept dropped files           | true           |
+| Register as URI scheme handler | true           |
+| Protocol                       | "org-protocol" |
+#+end_example
+
+To disable the "confirm" prompt in Chrome, you can also make Chrome
+show a checkbox to tick, so that the =OrgProtocol= app will be used
+without confirmation. To do this, run in a shell:
+
+#+BEGIN_SRC bash
+defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true
+#+END_SRC
+
+
+If you're using [[https://github.com/railwaycat/homebrew-emacsmacport][Emacs Mac Port]], it registered its `Emacs.app` as the default
+handler for the URL scheme `org-protocol`. To make =OrgProtocol.app=
+the default handler instead, run:
+
+#+BEGIN_SRC bash
+defaults write com.apple.LaunchServices/com.apple.launchservices.secure LSHandlers -array-add \
+'{"LSHandlerPreferredVersions" = { "LSHandlerRoleAll" = "-"; }; LSHandlerRoleAll = "org.yourusername.OrgProtocol"; LSHandlerURLScheme = "org-protocol";}'
+#+END_SRC
+
+Then restart your computer.
+
+
+** The =roam-file= protocol
+
+This is a simple protocol that opens the path specified by the =file=
+key (e.g. =org-protocol://roam-file?file=/tmp/file.org=). This is used
+in the generated graph.
+
+** The =roam-ref= Protocol
+
+This protocol finds or creates a new note with a given =ROAM_KEY= (see [[*Anatomy of an Org-roam File][Anatomy of an Org-roam File]]):
+
+[[file:images/roam-ref.gif]]
+
+To use this, create a Firefox bookmarklet as follows:
+
+#+BEGIN_SRC javascript
+javascript:location.href =
+'org-protocol://roam-ref?template=r&ref='
+ encodeURIComponent(location.href)
+ '&title='
+ encodeURIComponent(document.title)
+#+END_SRC
+
+or as a keybinding in =qutebrowser=, adding the following to the =autoconfig.yml= file:
+
+#+BEGIN_SRC yaml
+settings:
+  bindings.commands:
+    global:
+      normal:
+        gc: open javascript:void(location.href='org-protocol://roam-ref?template=r&ref='+encodeURIComponent(location.href)+'&title='+encodeURIComponent(document.title))
+#+END_SRC
+
+where =template= is the template key for a template in
+=org-roam-capture-ref-templates= (see [[*The Templating System][The Templating System]]). These templates
+should contain a =#+ROAM_KEY: ${ref}= in it.
+
+* Diagnosing and Repairing Files
+
+Org-roam provides a utility for diagnosing and repairing problematic files via
+=org-roam-doctor=. By default, =org-roam-doctor= runs the check across all Org-roam
+files, and this can take some time. To run the check only for the current file,
+run =C-u M-x org-roam-doctor=.
+
+- Function: org-roam-doctor &optional this-buffer
+
+  Perform a check on Org-roam files to ensure cleanliness. If THIS-BUFFER, run
+  the check only for the current buffer.
+
+The checks run are defined in =org-roam-doctor--checkers=. Each checker is an instance of =org-roam-doctor-checker=. To define a checker, use =make-org-roam-doctor-checker=. Here is a sample definition:
+
+#+BEGIN_SRC emacs-lisp
+(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))))
+#+END_SRC
+
+The =:name= property is the name of the function run. The function takes in the
+Org parse tree, and returns a list of =(point error-message)=. =:description= is a
+short description of what the checker does. =:actions= is an alist containing
+elements of the form =(char . (prompt . function))=. These actions are defined per
+checker, to perform autofixes for the errors. For each error detected,
+=org-roam-doctor= will move the point to the current error, and pop-up a help
+window displaying the error message, as well as the list of actions that can be
+taken provided in =:actions=.
+
+* _ Copying
+:PROPERTIES:
+:COPYING:    t
+:END:
+
+#+BEGIN_QUOTE
+Copyright (C) 2020-2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+You can redistribute this document 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 document 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.
+#+END_QUOTE
+
+* Appendix
+** Note-taking Workflows
+- Books ::
+  - [[https://www.goodreads.com/book/show/34507927-how-to-take-smart-notes][How To Take Smart Notes]]
+- Articles ::
+  - [[https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettelkasten-method-1][The Zettelkasten Method - LessWrong 2.0]]
+  - [[https://reddit.com/r/RoamResearch/comments/eho7de/building_a_second_brain_in_roamand_why_you_might][Building a Second Brain in Roam...And Why You Might Want To : RoamResearch]]
+  - [[https://www.nateliason.com/blog/roam][Roam Research: Why I Love It and How I Use It - Nat Eliason]]
+  - [[https://twitter.com/adam_keesling/status/1196864424725774336?s=20][Adam Keesling's Twitter Thread]]
+  - [[https://blog.jethro.dev/posts/how_to_take_smart_notes_org/][How To Take Smart Notes With Org-mode · Jethro Kuan]]
+- Threads ::
+  - [[https://news.ycombinator.com/item?id=22473209][Ask HN: How to Take Good Notes]]
+- Videos ::
+  - [[https://www.youtube.com/watch?v=RvWic15iXjk][How to Use Roam to Outline a New Article in Under 20 Minutes]]
+** Ecosystem
+A number of packages work well combined with Org-Roam:
+
+*** Deft
+   :PROPERTIES:
+   :CUSTOM_ID: deft
+   :END:
+
+[[https://jblevins.org/projects/deft/][Deft]] provides a nice interface
+for browsing and filtering org-roam notes.
+
+#+BEGIN_SRC emacs-lisp
+  (use-package deft
+    :after org
+    :bind
+    ("C-c n d" . deft)
+    :custom
+    (deft-recursive t)
+    (deft-use-filter-string-for-filename t)
+    (deft-default-extension "org")
+    (deft-directory "/path/to/org-roam-files/"))
+#+END_SRC
+
+If the title of the Org file is not the first line, you might not get
+nice titles. You may choose to patch this to use =org-roam='s
+functionality. Here I'm using
+[[https://github.com/raxod502/el-patch][el-patch]]:
+
+#+BEGIN_SRC emacs-lisp
+  (use-package el-patch
+    :straight (:host github
+                     :repo "raxod502/el-patch"
+                     :branch "develop"))
+
+  (eval-when-compile
+    (require 'el-patch))
+
+  (use-package deft
+    ;; same as above...
+    :config/el-patch
+    (defun deft-parse-title (file contents)
+      "Parse the given FILE and CONTENTS and determine the title.
+  If `deft-use-filename-as-title' is nil, the title is taken to
+  be the first non-empty line of the FILE.  Else the base name of the FILE is
+  used as title."
+      (el-patch-swap (if deft-use-filename-as-title
+                         (deft-base-filename file)
+                       (let ((begin (string-match "^.+$" contents)))
+                         (if begin
+                             (funcall deft-parse-title-function
+                                      (substring contents begin (match-end 0))))))
+                     (org-roam--get-title-or-slug file))))
+#+END_SRC
+
+The Deft interface can slow down quickly when the number of files get
+huge. [[https://github.com/hasu/notdeft][Notdeft]] is a fork of Deft
+that uses an external search engine and indexer.
+
+*** Org-journal
+   :PROPERTIES:
+   :CUSTOM_ID: org-journal
+   :END:
+
+[[https://github.com/bastibe/org-journal][Org-journal]] is a more
+powerful alternative to the simple function =org-roam-dailies-today=. It
+provides better journaling capabilities, and a nice calendar interface
+to see all dated entries.
+
+#+BEGIN_SRC emacs-lisp
+  (use-package org-journal
+    :bind
+    ("C-c n j" . org-journal-new-entry)
+    :custom
+    (org-journal-date-prefix "#+TITLE: ")
+    (org-journal-file-format "%Y-%m-%d.org")
+    (org-journal-dir "/path/to/org-roam-files/")
+    (org-journal-date-format "%A, %d %B %Y"))
+#+END_SRC
+
+*** Note-taking Add-ons
+   :PROPERTIES:
+   :CUSTOM_ID: note-taking-add-ons
+   :END:
+
+These are some plugins that make note-taking in Org-mode more enjoyable.
+
+**** Org-download
+    :PROPERTIES:
+    :CUSTOM_ID: org-download
+    :END:
+
+[[https://github.com/abo-abo/org-download][Org-download]] lets you
+screenshot and yank images from the web into your notes:
+
+#+CAPTION: org-download
+[[file:images/org-download.gif]]
+
+#+BEGIN_SRC emacs-lisp
+  (use-package org-download
+    :after org
+    :bind
+    (:map org-mode-map
+          (("s-Y" . org-download-screenshot)
+           ("s-y" . org-download-yank))))
+#+END_SRC
+
+**** mathpix.el
+    :PROPERTIES:
+    :CUSTOM_ID: mathpix.el
+    :END:
+
+[[https://github.com/jethrokuan/mathpix.el][mathpix.el]] uses
+[[https://mathpix.com/][Mathpix's]] API to convert clips into latex
+equations:
+
+#+CAPTION: mathpix
+[[file:images/mathpix.gif]]
+
+#+BEGIN_SRC emacs-lisp
+  (use-package mathpix.el
+    :straight (:host github :repo "jethrokuan/mathpix.el")
+    :custom ((mathpix-app-id "app-id")
+             (mathpix-app-key "app-key"))
+    :bind
+    ("C-x m" . mathpix-screenshot))
+#+END_SRC
+
+**** Org-noter / Interleave
+    :PROPERTIES:
+    :CUSTOM_ID: org-noter-interleave
+    :END:
+
+[[https://github.com/weirdNox/org-noter][Org-noter]] and
+[[https://github.com/rudolfochrist/interleave][Interleave]] are both
+projects that allow synchronised annotation of documents (PDF, EPUB
+etc.) within Org-mode.
+
+**** Bibliography
+    :PROPERTIES:
+    :CUSTOM_ID: bibliography
+    :END:
+
+[[https://github.com/zaeph/org-roam-bibtex][org-roam-bibtex]] offers
+tight integration between
+[[https://github.com/jkitchin/org-ref][org-ref]],
+[[https://github.com/tmalsburg/helm-bibtex][helm-bibtex]] and
+=org-roam=. This helps you manage your bibliographic notes under
+=org-roam=.
+
+**** Spaced Repetition
+    :PROPERTIES:
+    :CUSTOM_ID: spaced-repetition
+    :END:
+
+[[https://github.com/l3kn/org-fc/][Org-fc]] is a spaced repetition
+system that scales well with a large number of files. Other alternatives
+include
+[[https://orgmode.org/worg/org-contrib/org-drill.html][org-drill]], and
+[[https://github.com/abo-abo/pamparam][pamparam]].
+
+* FAQ
+** How do I have more than one Org-roam directory?
+
+Emacs supports directory-local variables, allowing the value of
+=org-roam-directory= to be different in different directories. It does this by
+checking for a file named =.dir-locals.el=.
+
+To add support for multiple directories, override the =org-roam-directory=
+variable using directory-local variables. This is what =.dir-locals.el= may
+contain:
+
+#+BEGIN_SRC emacs-lisp
+  ((nil . ((org-roam-directory . "/path/to/here/"))))
+#+END_SRC
+
+All files within that directory will be treated as their own separate
+set of Org-roam files. Remember to run =org-roam-db-build-cache= from a
+file within that directory, at least once.
+
+* _ :ignore:
+# Local Variables:
+# eval: (refill-mode +1)
+# before-save-hook: org-make-toc
+# after-save-hook: (lambda nil (progn (require 'ox-texinfo nil t) (org-texinfo-export-to-info)))
+# indent-tabs-mode: nil
+# org-src-preserve-indentation: nil
+# End:
--- a/doc/org-roam.texi
+++ b/doc/org-roam.texi
--- a/doc/org_export.md
+++ b/doc/org_export.md
@ -1,61 +0,0 @@
-While exporting your documents to another format such as HTML -- whether using Org's in-built export or ox-hugo -- you can add a backlinks section which would display the backlinks to the current file. This is done via org-export's preprocessing hooks. See more at [Advanced Export Configuration (The Org Manual)](https://orgmode.org/manual/Advanced-Export-Configuration.html#Advanced-Export-Configuration).
-
-Following are two different configs that might be suitable for different use-cases. Add one of these snippets in your Emacs init file.
-
-### Only Backlinks
-
-This will display only the backlinks and not the contents.
-
-```emacs-lisp
-(defun my/org-roam--backlinks-list (file)
-  (if (org-roam--org-roam-file-p file)
-      (--reduce-from
-       (concat acc (format "- [[file:%s][%s]]\n"
-                           (file-relative-name (car it) org-roam-directory)
-			                     (org-roam--get-title-or-slug (car it))))
-       "" (org-roam-db-query [:select [from] :from links :where (= to $s1)] file))
-    ""))
-
-(defun my/org-export-preprocessor (backend)
-  (let ((links (my/org-roam--backlinks-list (buffer-file-name))))
-    (unless (string= links "")
-      (save-excursion
-      	(goto-char (point-max))
-      	(insert (concat "\n* Backlinks\n") links)))))
-
-(add-hook 'org-export-before-processing-hook 'my/org-export-preprocessor)
-```
-
-### Backlinks and Contents
-
-This would insert both backlinks and the contents, just like the org-roam buffer. This might be especially useful if you host a web version of your personal knowledgebase and want to browse the files along with the backlinks from mobile devices.
-
-```emacs-lisp
-(defun my/org-roam--backlinks-list-with-content (file)
-  (with-temp-buffer
-    (if-let* ((backlinks (org-roam--get-backlinks file))
-              (grouped-backlinks (--group-by (nth 0 it) backlinks)))
-        (progn
-          (insert (format "\n\n* %d Backlinks\n"
-                          (length backlinks)))
-          (dolist (group grouped-backlinks)
-            (let ((file-from (car group))
-                  (bls (cdr group)))
-              (insert (format "** [[file:%s][%s]]\n"
-                              file-from
-                              (org-roam--get-title-or-slug file-from)))
-              (dolist (backlink bls)
-                (pcase-let ((`(,file-from _ ,props) backlink))
-                  (insert (s-trim (s-replace "\n" " " (plist-get props :content))))
-                  (insert "\n\n")))))))
-    (buffer-string)))
-
-  (defun my/org-export-preprocessor (backend)
-    (let ((links (my/org-roam--backlinks-list-with-content (buffer-file-name))))
-      (unless (string= links "")
-        (save-excursion
-          (goto-char (point-max))
-          (insert (concat "\n* Backlinks\n") links)))))
-
