Fix link replacement optimization

We are searching for a string literal for speed, so don’t treat it as a
regexp.

Fixes: fc8638759b ("feat: Limit link replacement scope")
Fixes: #2529

.dir-locals.el

@@ -4,6 +4,9 @@
   (elisp-lint-ignored-validators . ("byte-compile" "package-lint"))
   (elisp-lint-indent-specs . ((describe . 1)
                               (it . 1)
+                              (thread-first . 0)
+                              (cl-flet . 1)
+                              (cl-flet* . 1)
                               (org-element-map . defun)
                               (org-roam-dolist-with-progress . 2)
                               (org-roam-with-temp-buffer . 1)

.github/FUNDING.yml

@@ -1,6 +1,6 @@
 # These are supported funding model platforms
 
-github: [jethrokuan, zaeph]
+github: [jethrokuan]
 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

.github/ISSUE_TEMPLATE/bug_report.md

@@ -39,5 +39,3 @@ Example:
 ### Environment
 
 <!-- Please M-x org-roam-diagnostics and paste results here -->
-
-- Org-roam commit: https://github.com/jethrokuan/org-roam/commit/commithashhere

.github/workflows/docs.yml

@@ -4,7 +4,7 @@ name: "Docs"
 on:
   push:
     branches:
-      - master
+      - main
 
 jobs:
   build:

.github/workflows/test.yml

@@ -28,7 +28,7 @@ on:
   pull_request:
   push:
     branches:
-      - master
+      - main
 
 jobs:
   build:
@@ -36,7 +36,11 @@ jobs:
     strategy:
       matrix:
         emacs_version:
-          - 27.1
+          # REVIEW: we do not yet have the bootstrapping in place to test
+          #         versions of emacs without built-in sqlite (pre 29.1)
+          # - 27.2
+          # - 28.2
+          - 29.4
           - snapshot
     steps:
       - uses: purcell/setup-emacs@master
@@ -46,7 +50,7 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Install Eldev
-        run: curl -fsSL https://raw.github.com/doublep/eldev/master/webinstall/github-eldev | sh
+        run: curl -fsSL https://raw.github.com/org-roam/org-roam/master/github-eldev | sh
 
       - name: Install dependencies
         run: make prepare

.github/workflows/tidy-issues.yml

@@ -0,0 +1,93 @@
+name: 'Manage stale/dormant issues and PRs'
+
+on:
+  schedule:
+    - cron: '0 1 * * *'  # Daily at 1 AM UTC
+  workflow_dispatch:  # Allow this to be run manually
+    inputs:
+      dry_run:
+        description: 'Dry run: Show what would happen without making changes'
+        required: false
+        default: 'false'
+        type: boolean
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    steps:
+      # Handle stale issues/PRs
+      - name: Mark/close stale issues and PRs
+        uses: actions/stale@v9
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+          # Dry run setting
+          debug-only: ${{ github.event.inputs.dry_run == 'true' }}
+
+          # Messages
+          stale-issue-message: |
+            📅 **Stale Issue Notice**
+
+            This issue has been automatically marked as stale because it has not had recent activity for **6 months**.
+
+            **⏰ This issue will be closed in 2 weeks** if no further activity occurs.
+
+            **To keep this issue open:**
+            - Comment on this issue
+            - Reference it in a commit or PR
+            - Add new information or updates
+
+            Thank you for your contributions to org-roam! 🙏
+
+          close-issue-message: |
+            🔒 **Issue Automatically Closed**
+
+            This issue was automatically closed due to **6 months of inactivity** followed by 2 weeks notice.
+
+            **To reopen:**
+            - If still relevant, comment below and we'll reopen
+            - Or create a new issue with updated information
+
+            If this issue is not reopened in 2 weeks, it will be locked.
+            
+            This helps keep our issue tracker focused and manageable.
+
+          stale-pr-message: |
+            📅 **Stale Pull Request Notice**
+
+            This pull request has been automatically marked as stale because it has not had recent activity for **6 months**.
+
+            **⏰ This PR will be closed in 2 weeks** if no further activity occurs.
+
+            **To keep this PR open:**
+            - Push new commits
+            - Comment with updates
+            - Rebase on latest main branch
+
+            Thank you for your contributions to org-roam! 🙏
+
+          close-pr-message: |
+            🔒 **Pull Request Automatically Closed**
+
+            This pull request was automatically closed due to **6 months of inactivity** followed by 2 weeks notice.
+
+          # Timing (6 months + 2 weeks)
+          days-before-stale: 182  # ~6 months
+          days-before-close: 14   # 2 weeks notice
+
+          # Performance
+          operations-per-run: 1000
+
+      # Show dry run summary
+      - name: Dry run summary
+        if: github.event.inputs.dry_run == 'true'
+        run: |
+          echo "🧪 DRY RUN COMPLETED"
+          echo "This was a dry run - no actual changes were made."
+          echo "Check the action logs above to see what would have happened."
+          echo ""
+          echo "To run for real:"
+          echo "1. Go to Actions tab"
+          echo "2. Click 'Run workflow'"
+          echo "3. Leave 'Dry run mode' unchecked"
+          echo "4. Click 'Run workflow'"