-  (add-hook 'org-export-before-processing-hook 'my/org-export-preprocessor)
-```
--- a/doc/requirements.txt
+++ b/doc/requirements.txt
@ -1,2 +0,0 @@
-mkdocs-material==4.6.2
-pymdown-extensions==6.3
--- a/doc/roam_protocol.md
+++ b/doc/roam_protocol.md
@ -1,161 +0,0 @@
-## What is Roam protocol?
-
-Org-roam extending `org-protocol` with 2 protocols: the `roam-file`
-and `roam-ref` protocol.
-
-## The `roam-file` protocol
-
-This is a simple protocol that opens the path specified by the `file`
-key (e.g. `org-protocol://roam-file?file=/tmp/file.org`). This is used
-in the generated graph.
-
-## The `roam-ref` Protocol
-
-This protocol finds or creates a new note with a given `ROAM_KEY` (see
-[Anatomy](anatomy.md)):
-
-![roam-ref](images/roam-ref.gif)
-
-To use this, create a Firefox bookmarklet as follows:
-
-```javascript
-javascript:location.href =
-'org-protocol:/roam-ref?template=r&ref='
-+ encodeURIComponent(location.href)
-+ '&title='
-+ encodeURIComponent(document.title)
-```
-
-where `template` is the template key for a template in
-`org-roam-capture-ref-templates`. More documentation on the templating
-system can be found [here](templating.md).
-
-These templates should contain a `#+ROAM_KEY: ${ref}` in it.
-
-## Setting up Org-roam protocol
-
-To enable org-roam's protocol extensions, you have to add the
-following to your init file:
-
-```emacs-lisp
-(require 'org-roam-protocol)
-```
-
-The instructions for setting up `org-protocol` can be found
-[here][org-protocol-inst], but they are reproduced below.
-
-We will also need to create a desktop application for `emacsclient`.
-The instructions for various platforms are shown below:
-
-## Linux
-
-Create a desktop application. I place mine in
-`~/.local/share/applications/org-protocol.desktop`:
-
-```
-[Desktop Entry]
-Name=Org-Protocol
-Exec=emacsclient %u
-Icon=emacs-icon
-Type=Application
-Terminal=false
-MimeType=x-scheme-handler/org-protocol
-```
-
-Associate `org-protocol://` links with the desktop application by
-running in your shell:
-
-```bash
-xdg-mime default org-protocol.desktop x-scheme-handler/org-protocol
-```
-
-To disable the "confirm" prompt in Chrome, you can also make Chrome
-show a checkbox to tick, so that the `Org-Protocol Client` app will be used
-without confirmation. To do this, run in a shell:
-
-```sh
-sudo mkdir -p /etc/opt/chrome/policies/managed/
-sudo tee /etc/opt/chrome/policies/managed/external_protocol_dialog.json >/dev/null <<'EOF'
-{
-  "ExternalProtocolDialogShowAlwaysOpenCheckbox": true
-}
-EOF
-sudo chmod 644 /etc/opt/chrome/policies/managed/external_protocol_dialog.json
-```
-
-and then restart Chrome (for example, by navigating to <chrome://restart>) to
-make the new policy take effect.
-
-See [here](https://www.chromium.org/administrators/linux-quick-start)
-for more info on the `/etc/opt/chrome/policies/managed` directory and
-[here](https://cloud.google.com/docs/chrome-enterprise/policies/?policy=ExternalProtocolDialogShowAlwaysOpenCheckbox)
-for information on the `ExternalProtocolDialogShowAlwaysOpenCheckbox`
-policy.
-
-
-## Mac OS
-
-One solution is to use
-[Platypus](https://github.com/sveinbjornt/Platypus). Here are the
-instructions for setting up with Platypus and Chrome:
-
-1. Install and launch Platypus (with [Homebrew](https://brew.sh/)):
-
-```sh
-brew cask install platypus
-```
-2. Create a script `launch_emacs.sh`:
-
-```
-#!/usr/bin/env bash
-/usr/local/bin/emacsclient --no-wait $1
-```
-
-3. Create a Platypus app with the following settings:
-
-```
-| Setting                        | Value                     |
-|--------------------------------+---------------------------|
-| App Name                       | "OrgProtocol"             |
-| Script Type                    | "env" · "/usr/bin/env"    |
-| Script Path                    | "path/to/launch-emacs.sh" |
-| Interface                      | None                      |
-| Accept dropped items           | true                      |
-| Remain running after execution | false                     |
-```
-
-Inside `Settings`:
-
-```
-| Setting                        | Value          |
-|--------------------------------+----------------|
-| Accept dropped files           | true           |
-| Register as URI scheme handler | true           |
-| Protocol                       | "org-protocol" |
-```
-
-To disable the "confirm" prompt in Chrome, you can also make Chrome
-show a checkbox to tick, so that the `OrgProtocol` app will be used
-without confirmation. To do this, run in a shell:
-
-```sh
-defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true
-```
-
-
-##### Note for Emacs Mac Port
-
-If you're using [Emacs Mac Port](https://github.com/railwaycat/homebrew-emacsmacport), it
-registered its `Emacs.app` as the default handler for the URL scheme
-`org-protocol`. We have to make our `OrgProtocol.app` the default
-handler instead (replace `org.yourusername.OrgProtocol` with your app
-identifier):
-
-```
-$ defaults write com.apple.LaunchServices/com.apple.launchservices.secure LSHandlers -array-add \
-'{"LSHandlerPreferredVersions" = { "LSHandlerRoleAll" = "-"; }; LSHandlerRoleAll = "org.yourusername.OrgProtocol"; LSHandlerURLScheme = "org-protocol";}'
-```
-
-Then restart your computer.
-
-[org-protocol-inst]: https://orgmode.org/worg/org-contrib/org-protocol.html
--- a/doc/templating.md
+++ b/doc/templating.md
@ -1,119 +0,0 @@
-Rather than creating blank files on `org-roam-insert` and
-`org-roam-find-file`, it is may be desirable to prefill the file with
-content. This may include:
-
- Time of creation
- File it was created from
- Clipboard content
- Any other data you may want to input manually
-
-This requires a complex template insertion system, but fortunately,
-Org ships with a powerful one: `org-capture`. However, org-capture was
-not designed for such use. Org-roam abuses `org-capture` to some
-extent, extending its syntax. To first understand how org-roam's
-templating system works, it may be useful to look into org-capture.
-
-## Org-roam Templates
-
-The org-roam capture template extends org-capture's template with 2
-additional properties:
-
-1. `:file-name`: This is the file name template used when a new note
-   is created.
-2. `:head`: This is the template that is inserted on initial note
-   creation.
-
-### Org-roam Template Expansion
-
-Org-roam's template definitions also extend org-capture's template
-syntax, to allow prefilling of strings. In many scenarios,
-`org-roam--capture` is passed a mapping between variables and strings.
-For example, during `org-roam-insert`, a title is prompted for. If the
-title doesn't already exist, we would like to create a new file,
-without prompting for the title again.
-
-Variables passed are expanded with the `${var}` syntax. For example,
-during `org-roam-insert`, `${title}` is prefilled for expansion. Any
-variables that do not contain strings, are prompted for values using
-`completing-read`.
-
-After doing this expansion, the org-capture's template expansion
-system is used to fill up the rest of the template. You may read up
-more on this on [org-capture's documentation
-page](https://orgmode.org/manual/Template-expansion.html#Template-expansion).
-
-For example, take the template: `"%<%Y%m%d%H%M%S>-${title}"`, with the title
-`"Foo"`. The template is first expanded into `%<%Y%m%d%H%M%S>-Foo`. Then
-org-capture expands `%<%Y%m%d%H%M%S>` with timestamp: e.g.
-`20200213032037-Foo`.
-
-All of the flexibility afforded by emacs and org-mode are
-available. For example, if you want to encode a UTC timestamp in the
-filename, you can take advantage of org-mode's `%(EXP)` template
-expansion to call `format-time-string` directly to provide its third
-argument to specify UTC.
-
-``` emacs-lisp
-("d" "default" plain (function org-roam--capture-get-point)
-     "%?"
-     :file-name "%(format-time-string \"%Y-%m-%d--%H-%M-%SZ--${slug}\" (current-time) t)"
-     :head "#+TITLE: ${title}\n"
-     :unnarrowed t)
-```
-
-Similarly, if you want to change how titles are transformed into
-slugs, you can override `org-roam--title-to-slug`. For example, to use
-hyphens instead of underscores:
-
-
-``` emacs-lisp
-  (defun org-roam--title-to-slug (title)
-    "Convert TITLE to a filename-suitable slug. Uses hyphens rather than underscores."
-    (cl-flet* ((nonspacing-mark-p (char)
-                                  (eq 'Mn (get-char-code-property char 'general-category)))
-               (strip-nonspacing-marks (s)
-                                       (apply #'string (seq-remove #'nonspacing-mark-p
-                                                                   (ucs-normalize-NFD-string s))))
-               (cl-replace (title pair)
-                           (replace-regexp-in-string (car pair) (cdr pair) title)))
-      (let* ((pairs `(("[^[:alnum:][:digit:]]" . "-")  ;; convert anything not alphanumeric
-                      ("--*" . "-")  ;; remove sequential underscores
-                      ("^-" . "")  ;; remove starting underscore
-                      ("-$" . "")))  ;; remove ending underscore
-             (slug (-reduce-from #'cl-replace (strip-nonspacing-marks title) pairs)))
-        (s-downcase slug))))
-```
-
-This templating system is used throughout org-roam templates.
-
-### Template examples
-
-Here I walkthrough the default template, reproduced below.
-
-```
-("d" "default" plain (function org-roam--capture-get-point)
-     "%?"
-     :file-name "%<%Y%m%d%H%M%S>-${slug}"
-     :head "#+TITLE: ${title}\n"
-     :unnarrowed t)
-```
-
-1. The template has short key `"d"`. If you have only one template,
-   org-roam automatically chooses this template for you.
-2. The template is given a description of `"default"`.
-3. `plain` text is inserted. Other options include Org headings via
-   `entry`.
-4. `(function org-roam--capture-get-point)` should not be changed.
-5. `"%?"` is the template inserted on each call to `org-roam--capture`.
-   This template means don't insert any content, but place the cursor
-   here.
-6. `:file-name` is the file-name template for a new note, if it
-doesn't yet exist. This creates a file at path that looks like
-   `/path/to/org-roam-directory/20200213032037-foo.org`.
-7. `:head` contains the initial template to be inserted (once only),
-   at the beginning of the file. Here, the title global attribute is
-   inserted.
-8. `:unnarrowed t` tells org-capture to show the contents for the
-   whole file, rather than narrowing to just the entry.
-
-Other options you may want to learn about include `:immediate-finish`.
--- a/doc/tour.md
+++ b/doc/tour.md
@ -1,70 +0,0 @@
-Org-roam was built to support a workflow that was not possible with
-vanilla Org-mode. This flow is modelled after the [Zettelkasten
-method][zettelkasten], and many of [Roam Research][roam]'s workflows.
-It is crucial to understand that Org-roam does not auto-magically make
-note-taking better -- it's changing the note-taking workflow that
-does.
-
-To understand more about the methods and madness, the [Note-Taking
-Workflow][appendix:ntw] page contains a page of useful references. The
-author has also written [a post][jethro-blog-post] about how he uses
-Org-roam.
-
-## Activating Org-roam
-
-Org-roam's entry point is the global minor `org-roam-mode`. This sets
-up Emacs with several hooks, for keeping the org-roam cache
-consistently updated, as well as showing the backlinks buffer. 
-
-The cache is a sqlite database named `org-roam.db`, which resides at
-the root of the `org-roam-directory`. Activating `org-roam-mode`
-builds the cache, which may take a while the first time, but is
-generally instantaneous in subsequent runs. To build the cache
-manually again, run `M-x org-roam-db-build-cache`.
-
-## Finding a Note
-
-`org-roam-find-file` shows the list of titles for notes that reside in
-`org-roam-directory`. Selecting a note title will bring you to the
-corresponding note. Entering a title of a note that does not yet exist
-will create a new note with that title.
-
-![org-roam-find-file](images/org-roam-find-file.gif)
-
-Note that in the above image, the [ivy](https://github.com/abo-abo/swiper)
-completion frontend is used. The default frontend has some usability issues with
-non-matching candidates (e.g. when you want to enter a title of a new note,
-there is no completion candidate), so either `ivy` or `helm` is recommended.
-
-## Inserting Links
-
-`org-roam-insert` insert links to existing (or new) notes. Entering a
-non-existent title will also create a new note with that title.
-
-![org-roam-insert](images/org-roam-insert-filetag.gif)
-
-Good usage of Org-roam requires liberally linking files. This allows
-the build-up of a dense knowledge graph.
-
-## The Org-roam Buffer
-
-The Org-roam buffer is often displayed in the side window. It shows
-backlinks for the currently active Org-roam note, along with some
-surrounding context.
-
-![org-roam-buffer](images/org-roam-buffer.gif)
-
-## Exporting the Graph
-
-Org-roam also uses Graphviz to generate a graph, with notes as nodes,
-and links between them as edges. The generated graph can be used to
-navigate to the files, but this requires some additional setup
-described in the [Roam Protocol][appendix:roam-protocol] page.
-
-![org-roam-graph](images/org-roam-graph.gif)
-
-[zettelkasten]: https://zettelkasten.de/
-[appendix:ntw]: notetaking_workflow.md
-[appendix:roam-protocol]: roam_protocol.md
-[roam]: https://www.roamresearch.com/
-[jethro-blog-post]: https://blog.jethro.dev/posts/how_to_take_smart_notes_org/
--- a/makem.sh
+++ b/makem.sh
@ -155,7 +155,8 @@ function elisp-checkdoc-file {
    (when makem-checkdoc-errors-p
      (kill-emacs 1))))

-(setq checkdoc-spellcheck-documentation-flag t)
+(setq sentence-end-double-space nil)
+(setq checkdoc-spellcheck-documentation-flag nil)
 (makem-checkdoc-files-and-exit)
 EOF
    echo $file
@ -325,7 +326,7 @@ function dirnames {

 function filter-files-exclude-default {
    # Filter out paths (STDIN) which should be excluded by default.
-    egrep -v "(/\.cask/|-autoloads.el|.dir-locals)"
+    egrep -v "(/\.cask/|-autoloads.el|-macs.el|.dir-locals)"
 }

 function filter-files-exclude-args {
@ -694,7 +695,7 @@ function lint {
    lint-checkdoc
    lint-compile
    lint-declare
-    lint-indent
+    # lint-indent
    lint-package
    lint-regexps
 }
--- a/mkdocs.yml
+++ b/mkdocs.yml
@ -1,5 +1,5 @@
 site_name: "Org-roam"
-repo_url: https://github.com/jethrokuan/org-roam/
+repo_url: https://github.com/org-roam/org-roam/
 edit_uri: edit/master/doc/
 copyright: "Copyright (C) 2020 Jethro Kuan and contributors"
 docs_dir: doc
--- a/org-roam-buffer.el
+++ b/org-roam-buffer.el
@ -1,11 +1,11 @@
-;;; org-roam-buffer.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; 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/jethrokuan/org-roam
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
+;; Version: 1.1.1
 ;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))

 ;; This file is NOT part of GNU Emacs.
@ -40,6 +40,8 @@
 (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
+
 (declare-function org-roam-db--ensure-built   "org-roam-db")
 (declare-function org-roam--extract-ref       "org-roam")
 (declare-function org-roam--get-title-or-slug "org-roam")
@ -100,16 +102,28 @@ When non-nil, the window will not be closed when deleting other windows."
                       '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--insert-citelinks ()
  "Insert citation backlinks for the current buffer."
-  (if-let* ((roam-key (with-temp-buffer
-                        (insert-buffer-substring org-roam-buffer--current)
-                        (org-roam--extract-ref)))
-            (key-backlinks (org-roam--get-backlinks (s-chop-prefix "cite:" roam-key)))
+  (if-let* ((ref (with-temp-buffer
+                   (insert-buffer-substring org-roam-buffer--current)
+                   (org-roam--extract-ref)))
+            (org-ref-p (require 'org-ref nil t)) ; Ensure that org-ref is present
+            (key-backlinks (org-roam--get-backlinks (cdr ref)))
            (grouped-backlinks (--group-by (nth 0 it) key-backlinks)))
      (progn
-        (insert (format "\n\n* %d Cite backlinks\n"
-                        (length key-backlinks)))
+        (insert (let ((l (length key-backlinks)))
+                  (format "\n\n* %d %s\n"
+                          l (org-roam-buffer--pluralize "Cite backlink" l))))
        (dolist (group grouped-backlinks)
          (let ((file-from (car group))
                (bls (cdr group)))
@ -133,8 +147,9 @@ When non-nil, the window will not be closed when deleting other windows."
            (backlinks (org-roam--get-backlinks file-path))
            (grouped-backlinks (--group-by (nth 0 it) backlinks)))
      (progn
-        (insert (format "\n\n* %d Backlinks\n"
-                        (length backlinks)))
+        (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 (cdr group)))
@ -178,6 +193,7 @@ When non-nil, the window will not be closed when deleting other windows."
        (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
--- a/org-roam-capture.el
+++ b/org-roam-capture.el
@ -1,11 +1,11 @@
-;;; org-roam-capture.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-capture.el --- Capture functionality -*- 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
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
+;; Version: 1.1.1
 ;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))

 ;; This file is NOT part of GNU Emacs.
@ -33,6 +33,7 @@
 (require 'org-capture)
 (require 'dash)
 (require 's)
+(require 'cl-lib)

 ;; Declarations
 (defvar org-roam-encrypt-files)
@ -129,9 +130,11 @@ Details on how to specify for the template is given in `org-roam-capture-templat
 (defun org-roam-capture--in-process-p ()
  "Return non-nil if a `org-roam-capture' buffer exists."
  (cl-some (lambda (buffer)
-	     (and (eq (buffer-local-value 'major-mode (current-buffer)) 'org-mode)
-		  (plist-get (buffer-local-value 'org-capture-current-plist (current-buffer)) :org-roam)))
-	   (buffer-list)))
+             (and (eq (buffer-local-value 'major-mode buffer)
+                      'org-mode)
+                  (plist-get (buffer-local-value 'org-capture-current-plist buffer)
+                             :org-roam)))
+           (buffer-list)))

 (defun org-roam-capture--fill-template (str &optional info)
  "Expands the template STR, returning the string.
@ -277,23 +280,21 @@ This function is used solely in Org-roam's capture templates: see

 (defun org-roam-capture--convert-template (template)
  "Convert TEMPLATE from Org-roam syntax to `org-capture-templates' syntax."
-  (let* ((copy (copy-tree template))
-         converted
-         org-roam-plist
-         key
-         val)
-    ;;put positional args on converted template
-    (dotimes (_ 5)
-      (push (pop copy) converted))
-    (while (setq key (pop copy)
-                 val (pop copy))
-      (if (member key org-roam-capture--template-keywords)
-          (progn
-            (push val org-roam-plist)
-            (push key org-roam-plist))
-        (push key converted)
-        (push val converted)))
-    (append (nreverse converted) `(:org-roam ,org-roam-plist))))
+  (pcase template
+    (`(,_key ,_description) template)
+    (`(,key ,description ,type ,target . ,rest)
+     (let ((converted `(,key ,description ,type ,target
+                             ,(unless (keywordp (car rest)) (pop rest))))
+           org-roam-plist
+           options)
+       (while rest
+         (let* ((key (pop rest))
+                (val (pop rest))
+                (custom (member key org-roam-capture--template-keywords)))
+           (push val (if custom org-roam-plist options))
+           (push key (if custom org-roam-plist options))))
+       (append converted options `(:org-roam ,org-roam-plist))))
+    (_ (user-error "Invalid capture template format: %s" template))))

 (defun org-roam-capture--find-file-h ()
  "Opens the newly created template file.
@ -311,12 +312,13 @@ Suitable for moving point."
  :group 'org-roam
  :type 'hook)

-(defun org-roam--capture (&optional goto keys)
+(defun org-roam-capture--capture (&optional goto keys)
  "Create a new file, and return the path to the edited file.
 The templates are defined at `org-roam-capture-templates'.  The
 GOTO and KEYS argument have the same functionality as
 `org-capture'."
-  (let ((org-capture-templates (mapcar #'org-roam-capture--convert-template org-roam-capture-templates)))
+  (let ((org-capture-templates (mapcar #'org-roam-capture--convert-template org-roam-capture-templates))
+        org-capture-templates-contexts)
    (when (= (length org-capture-templates) 1)
      (setq keys (caar org-capture-templates)))
    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--save-file-maybe-h)
@ -330,14 +332,20 @@ This uses the templates defined at `org-roam-capture-templates'."
  (when (org-roam-capture--in-process-p)
    (user-error "Nested Org-roam capture processes not supported"))
  (let* ((completions (org-roam--get-title-path-completions))
-         (title (org-roam-completion--completing-read "File: " completions))
-         (file-path (cdr (assoc title completions))))
+         (title-with-keys (org-roam-completion--completing-read "File: "
+                                                                completions))
+         (res (cdr (assoc title-with-keys completions)))
+         (title (or (plist-get res :title) title-with-keys))
+         (file-path (plist-get res :file-path)))
    (let ((org-roam-capture--info (list (cons 'title title)
                                        (cons 'slug (org-roam--title-to-slug title))
                                        (cons 'file file-path)))
          (org-roam-capture--context 'capture))
      (setq org-roam-capture-additional-template-props (list :capture-fn 'org-roam-capture))
-      (org-roam--capture))))
+      (condition-case err
+          (org-roam-capture--capture)
+        (error (user-error "%s.  Please adjust `org-roam-capture-templates'"
+                           (error-message-string err)))))))