CHANGELOG.md

@@ -1,6 +1,147 @@
 # Changelog
 
-## 2.2.0
+## 2.3.1 (2025-06-26)
+
+* (fix): Use correct type specifications to suppress warnings by @okomestudio in https://github.com/org-roam/org-roam/pull/2522
+* perf: suppress extra org features in the temp buffer by @dustinfarris in https://github.com/org-roam/org-roam/pull/2524
+
+## 2.3.0 (2025-05-24)
+
+* (perf)node-read: filter before map to candidate by @russmatney in https://github.com/org-roam/org-roam/pull/2168
+* (chore): remove extraneous changelog line by @jethrokuan in https://github.com/org-roam/org-roam/pull/2172
+* (fix)org-roam-file-p: don't exclude org-roam-directory by @toregilhk in https://github.com/org-roam/org-roam/pull/2178
+* (chore) fix version numbers by @jethrokuan in https://github.com/org-roam/org-roam/pull/2182
+* (fix) org-roam-file-p handle opening a buffer with no path by @jethrokuan in https://github.com/org-roam/org-roam/pull/2185
+* (fix)db: update atime on file access by @jethrokuan in https://github.com/org-roam/org-roam/pull/2174
+* Fix org-roam-extract-subtree by @ralfdoering in https://github.com/org-roam/org-roam/pull/2191
+* (node): fix org-roam-node-at-point check by @jethrokuan in https://github.com/org-roam/org-roam/pull/2195
+* (chore): reapply #2178 by @jethrokuan in https://github.com/org-roam/org-roam/pull/2197
+* Solved issue #2192 (Respect blank lines in capture templates) by @alopezrivera in https://github.com/org-roam/org-roam/pull/2203
+* (chore)ci: /s/master/main by @jethrokuan in https://github.com/org-roam/org-roam/pull/2204
+* support custom minibuffer matching function by @cuttlefisch in https://github.com/org-roam/org-roam/pull/2177
+* (db)fix: org-roam-db-connector group by @jethrokuan in https://github.com/org-roam/org-roam/pull/2209
+* ensure unique candidates in `org-roam-ref-find` by @bdarcus in https://github.com/org-roam/org-roam/pull/2208
+* (db)fix: FOREIGN KEY error in narrowed buffer by @psii in https://github.com/org-roam/org-roam/pull/2215
+* (feat): org-roam-property-* code duplication removed (#2217) by @clanghans in https://github.com/org-roam/org-roam/pull/2218
+* (db)fix: file modification detection failing in some edge cases by @kisaragi-hiu in https://github.com/org-roam/org-roam/pull/2221
+* (fix): autoload org-roam-list-files by @jethrokuan in https://github.com/org-roam/org-roam/pull/2226
+* (fix): links not displayed properly in org-roam-buffer by @ntharim in https://github.com/org-roam/org-roam/pull/2236
+* (fix): remove use of deprecated org-font-lock-ensure by @jethrokuan in https://github.com/org-roam/org-roam/pull/2238
+* was missing the FULL parameter to `org-end-of-meta-data` - fixes #2242 by @jmay in https://github.com/org-roam/org-roam/pull/2246
+* (Docs): Fixed typos in the docs by @hnvy in https://github.com/org-roam/org-roam/pull/2256
+* Fix space chars in roam refs by @hwiorn in https://github.com/org-roam/org-roam/pull/2285
+* org-roam-tag-add: use tags separator as crm-separator by @Hugo-Heagren in https://github.com/org-roam/org-roam/pull/2282
+* Support multi-line org titles by @FelixBrendel in https://github.com/org-roam/org-roam/pull/2264
+* (Docs): orgmode.org/elpa has been shut down by @aviad in https://github.com/org-roam/org-roam/pull/2258
+* Minor typo in the commented text of the definition of `org-roam-refile` by @apc in https://github.com/org-roam/org-roam/pull/2263
+* fix outline of link in properties by @bhuztez in https://github.com/org-roam/org-roam/pull/2230
+* (fix): update `org-roam-unlinked-references-section` check by @Elilif in https://github.com/org-roam/org-roam/pull/2254
+* Add support for filtering backlinks. by @swflint in https://github.com/org-roam/org-roam/pull/2247
+* (docs): update documentation on database-connectors by @jethrokuan in https://github.com/org-roam/org-roam/pull/2298
+* (db): default to sqlite-builtin when possible by @jethrokuan in https://github.com/org-roam/org-roam/pull/2299
+* don't complete org-roam nodes in source blocks by @ParetoOptimalDev in https://github.com/org-roam/org-roam/pull/2292
+* (core): add org-roam-node-category by @jethrokuan in https://github.com/org-roam/org-roam/pull/2300
+* add discoverability support for age encrypted org files by @anticomputer in https://github.com/org-roam/org-roam/pull/2302
+* (minor): fix lints on main by @jethrokuan in https://github.com/org-roam/org-roam/pull/2320
+* utils: descendant-of-p: Defend against nils by @qzdl in https://github.com/org-roam/org-roam/pull/2319
+* Add customisable function for prompting when adding refs by @Hugo-Heagren in https://github.com/org-roam/org-roam/pull/2317