 (provide 'org-roam-capture)

--- a/org-roam-compat.el
+++ b/org-roam-compat.el
@ -1,11 +1,11 @@
-;;; org-roam-compat.el --- Compatibility Code -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-compat.el --- Compatibility Code -*- 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
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
+;; Version: 1.1.1
 ;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))

 ;; This file is NOT part of GNU Emacs.
@ -71,17 +71,22 @@
  "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")

 ;;;; 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")
-(make-obsolete-variable 'org-roam-graph-node-shape  'org-roam-graph-node-extra-config "org-roam 1.0.0")
-(defcustom org-roam-graph-node-shape "ellipse"
-  "Shape of graph nodes."
-  :type 'string
-  :group 'org-roam)
+(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
--- a/org-roam-completion.el
+++ b/org-roam-completion.el
@ -1,11 +1,11 @@
-;;; org-roam-completion.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-completion.el --- Completion features -*- 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
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
+;; Version: 1.1.1
 ;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))

 ;; This file is NOT part of GNU Emacs.
@ -47,11 +47,6 @@
          (function :tag "Custom function"))
  :group 'org-roam)

-(defcustom org-roam-completion-fuzzy-match nil
-  "Whether to fuzzy match Org-roam's completion candidates."
-  :type 'boolean
-  :group 'org-roam)
-
 (defun org-roam-completion--helm-candidate-transformer (candidates _source)
  "Transforms CANDIDATES for Helm-based completing read.
 SOURCE is not used."
@ -82,9 +77,7 @@ Return user choice."
                          :require-match require-match
                          :action (prog1 action
                                    (setq action nil))
-                          :caller 'org-roam--completing-read
-                          :re-builder (if org-roam-completion-fuzzy-match 'ivy--regex-fuzzy
-                                        'regexp-quote))
+                          :caller 'org-roam--completing-read)
              (user-error "Please install ivy from \
 https://github.com/abo-abo/swiper")))
           ((eq org-roam-completion-system 'helm)
@ -96,8 +89,7 @@ https://github.com/emacs-helm/helm"))
                            :candidates (mapcar #'car choices)
                            :filtered-candidate-transformer
                            (and (not require-match)
-                                 #'org-roam-completion--helm-candidate-transformer)
-                            :fuzzy-match org-roam-completion-fuzzy-match))
+                                 #'org-roam-completion--helm-candidate-transformer)))
                  (buf (concat "*org-roam "
                               (s-downcase (s-chop-suffix ":" (s-trim prompt)))
                               "*")))
--- a/org-roam-dailies.el
+++ b/org-roam-dailies.el
@ -1,11 +1,11 @@
-;;; org-roam-dialies.el --- Roam Research replica with Org-mode -*- 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>

 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
+;; Version: 1.1.1
 ;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))

 ;; This file is NOT part of GNU Emacs.
@ -34,6 +34,7 @@
 ;;; Library Requires
 (require 'org-capture)
 (require 'org-roam-capture)
+(require 'org-roam-macs)

 (defvar org-roam-dailies-capture-templates
  '(("d" "daily" plain (function org-roam-capture--get-point)
@ -52,7 +53,8 @@
        (org-roam-capture--info (list (cons 'time time)))
        (org-roam-capture--context 'dailies))
    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--find-file-h)
-    (org-roam--capture)))
+    (org-roam--with-template-error 'org-roam-dailies-capture-templates
+      (org-roam-capture--capture))))

 (defun org-roam-dailies-today ()
  "Create and find the daily note for today."
@ -69,7 +71,7 @@ With numeric argument N, use N days in the future."
  "Create and find the file for yesterday.
 With numeric argument N, use N days in the past."
  (interactive "p")
-  (org-roam-tomorrow (- n)))
+  (org-roam-dailies-tomorrow (- n)))

 (defun org-roam-dailies-date ()
  "Create the file for any date using the calendar interface."
@ -78,4 +80,5 @@ With numeric argument N, use N days in the past."
    (org-roam-dailies--file-for-time time)))

 (provide 'org-roam-dailies)
+
 ;;; org-roam-dailies.el ends here
--- a/org-roam-db.el
+++ b/org-roam-db.el
@ -1,11 +1,11 @@
-;;; org-roam-db.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-db.el --- Org-roam database API -*- 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
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
+;; Version: 1.1.1
 ;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))

 ;; This file is NOT part of GNU Emacs.
@ -39,11 +39,13 @@
 (defvar org-roam-directory)
 (defvar org-roam-verbose)

-(declare-function org-roam--extract-titles      "org-roam")
-(declare-function org-roam--extract-ref         "org-roam")
-(declare-function org-roam--extract-links       "org-roam")
-(declare-function org-roam--list-files          "org-roam")
-(declare-function org-roam-buffer--update-maybe "org-roam-buffer")
+(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-links                  "org-roam")
+(declare-function org-roam--list-all-files                 "org-roam")
+(declare-function org-roam-buffer--update-maybe            "org-roam-buffer")

 ;;;; Options
 (defcustom org-roam-db-location nil
@ -55,7 +57,7 @@ when used with multiple Org-roam instances."
  :type 'string
  :group 'org-roam)

-(defconst org-roam-db--version 2)
+(defconst org-roam-db--version 5)
 (defconst org-roam-db--sqlite-available-p
  (with-demoted-errors "Org-roam initialization: %S"
    (emacsql-sqlite-ensure-binary)
@ -93,7 +95,7 @@ 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--maybe-update conn version)))
+               (version (org-roam-db--update-maybe conn version)))
          (cond
           ((> version org-roam-db--version)
            (emacsql-close conn)
@ -119,7 +121,7 @@ SQL can be either the emacsql vector representation, or a string."
  '((files
     [(file :unique :primary-key)
      (hash :not-null)
-      (last-modified :not-null)])
+      (meta :not-null)])

    (links
     [(from :not-null)
@ -127,13 +129,18 @@ SQL can be either the emacsql vector representation, or a string."
      (type :not-null)
      (properties :not-null)])

+    (tags
+     [(file :unique :primary-key)
+      (tags)])
+
    (titles
     [(file :not-null)
      titles])

    (refs
     [(ref :unique :not-null)
-      (file :not-null)])))
+      (file :not-null)
+      (type :not-null)])))

 (defun org-roam-db--init (db)
  "Initialize database DB with the correct schema and user version."
@ -142,16 +149,16 @@ SQL can be either the emacsql vector representation, or a string."
      (emacsql db [:create-table $i1 $S2] table schema))
    (emacsql db (format "PRAGMA user_version = %s" org-roam-db--version))))

-(defun org-roam-db--maybe-update (db version)
+(defun org-roam-db--update-maybe (db version)
  "Upgrades the database schema for DB, if VERSION is old."
  (emacsql-with-transaction db
    'ignore
-    (when (= version 1)
-      (progn
-        (warn "No good way to perform a DB upgrade, rebuilding from scratch...")
-        (delete-file (org-roam-db--get))
-        (org-roam-db-build-cache)))
-    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)

 (defun org-roam-db--close (&optional db)
  "Closes the database connection for database DB.
@ -185,32 +192,27 @@ the current `org-roam-directory'."
  "Clears all entries in the caches."
  (interactive)
  (when (file-exists-p (org-roam-db--get))
-    (org-roam-db-query [:delete :from files])
-    (org-roam-db-query [:delete :from titles])
-    (org-roam-db-query [:delete :from links])
-    (org-roam-db-query [:delete :from refs])))
-
+    (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* ((path (or filepath
-                   (buffer-file-name)))
-         (file (file-truename path)))
-    (org-roam-db-query [:delete :from files
-                        :where (= file $s1)]
-                       file)
-    (org-roam-db-query [:delete :from links
-                        :where (= from $s1)]
-                       file)
-    (org-roam-db-query [:delete :from titles
-                        :where (= file $s1)]
-                       file)
-    (org-roam-db-query [:delete :from refs
-                        :where (= file $s1)]
-                       file)))
+  (let ((file (file-truename (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))))

 ;;;;; 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))))
+
 (defun org-roam-db--insert-links (links)
  "Insert LINKS into the Org-roam cache."
  (org-roam-db-query
@ -225,12 +227,20 @@ This is equivalent to removing the node from the graph."
    :values $v1]
   (list (vector file titles))))

+(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."
-  (org-roam-db-query
-   [:insert :into refs
-    :values $v1]
-   (list (vector ref file))))
+  (let ((key (cdr ref))
+        (type (car ref)))
+    (org-roam-db-query
+     [:insert :into refs :values $v1]
+     (list (vector key file type)))))

 ;;;;; Fetching
 (defun org-roam-db--get-current-files ()
@ -270,8 +280,9 @@ If the file does not have any connections, nil is returned."
    files))

 (defun org-roam-db--links-with-max-distance (file max-distance)
-  "Return all files reachable from/connected to FILE in at most MAX-DISTANCE steps,
-including the file itself.  If the file does not have any connections, nil is returned."
+  "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 roamlinks AS (SELECT * FROM links WHERE \"type\" = '\"roam\"'),
@ -302,13 +313,35 @@ including the file itself.  If the file does not have any connections, nil is re
    files))

 ;;;;; Updating
+(defun org-roam-db--update-meta ()
+  "Update the metadata of the current buffer into the cache."
+  (let* ((file (file-truename (buffer-file-name)))
+         (attr (file-attributes file))
+         (atime (file-attribute-access-time attr))
+         (mtime (file-attribute-modification-time attr))
+         (hash (secure-hash 'sha1 (current-buffer))))
+    (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 (file-truename (buffer-file-name))))
+  (let* ((file (file-truename (buffer-file-name)))
+         (title (org-roam--extract-titles)))
    (org-roam-db-query [:delete :from titles
                        :where (= file $s1)]
                       file)
-    (org-roam-db--insert-titles file (org-roam--extract-titles))))
+    (org-roam-db--insert-titles file title)))
+
+(defun org-roam-db--update-tags ()
+  "Update the tags of the current buffer into the cache."
+  (let* ((file (file-truename (buffer-file-name)))
+         (tags (org-roam--extract-tags)))
+    (org-roam-db-query [:delete :from tags
+                        :where (= file $s1)]
+                       file)
+    (org-roam-db--insert-tags file tags)))

 (defun org-roam-db--update-refs ()
  "Update the ref of the current buffer into the cache."
@ -330,43 +363,53 @@ including the file itself.  If the file does not have any connections, nil is re

 (defun org-roam-db--update-file (&optional file-path)
  "Update Org-roam cache for FILE-PATH."
-  (let (buf)
-    (if file-path
-        (setq buf (find-file-noselect file-path))
-      (setq buf (current-buffer)))
-    (with-current-buffer buf
-      (save-excursion
-        (org-roam-db--update-titles)
-        (org-roam-db--update-refs)
-        (org-roam-db--update-cache-links)
-        (org-roam-buffer--update-maybe :redisplay t)))))
+  (when (org-roam--org-roam-file-p file-path)
+    (let ((buf (or (and file-path
+                        (find-file-noselect file-path t))
+                   (current-buffer))))
+      (with-current-buffer buf
+        (save-excursion
+          (org-roam-db--update-meta)
+          (org-roam-db--update-tags)
+          (org-roam-db--update-titles)
+          (org-roam-db--update-refs)
+          (org-roam-db--update-cache-links)
+          (org-roam-buffer--update-maybe :redisplay t))))))

-;;;;; org-roam-db-build-cache
-(defun org-roam-db-build-cache ()
-  "Build the cache for `org-roam-directory'."
-  (interactive)
+(defun org-roam-db-build-cache (&optional force)
+  "Build the cache for `org-roam-directory'.
+If FORCE, force a rebuild of the cache from scratch."
+  (interactive "P")
+  (when force (delete-file (org-roam-db--get)))
  (org-roam-db--close) ;; Force a reconnect
  (org-roam-db) ;; To initialize the database, no-op if already initialized
-  (let* ((org-roam-files (org-roam--list-files org-roam-directory))
+  (let* ((org-roam-files (org-roam--list-all-files))
         (current-files (org-roam-db--get-current-files))
-         (time (current-time))
-         all-files all-links all-titles all-refs)
+         all-files all-links all-titles all-refs all-tags)
    (dolist (file org-roam-files)
-      (org-roam--with-temp-buffer
-        (insert-file-contents file)
-        (let ((contents-hash (secure-hash 'sha1 (current-buffer))))
-          (unless (string= (gethash file current-files)
-                           contents-hash)
-            (org-roam-db--clear-file file)
-            (setq all-files
-                  (cons (vector file contents-hash time) all-files))
-            (when-let (links (org-roam--extract-links file))
-              (setq all-links (append links all-links)))
-            (let ((titles (org-roam--extract-titles)))
-              (setq all-titles (cons (vector file titles) all-titles)))
-            (when-let ((ref (org-roam--extract-ref)))
-              (setq all-refs (cons (vector ref file) all-refs))))
-          (remhash file current-files))))
+      (let* ((attr (file-attributes file))
+             (atime (file-attribute-access-time attr))
+             (mtime (file-attribute-modification-time attr)))
+        (org-roam--with-temp-buffer
+          (insert-file-contents file)
+          (let ((contents-hash (secure-hash 'sha1 (current-buffer))))
+            (unless (string= (gethash file current-files)
+                             contents-hash)
+              (org-roam-db--clear-file file)
+              (push (vector file contents-hash (list :atime atime :mtime mtime))
+                    all-files)
+              (when-let (links (org-roam--extract-links file))
+                (push links all-links))
+              (when-let (tags (org-roam--extract-tags file))
+                (push (vector file tags) all-tags))
+              (let ((titles (org-roam--extract-titles)))
+                (push (vector file titles)
+                      all-titles))
+              (when-let* ((ref (org-roam--extract-ref))
+                          (type (car ref))
+                          (key (cdr ref)))
+                (setq all-refs (cons (vector key file type) all-refs))))
+            (remhash file current-files)))))
    (dolist (file (hash-table-keys current-files))
      ;; These files are no longer around, remove from cache...
      (org-roam-db--clear-file file))
@ -385,6 +428,11 @@ including the file itself.  If the file does not have any connections, nil is re
       [:insert :into titles
        :values $v1]
       all-titles))
+    (when all-tags
+      (org-roam-db-query
+       [:insert :into tags
+        :values $v1]
+       all-tags))
    (when all-refs
      (org-roam-db-query
       [:insert :into refs
@ -392,16 +440,17 @@ including the file itself.  If the file does not have any connections, nil is re
       all-refs))
    (let ((stats (list :files (length all-files)
                       :links (length all-links)
+                       :tags (length all-tags)
                       :titles (length all-titles)
                       :refs (length all-refs)
                       :deleted (length (hash-table-keys current-files)))))
-      (when org-roam-verbose
-        (message "files: %s, links: %s, titles: %s, refs: %s, deleted: %s"
-                 (plist-get stats :files)
-                 (plist-get stats :links)
-                 (plist-get stats :titles)
-                 (plist-get stats :refs)
-                 (plist-get stats :deleted)))
+      (org-roam-message "files: %s, links: %s, tags: %s, titles: %s, refs: %s, deleted: %s"
+                        (plist-get stats :files)
+                        (plist-get stats :links)
+                        (plist-get stats :tags)
+                        (plist-get stats :titles)
+                        (plist-get stats :refs)
+                        (plist-get stats :deleted))
      stats)))

 (provide 'org-roam-db)
--- a/org-roam-dev.el
+++ b/org-roam-dev.el
@ -0,0 +1,40 @@
+;;; 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: 1.1.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; 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)
+(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
@ -0,0 +1,231 @@
+;;; 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: 1.1.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; 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-roam-macs)
+(require 'org-element)
+
+(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")
+
+(defvar org-roam-verbose)
+
+(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))))))
+
+(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")
+  (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)))
+      (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-graph.el
+++ b/org-roam-graph.el
@ -1,11 +1,11 @@
-;;; org-roam-graph.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-graph.el --- Graphing API -*- 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
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
+;; Version: 1.1.1
 ;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))

 ;; This file is NOT part of GNU Emacs.
@ -53,8 +53,8 @@ It may be one of the following:
          (const    :tag "view-file"))
  :group 'org-roam)

-(defcustom org-roam-graph-executable (executable-find "dot")
-  "Path to graphing executable."
+(defcustom org-roam-graph-executable "dot"
+  "Path to graphing executable, or its name."
  :type 'string
  :group 'org-roam)

@ -65,14 +65,20 @@ Example:
  :type '(alist)
  :group 'org-roam)

-(defcustom org-roam-graph-node-extra-config nil
+(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\"))"
  :type '(alist)
  :group 'org-roam)

-(defcustom org-roam-graph-edge-extra-config nil
+(defcustom org-roam-graph-edge-extra-config
+  '(("color" . "#333333"))
  "Extra options for graphviz edges.
 Example:
 '((\"dir\" . \"back\"))"
@ -91,6 +97,19 @@ Example:
  :type 'number
  :group 'org-roam)

+(defcustom org-roam-graph-shorten-titles 'truncate
+  "Determines how long titles appear in graph nodes.
+Recognized values are the symbols `truncate' and `wrap', in which
+cases the title will be truncated or wrapped, respectively, if it
+is longer than `org-roam-graph-max-title-length'.
+
+All other values including nil will have no effect."
+  :type '(choice
+          (const :tag "truncate" truncate)
+          (const :tag "wrap" wrap)
+          (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
@ -154,7 +173,8 @@ into a digraph."
            `[: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"))
+                                                     (= 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)))
@ -163,7 +183,8 @@ into a digraph."
        (insert (org-roam-graph--dot-option option) ";\n"))
      (dolist (attribute '("node" "edge"))
        (insert (format " %s [%s];\n" attribute
-                        (mapconcat #'org-roam-graph--dot-option
+                        (mapconcat (lambda (var)
+                                     (org-roam-graph--dot-option var nil "\""))
                                   (symbol-value
                                    (intern (concat "org-roam-graph-" attribute "-extra-config")))
                                   ","))))
@ -171,7 +192,10 @@ into a digraph."
        (let* ((file (xml-escape-string (car node)))
               (title (or (caadr node)
                          (org-roam--path-to-slug file)))
-               (shortened-title (s-truncate org-roam-graph-max-title-length title))
+               (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)))
               (node-properties
                `(("label"   . ,(s-replace "\"" "\\\"" shortened-title))
                  ("URL"     . ,(concat "org-protocol://roam-file?file=" (url-hexify-string file)))
@ -195,19 +219,22 @@ into a digraph."

 (defun org-roam-graph--build (&optional node-query)
  "Generate a graph showing the relations between nodes in NODE-QUERY."
-  (unless org-roam-graph-executable
-    (user-error "Can't find %s executable.  Please check if it is in your path"
-                org-roam-graph-executable))
-  (let* ((node-query (or node-query
-                         `[:select [file titles]
-                           :from titles
-                           ,@(org-roam-graph--expand-matcher 'file t)]))
-         (graph      (org-roam-graph--dot node-query))
-         (temp-dot   (make-temp-file "graph." nil ".dot" graph))
-         (temp-graph (make-temp-file "graph." nil ".svg")))
-    (call-process org-roam-graph-executable nil 0 nil
-                  temp-dot "-Tsvg" "-o" temp-graph)
-    temp-graph))
+  (let ((name org-roam-graph-executable))
+    (unless (stringp name)
+      (user-error "`org-roam-graph-executable' is not a string"))
+    (unless (executable-find org-roam-graph-executable)
+      (user-error (concat "Cannot find executable \"%s\" to generate the graph.  "
+                          "Please adjust `org-roam-graph-executable'")
+                  name))
+    (let* ((node-query (or node-query
+                           `[:select [file titles]
+                             :from titles
+                             ,@(org-roam-graph--expand-matcher 'file t)]))
+           (graph (org-roam-graph--dot node-query))
+           (temp-dot (make-temp-file "graph." nil ".dot" graph))
+           (temp-graph (make-temp-file "graph." nil ".svg")))
+      (call-process name nil 0 nil temp-dot "-Tsvg" "-o" temp-graph)
+      temp-graph)))

 (defun org-roam-graph--open (file)
  "Open FILE using `org-roam-graph-viewer' with `view-file' as a fallback."
@ -216,7 +243,7 @@ into a digraph."
     (if (executable-find org-roam-graph-viewer)
         (condition-case err
             (call-process org-roam-graph-viewer nil 0 nil file)
-           ((error (user-error "Failed to open org-roam graph: %s" err))))
+           (error (user-error "Failed to open org-roam graph: %s" err)))
       (user-error "Executable not found: \"%s\"" org-roam-graph-viewer)))
    ((pred functionp) (funcall org-roam-graph-viewer file))
    ('nil (view-file file))
@ -248,15 +275,16 @@ ARG may be any of the following values:
  - `\\[universal-argument]' -   build the graph for FILE.
  - `\\[universal-argument]' -N  build the graph for FILE limiting nodes to N steps."
  (interactive "P")
-  (let ((file (or file (buffer-file-name))))
-    (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))
+  (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--open (org-roam-graph--build node-query)))
      ('(4)            (org-roam-graph--open (org-roam-graph--build-connected-component file)))
-      ((pred integerp) (let ((graph (org-roam-graph--build-connected-component (buffer-file-name) (abs arg))))
+      ((pred integerp) (let ((graph (org-roam-graph--build-connected-component file (abs arg))))
                         (when (>= arg 0)
                           (org-roam-graph--open graph))))
      ('(16)           (org-roam-graph--build node-query))
--- a/org-roam-macs.el
+++ b/org-roam-macs.el
@ -1,11 +1,11 @@
-;;; org-roam-macs.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-macs.el --- Macros/utility functions -*- 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
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
+;; Version: 1.1.1
 ;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))

 ;; This file is NOT part of GNU Emacs.
@ -27,12 +27,15 @@

 ;;; Commentary:
 ;;
-;; This library implements macros used throughout org-roam
+;; This library implements macros and utility functions used throughout
+;; org-roam.
 ;;
 ;;
 ;;; Code:
 ;;;; Library Requires

+(defvar org-roam-verbose)
+
 (defmacro org-roam--with-temp-buffer (&rest body)
  "Execute BODY within a temp buffer.
 Like `with-temp-buffer', but propagates `org-roam-directory'."
@ -43,6 +46,24 @@ Like `with-temp-buffer', but propagates `org-roam-directory'."
         (let ((org-roam-directory ,current-org-roam-directory))
           ,@body)))))

+(defmacro org-roam--with-template-error (templates &rest body)
+  "Eval BODY, and point to TEMPLATES on error.
+Provides more informative error messages so that users know where
+to look.
+
+\(fn TEMPLATES BODY...)"
+  (declare (debug (form body)) (indent 1))
+  `(condition-case err
+       ,@body
+     (error (user-error "%s.  Please adjust `%s'"
+                        (error-message-string err)
+                        ,templates))))
+
+(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))))
+
 (provide 'org-roam-macs)

 ;;; org-roam-macs.el ends here
--- a/org-roam-protocol.el
+++ b/org-roam-protocol.el
@ -1,10 +1,10 @@
-;;; org-roam-protocol.el --- Protocol handler for roam:// links  -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-protocol.el --- Protocol handler for roam:// links  -*- 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
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
+;; Version: 1.1.1
 ;; Package-Requires: ((emacs "26.1") (org "9.3"))

 ;; This file is NOT part of GNU Emacs.
@ -62,8 +62,9 @@ It opens or creates a note with the given ref.
           (org-roam-capture--info decoded-alist)
           (template (cdr (assoc 'template decoded-alist))))
      (raise-frame)
-      (org-roam--capture nil template)
-      (message "Item captured.")))
+      (org-roam--with-template-error 'org-roam-capture-ref-templates
+        (org-roam-capture--capture nil template))
+      (org-roam-message "Item captured.")))
  nil)

 (defun org-roam-protocol-open-file (info)
--- a/org-roam.el
+++ b/org-roam.el
--- a/tests/roam-files/base.org
+++ b/tests/roam-files/base.org
@ -0,0 +1 @@
+#+TITLE: Base
--- a/tests/roam-files/nested/deeply/deeply_nested_file.org
+++ b/tests/roam-files/nested/deeply/deeply_nested_file.org
@ -0,0 +1 @@
+#+TITLE: Deeply Nested File
--- a/tests/roam-files/no-title.org
+++ b/tests/roam-files/no-title.org
@ -1,3 +1,5 @@
 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
@ -0,0 +1,3 @@
+#+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
@ -0,0 +1,4 @@
+#+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
@ -0,0 +1 @@
+#+ROAM_ALIAS: "roam" "alias"
--- a/tests/roam-files/titles/combination.org
+++ b/tests/roam-files/titles/combination.org
@ -0,0 +1,4 @@
+#+TITLE: TITLE PROP
+#+ROAM_ALIAS: "roam" "alias"
+
+* Headline
--- a/tests/roam-files/titles/headline.org
+++ b/tests/roam-files/titles/headline.org
@ -0,0 +1 @@
+* Headline
--- a/tests/roam-files/titles/title.org
+++ b/tests/roam-files/titles/title.org
@ -0,0 +1 @@
+#+TITLE: Title
--- a/tests/test-org-roam.el
+++ b/tests/test-org-roam.el
@ -1,4 +1,4 @@
-;;; test-org-roam.el --- Tests for org-roam -*- lexical-binding: t; -*-
+;;; test-org-roam.el --- Tests for Org-roam -*- lexical-binding: t; -*-

 ;; Copyright (C) 2020 Jethro Kuan

@ -19,237 +19,395 @@
 ;; along with this program.  If not, see <https://www.gnu.org/licenses/>.