+* Fix org-fold-core-style in org-roam-buffer by @hwiorn in https://github.com/org-roam/org-roam/pull/2325
+* depend on snapshot of emacsql by @jethrokuan in https://github.com/org-roam/org-roam/pull/2327
+* (node): org-roam-node-at-point: don't error in non-org buffers by @Hugo-Heagren in https://github.com/org-roam/org-roam/pull/2329
+* (node) add optional NOCASE parameter to org-roam-node-from-title-or-alias by @nuthub in https://github.com/org-roam/org-roam/pull/2403
+* (docs): update org-protocol instructions by @benthamite in https://github.com/org-roam/org-roam/pull/2401
+* Fix some typos by @feltcat in https://github.com/org-roam/org-roam/pull/2430
+* (docs): fix name of my-org-roam-show-backlink-p by @Delapouite in https://github.com/org-roam/org-roam/pull/2447
+* Link Martin Edström's knowledge base by @meedstrom in https://github.com/org-roam/org-roam/pull/2394
+* Update org-roam.org by @marcosbodio in https://github.com/org-roam/org-roam/pull/2441
+* (chore): fix indent blocking ci lint execution by @Delapouite in https://github.com/org-roam/org-roam/pull/2448
+* Fix Issue #2410 - Unlinked References doesnt work if the org-roam-directory has a space in it.  by @vikram-mandyam in https://github.com/org-roam/org-roam/pull/2411
+* (test): add "org-roam--list-files-search-globs" by @Delapouite in https://github.com/org-roam/org-roam/pull/2449
+* Backlink heading by @toregilhk in https://github.com/org-roam/org-roam/pull/2333
+* (test): add org-roam-id-find by @Delapouite in https://github.com/org-roam/org-roam/pull/2450
+* (test): add org-roam-id-at-point by @Delapouite in https://github.com/org-roam/org-roam/pull/2451
+* (test): add org-roam--buffer-promoteable-p by @Delapouite in https://github.com/org-roam/org-roam/pull/2452
+* (test): add org-roam--get-titles by @Delapouite in https://github.com/org-roam/org-roam/pull/2453
+* (test): add org-roam-node-from-{id|title-or-alias} by @Delapouite in https://github.com/org-roam/org-roam/pull/2454
+* (test): add org-roam-alias-{add|remove} by @Delapouite in https://github.com/org-roam/org-roam/pull/2455
+* (docs): add missing versions dates and obsolete notice by @Delapouite in https://github.com/org-roam/org-roam/pull/2456
+* (docs): explain org-roam-file-exclude-regexp by @adamoudad in https://github.com/org-roam/org-roam/pull/2458
+* (test): add org-roam-demote-entire-buffer by @Delapouite in https://github.com/org-roam/org-roam/pull/2459
+* (test): add org-roam-file-p by @Delapouite in https://github.com/org-roam/org-roam/pull/2460
+* (test): add org-roam-buffer-p by @Delapouite in https://github.com/org-roam/org-roam/pull/2461
+* (fix): remove dead-code about org-roam-shield feature by @Delapouite in https://github.com/org-roam/org-roam/pull/2462
+* (test): add org-roam-db--file-hash by @Delapouite in https://github.com/org-roam/org-roam/pull/2464
+* (test): add org-roam-db-get-{scheduled|deadline}-time by @Delapouite in https://github.com/org-roam/org-roam/pull/2465
+* Doc formatting: 2 fixes by @kevinrineer in https://github.com/org-roam/org-roam/pull/2475
+* Take org-roam-node as argument to #'org-roam-refile by @pestctrl in https://github.com/org-roam/org-roam/pull/2388
+* Compatibility with latest org-id version: advise org-id-find rather than overwriting id link by @ricklupton in https://github.com/org-roam/org-roam/pull/2432
+* Depend on emacsql 4.0.0 by @bcc32 in https://github.com/org-roam/org-roam/pull/2466
+* Use regexp match to replace hard-coded path equal test by @manphiz in https://github.com/org-roam/org-roam/pull/2497
+* Align sqlite integration with emacsql 4.0 by @dustinfarris in https://github.com/org-roam/org-roam/pull/2503
+* fix #2425 Prevent data loss when user has called org-roam-extract-subtree on folded org headline by @akashpal-21 in https://github.com/org-roam/org-roam/pull/2444
+* Rely on emacsql-sqlite-open to pick the best available back-end by @tarsius in https://github.com/org-roam/org-roam/pull/2486
+* Set org-roam-directory to a non-existent path to ensure robust test by @manphiz in https://github.com/org-roam/org-roam/pull/2499
+* (perf): Deprecate link :outline properties by @meedstrom in https://github.com/org-roam/org-roam/pull/2509
+* Bump DB version to avoid error by @meedstrom in https://github.com/org-roam/org-roam/pull/2514
+
+
+## 2.2.2 (2022-04-25)
+
+### Breaking
+### Added
+- [#2138](https://github.com/org-roam/org-roam/pull/2138) export: add new module
+- [#2170](https://github.com/org-roam/org-roam/pull/2170) log: add new module for working with org logs