 ;;; Commentary:
-
-;;
-
 ;;; Code:

-;;;; Requirements
-
 (require 'buttercup)
 (require 'with-simulated-input)
 (require 'org-roam)
 (require 'dash)

-(defun org-roam-test-abs-path (file-path)
+(defun test-org-roam--abs-path (file-path)
  "Get absolute FILE-PATH from `org-roam-directory'."
  (file-truename (expand-file-name file-path org-roam-directory)))

-(defun org-roam-test-find-new-file (path)
+(defun test-org-roam--find-file (path)
  "PATH."
-  (let ((path (org-roam-test-abs-path path)))
+  (let ((path (test-org-roam--abs-path path)))
    (make-directory (file-name-directory path) t)
    (find-file path)))

-(defvar org-roam-test-directory (file-truename (concat default-directory "tests/roam-files"))
+(defvar test-org-roam-directory (file-truename (concat default-directory "tests/roam-files"))
  "Directory containing org-roam test org files.")

-(defun org-roam-test-init ()
+(defun test-org-roam--init ()
  "."
-  (org-roam-db--close)
-  (let ((original-dir org-roam-test-directory)
+  (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)))
+    (org-roam-mode +1)
+    (sleep-for 2)))
+
+(defun test-org-roam--teardown ()
+  (org-roam-mode -1)
+  (delete-file (org-roam-db--get))
+  (org-roam-db--close))
+
+(describe "Title extraction"
+  :var (org-roam-title-sources)
+  (before-all
+    (test-org-roam--init))
+
+  (after-all
+    (test-org-roam--teardown))
+
+  (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")))
+
+    (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"))))))

 ;;; Tests
-(describe "org-roam-db-build-cache"
-  (it "initializes correctly"
-    (org-roam-test-init)
-    (org-roam-db-build-cache)
+(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 2)
+                                      :where titles :is-null])) :to-be 1)
    (expect (caar (org-roam-db-query [:select (funcall count) :from refs])) :to-be 1)

-    ;; TODO Test files
-
    ;; Links
    (expect (caar (org-roam-db-query [:select (funcall count) :from links
                                      :where (= from $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 1)
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 1)
    (expect (caar (org-roam-db-query [:select (funcall count) :from links
                                      :where (= from $s1)]
-                                     (org-roam-test-abs-path "nested/bar.org"))) :to-be 2)
+                                     (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)]
-                                     (org-roam-test-abs-path "nested/foo.org"))) :to-be 1)
+                                     (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)]
-                                     (org-roam-test-abs-path "nested/bar.org"))) :to-be 1)
+                                     (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)]
-                                     (org-roam-test-abs-path "unlinked.org"))) :to-be 0)
+                                     (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 (org-roam-test-abs-path "alias.org")
+            (list (list (test-org-roam--abs-path "alias.org")
                        (list "t1" "a1" "a 2"))
-                  (list (org-roam-test-abs-path "bar.org")
+                  (list (test-org-roam--abs-path "bar.org")
                        (list "Bar"))
-                  (list (org-roam-test-abs-path "foo.org")
+                  (list (test-org-roam--abs-path "foo.org")
                        (list "Foo"))
-                  (list (org-roam-test-abs-path "nested/bar.org")
+                  (list (test-org-roam--abs-path "nested/bar.org")
                        (list "Nested Bar"))
-                  (list (org-roam-test-abs-path "nested/foo.org")
+                  (list (test-org-roam--abs-path "nested/foo.org")
                        (list "Nested Foo"))
-                  (list (org-roam-test-abs-path "no-title.org") nil)
-                  (list (org-roam-test-abs-path "web_ref.org") nil)
-                  (list (org-roam-test-abs-path "unlinked.org")
+                  (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/" (org-roam-test-abs-path "web_ref.org"))))
+            (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 :titles 0 :refs 0 :deleted 0))))
+            (list :files 0 :links 0 :tags 0 :titles 0 :refs 0 :deleted 0))))

-(describe "org-roam-insert"
+(xdescribe "org-roam-insert"
  (before-each
-    (org-roam-test-init)
-    (org-roam-db--clear)
-    (org-roam-db-build-cache))
+    (test-org-roam--init))
+
+  (after-each
+    (test-org-roam--teardown))

  (it "temp1 -> foo"
-    (let ((buf (org-roam-test-find-new-file "temp1.org")))
+    (let ((buf (test-org-roam--find-file "temp1.org")))
      (with-current-buffer buf
        (with-simulated-input
         "Foo RET"
-         (org-roam-insert nil))))
+         (org-roam-insert))))
    (expect (buffer-string) :to-match (regexp-quote "file:foo.org")))

  (it "temp2 -> nested/foo"
-    (let ((buf (org-roam-test-find-new-file "temp2.org")))
+    (let ((buf (test-org-roam--find-file "temp2.org")))
      (with-current-buffer buf
        (with-simulated-input
-         "Nested SPC Foo RET"
-         (org-roam-insert nil))))
+         "(nested) SPC Nested SPC Foo RET"
+         (org-roam-insert))))
    (expect (buffer-string) :to-match (regexp-quote "file:nested/foo.org")))

  (it "nested/temp3 -> foo"
-    (let ((buf (org-roam-test-find-new-file "nested/temp3.org")))
+    (let ((buf (test-org-roam--find-file "nested/temp3.org")))
      (with-current-buffer buf
        (with-simulated-input
         "Foo RET"
-         (org-roam-insert nil))))
+         (org-roam-insert))))
    (expect (buffer-string) :to-match (regexp-quote "file:../foo.org")))

  (it "a/b/temp4 -> nested/foo"
-    (let ((buf (org-roam-test-find-new-file "a/b/temp4.org")))
+    (let ((buf (test-org-roam--find-file "a/b/temp4.org")))
      (with-current-buffer buf
        (with-simulated-input
-         "Nested SPC Foo RET"
-         (org-roam-insert nil))))
+         "(nested) SPC Nested SPC Foo RET"
+         (org-roam-insert))))
    (expect (buffer-string) :to-match (regexp-quote "file:../../nested/foo.org"))))

-(describe "rename file updates cache"
+(xdescribe "rename file updates cache"
  (before-each
-    (org-roam-test-init)
-    (org-roam-db--clear)
-    (org-roam-db-build-cache))
+    (test-org-roam--init))
+
+  (after-each
+    (test-org-roam--teardown))

  (it "foo -> new_foo"
-    (rename-file (org-roam-test-abs-path "foo.org")
-                 (org-roam-test-abs-path "new_foo.org"))
+    (rename-file (test-org-roam--abs-path "foo.org")
+                 (test-org-roam--abs-path "new_foo.org"))
    ;; Cache should be cleared of old file
    (expect (caar (org-roam-db-query [:select (funcall count)
                                      :from titles
                                      :where (= file $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
    (expect (caar (org-roam-db-query [:select (funcall count)
                                      :from refs
                                      :where (= file $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
    (expect (caar (org-roam-db-query [:select (funcall count)
                                      :from links
                                      :where (= from $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)

    ;; Cache should be updated
    (expect (org-roam-db-query [:select [to]
                                :from links
                                :where (= from $s1)]
-                               (org-roam-test-abs-path "new_foo.org"))
+                               (test-org-roam--abs-path "new_foo.org"))
            :to-have-same-items-as
-            (list (list (org-roam-test-abs-path "bar.org"))))
+            (list (list (test-org-roam--abs-path "bar.org"))))
    (expect (org-roam-db-query [:select [from]
                                :from links
                                :where (= to $s1)]
-                               (org-roam-test-abs-path "new_foo.org"))
+                               (test-org-roam--abs-path "new_foo.org"))
            :to-have-same-items-as
-            (list (list (org-roam-test-abs-path "nested/bar.org"))))
+            (list (list (test-org-roam--abs-path "nested/bar.org"))))

    ;; Links are updated
    (expect (with-temp-buffer
-              (insert-file-contents (org-roam-test-abs-path "nested/bar.org"))
+              (insert-file-contents (test-org-roam--abs-path "nested/bar.org"))
              (buffer-string))
            :to-match
            (regexp-quote "[[file:../new_foo.org][Foo]]")))

  (it "foo -> foo with spaces"
-    (rename-file (org-roam-test-abs-path "foo.org")
-                 (org-roam-test-abs-path "foo with spaces.org"))
+    (rename-file (test-org-roam--abs-path "foo.org")
+                 (test-org-roam--abs-path "foo with spaces.org"))
    ;; Cache should be cleared of old file
    (expect (caar (org-roam-db-query [:select (funcall count)
                                      :from titles
                                      :where (= file $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
    (expect (caar (org-roam-db-query [:select (funcall count)
                                      :from refs
                                      :where (= file $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
    (expect (caar (org-roam-db-query [:select (funcall count)
                                      :from links
                                      :where (= from $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)

    ;; Cache should be updated
    (expect (org-roam-db-query [:select [to]
                                :from links
                                :where (= from $s1)]
-                               (org-roam-test-abs-path "foo with spaces.org"))
+                               (test-org-roam--abs-path "foo with spaces.org"))
            :to-have-same-items-as
-            (list (list (org-roam-test-abs-path "bar.org"))))
+            (list (list (test-org-roam--abs-path "bar.org"))))
    (expect (org-roam-db-query [:select [from]
                                :from links
                                :where (= to $s1)]
-                               (org-roam-test-abs-path "foo with spaces.org"))
+                               (test-org-roam--abs-path "foo with spaces.org"))
            :to-have-same-items-as
-            (list (list (org-roam-test-abs-path "nested/bar.org"))))
+            (list (list (test-org-roam--abs-path "nested/bar.org"))))

    ;; Links are updated
    (expect (with-temp-buffer
-              (insert-file-contents (org-roam-test-abs-path "nested/bar.org"))
+              (insert-file-contents (test-org-roam--abs-path "nested/bar.org"))
              (buffer-string))
            :to-match
            (regexp-quote "[[file:../foo with spaces.org][Foo]]")))

  (it "no-title -> meaningful-title"
-    (rename-file (org-roam-test-abs-path "no-title.org")
-                 (org-roam-test-abs-path "meaningful-title.org"))
+    (rename-file (test-org-roam--abs-path "no-title.org")
+                 (test-org-roam--abs-path "meaningful-title.org"))
    ;; File has no forward links
    (expect (caar (org-roam-db-query [:select (funcall count)
                                      :from links
                                      :where (= from $s1)]
-                                     (org-roam-test-abs-path "no-title.org"))) :to-be 0)
+                                     (test-org-roam--abs-path "no-title.org"))) :to-be 0)
    (expect (caar (org-roam-db-query [:select (funcall count)
                                      :from links
                                      :where (= from $s1)]
-                                     (org-roam-test-abs-path "meaningful-title.org"))) :to-be 1)
+                                     (test-org-roam--abs-path "meaningful-title.org"))) :to-be 1)

    ;; Links are updated with the appropriate name
    (expect (with-temp-buffer
-              (insert-file-contents (org-roam-test-abs-path "meaningful-title.org"))
+              (insert-file-contents (test-org-roam--abs-path "meaningful-title.org"))
              (buffer-string))
            :to-match
            (regexp-quote "[[file:meaningful-title.org][meaningful-title]]")))
@ -260,47 +418,47 @@
              :where (= ref $s1)]
             "https://google.com/")
            :to-equal
-            (list (list (org-roam-test-abs-path "web_ref.org"))))
-    (rename-file (org-roam-test-abs-path "web_ref.org")
-                 (org-roam-test-abs-path "hello.org"))
+            (list (list (test-org-roam--abs-path "web_ref.org"))))
+    (rename-file (test-org-roam--abs-path "web_ref.org")
+                 (test-org-roam--abs-path "hello.org"))
    (expect (org-roam-db-query
             [:select [file] :from refs
              :where (= ref $s1)]
             "https://google.com/")
-            :to-equal (list (list (org-roam-test-abs-path "hello.org"))))
+            :to-equal (list (list (test-org-roam--abs-path "hello.org"))))
    (expect (caar (org-roam-db-query
                   [:select [ref] :from refs
                    :where (= file $s1)]
-                   (org-roam-test-abs-path "web_ref.org")))
+                   (test-org-roam--abs-path "web_ref.org")))
            :to-equal nil)))

-(describe "delete file updates cache"
+(xdescribe "delete file updates cache"
  (before-each
-    (org-roam-test-init)
-    (org-roam-db--clear)
-    (org-roam-db-build-cache)
-    (sleep-for 1))
+    (test-org-roam--init))
+
+  (after-each
+    (test-org-roam--teardown))

  (it "delete foo"
-    (delete-file (org-roam-test-abs-path "foo.org"))
+    (delete-file (test-org-roam--abs-path "foo.org"))
    (expect (caar (org-roam-db-query [:select (funcall count)
                                      :from titles
                                      :where (= file $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
    (expect (caar (org-roam-db-query [:select (funcall count)
                                      :from refs
                                      :where (= file $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
    (expect (caar (org-roam-db-query [:select (funcall count)
                                      :from links
                                      :where (= from $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0))
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 0))