+- [#2158](https://github.com/org-roam/org-roam/pull/2158) db: support emacsql-sqlite-builtin and emacsql-sqlite-module
+- [#2160](https://github.com/org-roam/org-roam/pull/2160) core: support a list of `org-roam-file-exclude-regexp`
+
+### Removed
+### Fixed
+- [#2091](https://github.com/org-roam/org-roam/pull/2091) node: fix org-roam-promote-entire-buffer structural errors
+- [#2130](https://github.com/org-roam/org-roam/pull/2130) buffer: unlinked-references section now also searches within symlinked directories
+- [#2152](https://github.com/org-roam/org-roam/pull/2152) org-roam-preview-default-function: doesn't copy copy content of next heading node when current node's content is empty
+- [#2159](https://github.com/org-roam/org-roam/pull/2159) db: fix db syncs on narrowed buffers
+- [#2156](https://github.com/org-roam/org-roam/pull/2157) capture: templates with functions are handled correctly to avoid signaling `char-or-string-p`
+
+### Changed
+- [#2160](https://github.com/org-roam/org-roam/pull/2160) core: ignore files in `org-attach-id-dir` by default
+
+## 2.2.1 (2022-03-15)
+
+### Breaking
+- [#2054](https://github.com/org-roam/org-roam/pull/2054) node: simplify default `org-roam-node-display-template`.
+  This was done so completions work fine by default on all completion systems. To restore the tabular vertical completion interface, set this in your configuration:
+
+  ```emacs-lisp
+  (setq org-roam-node-display-template
+        (concat "${title:*} "
+                (propertize "${tags:10}" 'face 'org-tag)))
+  ```
+
+### Added
+- [#2042](https://github.com/org-roam/org-roam/pull/2042) db: add `org-roam-db-extra-links-elements` and `org-roam-db-extra-links-exclude-keys` for fine-grained control over additional link parsing
+- [#2049](https://github.com/org-roam/org-roam/pull/2049) capture: allow ID to be used as part of `org-roam-capture-templates`
+- [#2050](https://github.com/org-roam/org-roam/pull/2050) core: add `FILTER-FN` to `org-roam-node-random`
+- [#2065](https://github.com/org-roam/org-roam/pull/2065) dailies: add `keys` argument to the remaining dailies functions `org-roam-dailies-goto-yesterday`/`-today`/`-tomorrow`/`-date` and `org-roam-dailies-capture-yesterday`/`-tomorrow`/`-date` to give the abilty to get into a capture buffer bypassing the selection screen in all dailies commands. Extension of #2055
+- [#2079](https://github.com/org-roam/org-roam/pull/2079) capture: ensure that `:ref` info captured in all cases.
+- [#2121](https://github.com/org-roam/org-roam/pull/2121) buffer: add unique option to `org-roam-backlinks-section`
+
+### Removed
+### Fixed
+- [#2086](https://github.com/org-roam/org-roam/pull/2086) capture: correctly update org-id-locations on capture
+- [#2082](https://github.com/org-roam/org-roam/pull/2082) buffer: don't destroy window if `org-roam-node-toggle` reuses window
+- [#2080](https://github.com/org-roam/org-roam/pull/2080) dailies: prevent multiple "dailies/" subdir expansions
+- [#2055](https://github.com/org-roam/org-roam/pull/2055) dailies: removed stray f require, which was causing require and compilation errors
+- [#2117](https://github.com/org-roam/org-roam/pull/2117) capture: preserve trailing whitespace content in capture templates
+
+### Changed
+- [#2060](https://github.com/org-roam/org-roam/pull/2060) node: added double acute accent normalization for Unicode characters in titles
+- [#2040](https://github.com/org-roam/org-roam/pull/2040) completions: fix completions display-width for Helm users
+- [#2025](https://github.com/org-roam/org-roam/pull/2025) chore: removed the dependencies on f.el and s.el
+- [#2109](https://github.com/org-roam/org-roam/pull/2109) capture: `org-roam-node-insert` places cursor after inserted link where appropriate
+- [#2123](https://github.com/org-roam/org-roam/pull/2123), [#2124](https://github.com/org-roam/org-roam/pull/2124) buffer: `org-roam-mode-section-functions` renamed to `org-roam-mode-sections`, supports passing args into the section-rendering function
+
+## 2.2.0 (2022-01-14)
+
 ### Added
 - [#1806](https://github.com/org-roam/org-roam/pull/1806), [#2017](https://github.com/org-roam/org-roam/pull/2017) db: support caching and usage of Org 9.5's in-built citations
 - [#1963](https://github.com/org-roam/org-roam/pull/1963) db: cache file title into files table
@@ -31,7 +172,8 @@
 - [#2016](https://github.com/org-roam/org-roam/pull/2016) db: fix node caching being affected by agenda variables
 - [#2033](https://github.com/org-roam/org-roam/pull/2023) db: respect local variables during db parsing
 
-## 2.1.0
+## 2.1.0 (2021-08-20)
+
 ### Added
 - [#1693](https://github.com/org-roam/org-roam/pull/1693) added `filter-fn` and `templates` parameter to `org-roam-capture`, `org-roam-node-find`, and `org-roam-node-insert`
 - [#1709](https://github.com/org-roam/org-roam/pull/1709) added ability to specify default value in org-roam capture templates
@@ -61,7 +203,10 @@
 - [#1713](https://github.com/org-roam/org-roam/pull/1713) capture: check for file-existence before template insertion
 - [#1725](https://github.com/org-roam/org-roam/pull/1725) db: always compute hash of encrypted file to prevent re-processing of encrypted files
 
-## 2.0.0
+## 2.0.0 (2021-07-17)
+
+A few symbols have been marked as obsolete. Have a look at the content of [org-roam-compat.el](https://github.com/org-roam/org-roam/blob/f819720c510185af713522c592833ec9f2934251/org-roam-compat.el#L159)
+
 ### Added
 - [#1396](https://github.com/org-roam/org-roam/pull/1396) add option to choose between prepending, appending, and omitting `roam_tags` in file completion
 - [#1270](https://github.com/org-roam/org-roam/pull/1270) capture: create OLP if it does not exist. Removes need for OLP setup in `:head`.
@@ -88,7 +233,7 @@
 - [#1409](https://github.com/org-roam/org-roam/issues/1398) prevent inclusion of non-org-roam files in `org-roam-dailies--list-files`
 - [#1542](https://github.com/org-roam/org-roam/issues/1542) fix files not excluded when `org-roam-list-files-commands` is nil
 
-## 1.2.3 (13-11-2020)
+## 1.2.3 (2020-11-13)
 
 Primarily a stabilization and bug-fix release.
 