  (it "delete web_ref"
    (expect (org-roam-db-query [:select * :from refs])
            :to-have-same-items-as
-            (list (list "https://google.com/" (org-roam-test-abs-path "web_ref.org"))))
-    (delete-file (org-roam-test-abs-path "web_ref.org"))
+            (list (list "https://google.com/" (test-org-roam--abs-path "web_ref.org") "website")))
+    (delete-file (test-org-roam--abs-path "web_ref.org"))
    (expect (org-roam-db-query [:select * :from refs])
            :to-have-same-items-as
            (list))))
Author	SHA1	Message	Date
Jethro Kuan	cce2db8b5a	(release): v1.1.1 (#668 )	2020-05-18 22:04:51 +08:00
Jethro Kuan	2147adf95c	Create FUNDING.yml	2020-05-18 21:27:31 +08:00
Jethro Kuan	d2654f6023	(docs): add a nice default theme (#667 )	2020-05-18 19:15:12 +08:00
N V	78b518efd3	(fix): org-roam-capture--capture shadow org-capture-templates-contexts (#662 ) Lexically bind org-capture-templates-contexts to nil before calling org-capture with org-roam-capture-templates. Otherwise, contexts may shadow org-roam-templates which have same keys as org-capture-templates. mentioned in #651	2020-05-17 11:51:25 -04:00
N V	1b5e55b6c4	(fix): org-roam-capture allow creating new file (#661 ) Set title correctly when no match found in prompt's candidates. fixes #651	2020-05-17 11:36:15 -04:00
Jethro Kuan	4b45f1dbf5	(fix): fix link updating on file-renames (#660 ) Fixes #647: file: links are now updated to reflect the directory change. Also fixes #554: rename-files to directories are also resolved correctly now. Co-authored-by: Leo Vivier <leo.vivier+dev@gmail.com>	2020-05-17 18:51:52 +08:00
N V	e0aee184a7	(fix): prevent org-roam-version from loading org-roam-dev (#659 ) Instead of visiting file, insert library into temp buffer. Prevents loading .dir-local dev environment, accompanying unsafe-variable prompt. Prevents interference with org-roam.el if already open.	2020-05-17 03:41:40 -04:00
N V	eae97487dc	(internal): fix free variable reference (#658 ) Define org-roam-backlinks-mode before it is referenced.	2020-05-17 02:56:15 -04:00
N V	f5a9dfab9b	(fix): Require seq.el (#657 ) seq.el is is not guaranteed to be loaded otherwise.	2020-05-17 02:20:48 -04:00
N V	7844827757	(feature): org-roam-diagnostics command (#653 ) Automates collection of user environment information.	2020-05-17 01:57:38 -04:00
N V	74f12ee8aa	(internal): org-roam-version save-excursion (#656 ) Restore user's point in org-roam.el	2020-05-17 01:46:41 -04:00
N V	055669817a	(feature): org-roam-version command (#655 ) Useful for diagnostic information. Should be supplemented with finer grained info (commit hash would be ideal) once we figure out a more sophisticated approach.	2020-05-17 13:33:53 +08:00
N V	1fc08b4428	(internal): inline minor-mode keymaps (#654 ) define-minor-mode macro creates appropriate symbol/documentation for inlined keymaps.	2020-05-17 01:24:21 -04:00
N V	cfe3b19a73	(doc): bug_report.md request more info (#652 ) Request interactive commands for more build/version info. Request Org mode version.	2020-05-16 23:24:29 -04:00
Leo Vivier	1bc1559743	(fix): fix regression in find-ref (#650 ) Fixes #649.	2020-05-17 00:09:58 +02:00
Leo Vivier	265182a698	(fix): adapt find-ref to new format (#646 )	2020-05-16 14:03:37 +02:00
Jethro Kuan	4b4ebf76c7	(fix): fix parsing for ido (#645 ) This reverts commit `47763f49fd`, after #643 reverted completions from hash-table to alist.	2020-05-16 19:38:52 +08:00
Leo Vivier	3bc174a6f0	(fix): reimplement mtime sorting (#642 )	2020-05-16 19:32:23 +08:00
Jethro Kuan	8091f4598e	(internal): revert completions from hash table to alist (#643 ) Initially we thought that using hash-tables would shave some seconds because searching for a key is O(1), but when we present completions, we typically want them sorted, and hash-tables do not support sorted keys. Co-authored-by: Leo Vivier <leo.vivier+dev@gmail.com>	2020-05-16 18:17:37 +08:00
Leo Vivier	1267a43043	(fix): refactor get-ref-path-completions (#633 ) * (fix): refactor get-ref-path-completions * Remove leftover variable Co-authored-by: Jethro Kuan <jethrokuan95@gmail.com>	2020-05-16 08:40:41 +02:00
N V	8ff09b4b6d	(docs): Mention steps to provide backtrace in bug_report.md (#641 )	2020-05-15 22:54:37 -04:00
Leo Vivier	2499c7e220	(feat): add COMPLETIONS argument to insert and find-file (#637 ) Needed for smoother interaction with ORB. I’ve elected to keep FILTER-FN for the moment, even though it’s a bit redundant, and the description in the docstring is not correct with the addition of tags.	2020-05-16 01:29:18 +02:00
Leo Vivier	d816250614	(fix): move from alist to hash for find-ref (#640 )	2020-05-16 01:23:36 +02:00
p4v4n	47763f49fd	(fix): fix parsing of new hash-table for ido * Use hash-table-keys to extract titles for ido * Same change for helm	2020-05-16 01:01:35 +02:00
Leo Vivier	9961a22a8c	(fix): replace `if` with `when` (#632 )	2020-05-15 20:23:06 +08:00
Jethro Kuan	f390593cfb	(feat): Add a tagging system (#604 ) Tags are used as meta-data for files: they facilitate interactions with notes where titles are insufficient. For example, tags allow for categorization of notes: differentiating between bibliographical and structure notes during interactive commands. Co-authored-by: Leo Vivier <leo.vivier+dev@gmail.com> Co-authored-by: N V <44036031+progfolio@users.noreply.github.com>	2020-05-15 16:10:11 +08:00
N V	59c18c0e8c	(internal): org-roam-dev -> sentence-end-double-space nil (#629 ) Required by CI.	2020-05-15 13:11:19 +08:00
Allard Hendriksen	3df3b6519c	(doc): fix org-roam-buffer-no-delete-other-windows (#628 ) It appears the option has changed name, but this was not yet reflected in the documentation.	2020-05-14 22:52:27 +02:00
Jethro Kuan	b47b76aa41	(refactor): refactor title extraction (#625 ) Introduces '(org-roam-title-sources), which can be a list of lists. Each symbol corresponds to a function, that when called returns a list of titles. If the element is a list, use the first function in the list that returns a successful result.	2020-05-14 19:45:07 +08:00
Günter Zöchbauer	abb36d11ef	(docs): remove redundant word in docstring (#626 )	2020-05-14 19:04:59 +08:00
Jethro Kuan	e55a38530d	(fix): fix org-roam-doctor broken-link checker (#624 ) The checker originally returns reports of wrong format when there are no errors	2020-05-14 13:51:35 +08:00
Jethro Kuan	80bc19cbda	(docs): update manual location (#622 )	2020-05-13 20:19:31 +08:00
Jethro Kuan	85b3e488b2	(ci): fix	2020-05-13 19:56:06 +08:00
Jethro Kuan	5a9f765a49	(ci): move images to the correct location	2020-05-13 19:54:08 +08:00
Jethro Kuan	1c7c5b3b9b	(ci): add nojekyll to docs	2020-05-13 19:48:39 +08:00
Jethro Kuan	4266a81b51	(ci): build the correct folder, clean builds	2020-05-13 19:43:36 +08:00
Jethro Kuan	36940e1eef	Revert "(ci): deploy docs to docs branch" This reverts commit `176aac67e6`.	2020-05-13 19:39:12 +08:00
Jethro Kuan	176aac67e6	(ci): deploy docs to docs branch	2020-05-13 19:36:36 +08:00
Jethro Kuan	376ff71616	(ci): run doc build commands directly (#621 )	2020-05-13 19:35:48 +08:00
Jethro Kuan	232921b9a1	(docs): track landing page (#620 )	2020-05-13 19:26:37 +08:00
Jethro Kuan	9e2998c580	(ci): remove old docs, add landing page (#619 )	2020-05-13 19:24:17 +08:00
Jethro Kuan	e44b84b791	(ci): make multi-page manual (#618 )	2020-05-13 18:56:42 +08:00
Jethro Kuan	5e63bf32ed	(ci): makeinfo -> texinfo (#617 )	2020-05-13 18:49:18 +08:00
Jethro Kuan	e62bda799a	(docs): use gh actions to deploy documentation (#616 )	2020-05-13 18:45:32 +08:00
Jethro Kuan	46975107a2	(internal): remove assignment in issue templates (#615 )	2020-05-13 17:58:34 +08:00
N V	b388fd3db2	(refactor): org-roam-db--clear pull tables from schemata (#611 ) Programatically pull tables from schemata, rather than manually specifying each table.	2020-05-13 02:24:50 -04:00
N V	e0cefa7377	(refactor): org-roam-db--clear-file pull tables from schemata (#613 ) Programatically pull tables from schemata, rather than manually specifying.	2020-05-13 14:14:46 +08:00
N V	fca1777648	(internal): Summarize features (#608 ) * (internal): Summarize features Replace generic package description in features' first line summary. Co-authored-by: Leo Vivier <leo.vivier+dev@gmail.com>	2020-05-12 15:06:19 -04:00
N V	1722fae9af	(internal): org-roam-dev use directory-local variable (#607 ) Add .dir-locals.el to load org-roam-dev for all source files.	2020-05-12 13:46:12 -04:00
N V	3727f015cd	(internal): add org-roam-dev.el (#606 ) Help ensure source code consistency. emacsql indentation for now, but can easily be expanded as needed.	2020-05-13 01:21:54 +08:00
Jethro Kuan	a85205e7bc	(fix): Respect `org-roam-file-extensions` during file creation (#602 )	2020-05-12 19:08:00 +08:00
Leo Vivier	b4927abbd7	(fix): Enforce default for ‘org-roam-index-file’ (#599 )	2020-05-12 16:12:14 +08:00
N V	ad5fca5440	"Refactor org-roam-message as a function" (#595 ) * Refactor org-roam-message as a function Add to commentary that org-roam-macs may contain other utility functions (similar to org-macs). * Fix typos * Try again * Fix typo * fix syntax error * fix syntax error * Apply args correctly * Refactor with funcall * Revert "Refactor with funcall" This reverts commit `0807252d64`. Co-authored-by: Leo Vivier <leo.vivier+dev@gmail.com>	2020-05-10 23:17:55 +02:00
Jethro Kuan	3efe315ff1	(internal): add `org-roam-message` (#593 ) This macro simplifies message printing, so we can respect `org-roam-verbose` in more places. Also silences more messages when `org-roam-verbose` set to false.	2020-05-10 16:44:28 +08:00
Jethro Kuan	d68d1f8ebb	(feat): add `org-roam-doctor` (#570 ) `org-roam-doctor` provides a diagnostic tool for checking an Org-roam file for things that are broken. Currently implemented is a check for broken links, and methods to fix them. The checker is designed to be extensible.	2020-05-10 13:57:18 +08:00
Leo Vivier	c70f2d5f54	(fix): update repo root to group (#591 )	2020-05-10 13:48:16 +08:00
Günter Zöchbauer	d3206b797a	(docs): link to discourse in README (#577 ) Also, add information about Graphviz on the README. Co-authored-by: Jethro Kuan <jethrokuan95@gmail.com>	2020-05-09 19:54:05 +08:00
Leo Vivier	dee540b62f	(fix): do not store empty-string refs in db (#586 ) * (fix): do not store empty-string refs in db * Error when ROAM_KEY is empty * Handle nil Co-authored-by: Jethro Kuan <jethrokuan95@gmail.com>	2020-05-09 13:47:56 +02:00
Leo Vivier	46fd2a9a68	(fix): allow group templates in capture-templates (#584 ) Co-authored-by: N V <44036031+progfolio@users.noreply.github.com>	2020-05-09 18:08:08 +08:00
Leo Vivier	c1bfa99ace	(fix): make graph--build error on non-string (#580 ) * (fix): make graph--build error on non-string * Replace let* with let * Fix wording	2020-05-07 20:38:17 +02:00
Leo Vivier	9bc80ff9f7	(fix): improve error message on missing executable (#579 )	2020-05-08 01:44:28 +08:00
Jethro Kuan	1912beebc3	(docs): mention where to modify org-roam templates (#575 ) Addresses #573	2020-05-07 16:33:42 +08:00
Jethro Kuan	f8f7e6009c	(internal): add longer sleep time to tests (#574 )	2020-05-07 15:41:58 +08:00
Leo Vivier	689f559080	(doc): Add a gif for ORB (#571 )	2020-05-06 18:59:09 +08:00
Leo Vivier	3ca2d9f4ca	(doc): Improve wording 'A Preview' (#568 ) * (doc): Improve wording of the first paragraph Can’t believe nobody told us that we used ‘screenshot’ instead of ‘screencast’. :( * Fill to 72	2020-05-05 14:19:00 +08:00
Leo Vivier	cd0850f1c1	(feat): simplify format of `INFO` for find-ref and add `FILTER` (#567 ) * (feat): simplify format of `INFO` for find-ref The format of the `INFO` argument of `org-roam-find` has been simplified, thanks to the split of `type` and `ref` in the db permitted by #547. The non-interactive behaviour of `org-roam-find-ref` has also been isolated into `org-roam--find-ref`. Even if it makes us repeat ourselves a bit, it avoids having to nil the interactive argument just to get the non-interactive us, which I think is better syntax. * (feat): implement get-ref-path-completions filtering	2020-05-04 22:31:28 +02:00
Leo Vivier	11e15594cc	(feat): add custom face for invalid links (#564 ) * (feat): add custom face for links without destinations * Rename to ‘invalid’ * Update docstring * Remove ‘typically’	2020-05-04 15:47:27 +02:00
Jethro Kuan	f6e84caf72	(chore): inherit org-roam-link-current from org-link (#563 ) A better default for org-roam-link-current is the original org-link face, rather than org-block.	2020-05-04 20:58:12 +08:00
Göktuğ Karakaşlı	11d239d661	(feat): fix citation links not showing up in graph (#547 ) This change adds a `type` column to the refs column, and strips the prefix before storing the key in the `refs` table.	2020-05-04 20:44:15 +08:00
Jethro Kuan	7df50c14ec	(internal): make lint errors fail CI, and disable spellcheck during linting (#561 ) - make lint errors fail CI - disable indentation linting - disable package linting for org-roam-macs.el - disable spellcheck for checkdoc - fixes compilation errors	2020-05-04 15:17:39 +08:00
Jethro Kuan	a723199d68	(feat): apply error face if file link is broken (#560 )	2020-05-04 12:57:43 +08:00
N V	1bbfb0cdc9	(ehancement): Improve org-roam-graph (#559 ) Allow showing/building the whole graph from any buffer. Allow programatically specifying connected component path.	2020-05-03 18:03:02 -04:00
Jethro Kuan	69d4f05a13	(feat): add prefix argument to force database rebuild (#553 ) * (feat): add prefix argument to force database rebuild * Update changelog	2020-05-03 18:40:32 +08:00
Jethro Kuan	4cad2cf6e6	(internal): use Make and Org to build manual (#546 )	2020-05-03 18:06:27 +08:00
Tim Quelch	e698ed7f53	Generate cite backlinks using all org ref cite types (#551 ) This would fail on pathological cases where the key itself contains other prefixes e.g. if the key is `cite:parencite:autocite:key`. Although this is unlikely... To use org-ref-cite-types, we must ensure that org-ref is loaded. This would likely already be done otherwise as the user is obviously using cite links.	2020-05-02 18:50:11 +08:00
Jethro Kuan	0132546e56	Create stale.yml	2020-05-01 20:16:57 +08:00
Mykhailo Shevchuk	a8e2544435	graph: add an option of wrapping the title (#542 ) Co-authored-by: Jethro Kuan <jethrokuan95@gmail.com>	2020-05-01 19:49:46 +08:00
Tim Quelch	1ad3539c54	(fix): ensure that multicite links are correctly split (#545 ) * Ensure that multicite links are correctly split org-ref multi-citations are handled by "cite:key1,key2". In the org-roam databases this was previously stored as a single "cite" link to the (non-existing) key "key1,key2". This means that cite backlinks and cite graph behaviour does not work correctly for these links. This fix will split any cite links with a comma into separate links to each individual ref * Refactor with ->> * Refactor to use org-ref-split-and-strip-string instead * Update changelog with #545 * (fix): optimize processing * (fix): avoid repetition Co-authored-by: Leo Vivier <leo.vivier+dev@gmail.com>	2020-05-01 11:57:28 +02:00
Leo Vivier	5b773b687b	(doc): add key-binding for index in default configs (#543 ) * (doc): add key-binding for index in default configs * (fix): rename org-roam-find-index to -jump-to-index	2020-05-01 09:07:37 +02:00
Leo Vivier	08aa5c630d	(feat): reintroduce org-roam-link-current face (#516 )	2020-04-30 20:20:33 +08:00
Leo Vivier	e05ee1240d	(feat) cond display relative subdir in title for selection (#427 ) * (feat) cond display relative subdir in title for selection A title can now be constructed as ‘subdir/file-title’ where ‘subdir’ is the sub-directory relative from ‘org-roam-directory’. When ‘org-roam-title-include-subdirs’ is non-nil, ‘org-roam--extract-titles’ now outputs titles in this format. * (fix) improve docstrings * (feat) add var for modifying subdir-separator * (fix) nitpick docstring * (doc) document subdir creation in templates with :file-name * (feat) make subdir-format accept a function * (fix) respect docstring one-line-description * (fix) address checkdoc errors * (fix) also add subdirs when db--update-titles * (feat) improve modularisation `org-roam--extract-titles' is now reverted to its default definition, i.e. it doesn’t format the titles. In its stead, `org-roam--extract-and-format-titles' is created to both extract the titles and process all of them with `org-roam--format-title', which is a much better way to do this. * Refactor with ->> * Refactor with let* Pretty sure I got confused because I thought I needed to use the result of the db-queryr. * Remove useless ->>	2020-04-30 13:13:19 +02:00
Jethro Kuan	65d99e998c	(feat): prettier graph defaults (#541 ) Use settings provided by @tecosaur. Closes #539.	2020-04-30 13:56:54 +08:00
Leo Vivier	ea3f5d00a0	(feat) expand rel-links upon extraction (#520 )	2020-04-30 13:44:45 +08:00
Jethro Kuan	7680663205	(feat): optionally use headline as title (#538 ) Optionally pulls title from the first headline in Org file. Closes #506.	2020-04-29 12:42:55 +08:00
Leo Vivier	d0819aeffb	(feat) implement org-roam-find-index (#513 )	2020-04-29 12:08:42 +08:00
Jethro Kuan	bd4b9d41e8	(bugfix): quote graphviz configuration options (#537 ) Always quote graphviz configuration options. This allows passing configurations with spaces. Fixes #535.	2020-04-29 11:30:39 +08:00
Leo Vivier	4142300501	(internal): refactor org-roam--pluralize (#525 )	2020-04-26 19:07:19 +08:00
Jethro Kuan	487025aa2f	(chore): remove org-roam-completion-fuzzy-match (#523 ) Remove the fuzzy matching variable introduced in #289. The rationale is addressed in https://github.com/jethrokuan/org-roam/issues/514#issuecomment-619438401: Helm, Ido and Ivy have their own mechanisms for fuzzy search, and can be tweaked using their own configuration options outside of org-roam, e.g. through `ivy-re-builders-alist`.	2020-04-26 18:32:27 +08:00
Leo Vivier	bd3c97bb30	(feat) conditionally pluralize heading in org-roam-buffer (#521 )	2020-04-26 17:51:32 +08:00
Jethro Kuan	265a3054be	(fix): resolve symlinks during cache build (#524 ) Fixes #518.	2020-04-26 17:42:57 +08:00
Michael Glaesemann	8bb2465e61	(docs): update reference to Roam Protocol documentation (#519 ) Co-authored-by: Jethro Kuan <jethrokuan95@gmail.com>	2020-04-26 17:29:21 +08:00
Rafael Accácio Nogueira	c3a5544da9	(docs): add docs for qutebrowser keybindings (#512 )	2020-04-26 17:23:11 +08:00
Jürgen Hötzel	963692f353	(bugfix): Fix invalid usage of error handler (#511 ) The error handler was never invoked when executing `org-roam-graph-viewer` failed	2020-04-25 18:53:09 +08:00
Jethro Kuan	d01f7b2daf	(bugfix): fix inserting backup files into database (#509 ) In #470, the `and` clause was removed, so `org-roam--org-roam-file-p` returns `t` on `foo.org~` backup files. This PR adds that back in. In addition, the `after-save-hook` function was not checking for whether the file was within the org-roam system, which meant files from outside `org-roam` would also be added into the database. This PR adds a guard clause.	2020-04-22 14:35:47 +08:00
Leo Vivier	8a99febd0b	(fix): lowercase username in url to org-roam-bibtex (#505 )	2020-04-22 14:28:30 +08:00
Josh English	b5786edb30	(docs): Fix org-roam-protocol JS Bookmarklet (#508 )	2020-04-22 13:57:12 +08:00
Jethro Kuan	dce8c47d6e	(docs): mention org-roam-bibtex (#503 )	2020-04-21 20:55:12 +08:00