@@ -119,7 +264,7 @@ Org-roam-dailies has also been revamped to include new features, see [this video
 - [#1233](https://github.com/org-roam/org-roam/issues/1233) fixes bug where descriptive file links become plain links during update for relative paths
 - [#1252](https://github.com/org-roam/org-roam/issues/1252) respect original link type during automatic replacement
 
-## 1.2.2 (06-10-2020)
+## 1.2.2 (2020-10-06)
 
 In this release we support fuzzy links of the form `[[roam:Title]]`, `[[roam:*Headline]]` and `[[roam:Title*Headline]]`. Completion for these fuzzy links is supported via `completion-at-point`.
 
@@ -157,7 +302,7 @@ This change requires you to set `org-roam-directory` to the resolved path of a f
 - [#1057](https://github.com/org-roam/org-roam/pull/1057) Improve performance of database builds by preventing generation of LaTeX and image previews.
 - [#1103](https://github.com/org-roam/org-roam/pull/1103) Fix long build-times for Windows on files with URL links
 
-## 1.2.1 (27-07-2020)
+## 1.2.1 (2020-07-27)
 
 This release consisted of a big deal of refactoring and bug fixes. Notably, we fixed several catastrophic failures on db builds with bad setups (#854), and modularized tag and title extractions.
 
@@ -190,7 +335,7 @@ We also added some new features that had been a long time coming:
 - [#894](https://github.com/org-roam/org-roam/pull/894) Perform link fixes on all Org-roam files
 - [#952](https://github.com/org-roam/org-roam/pull/952) Cache `${foo}` template variables so they do not need to be re-entered twice
 
-## 1.2.0 (12-06-2020)
+## 1.2.0 (2020-06-12)
 
 In this release, we improved the linking process by achieving feature parity between links to files and links to headlines. Before, we used the `file:foo::*bar` format to link to the headline `bar` in file `foo`, but this was prone to breakage upon renaming the file or modifying the headline. This is not the case anymore. Now, we use `org-id` to create IDs for those headlines, which are then stored in our database to compute the relationships and jump around. Note that this will work even if you’re not using `org-id` in your global configuration for Org-mode.
 
@@ -218,7 +363,7 @@ We also add `org-roam-unlinked-references`, which naively finds text that could
 - [#759](https://github.com/org-roam/org-roam/pull/759), [#760](https://github.com/org-roam/org-roam/pull/760) Tags are only added to the tags table if there are actually tags present
 - [#700](https://github.com/org-roam/org-roam/pull/700), [#733](https://github.com/org-roam/org-roam/pull/733) Allow symlinks within the `org-roam` directory
 
-## 1.1.1 (18-05-2020)
+## 1.1.1 (2020-05-18)
 
 In this release, we added two new features:
 
@@ -258,7 +403,7 @@ As usual, this release comes with a multitude of bug-fixes and refactorings.
 - [#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)
+## 1.1.0 (2020-04-21)
 
 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:
 
@@ -296,7 +441,7 @@ In the coming months, you can expect work on bigger projects (e.g. revamping the
 - [#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)
+## 1.0.0 (2020-03-23)
 
 Org-roam is now on MELPA! We have squashed most of the bugs, and Org-roam has
 been stable for the most part.
@@ -315,7 +460,7 @@ been stable for the most part.
 - [#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)
+## 1.0.0-rc1 (2020-03-06)
 
 This is a pre-release before the push to MELPA. It contains large
 internal changes, with little user-facing changes. Most notably, the

README.md

@@ -47,30 +47,6 @@ Stable](https://stable.melpa.org/) using `package.el`:
 ```
 M-x package-install RET org-roam RET
 ```
-
-Here's a very basic sample for configuration of `org-roam` using `use-package`:
-
-```emacs-lisp
-(use-package org-roam
-  :ensure t
-  :custom
-  (org-roam-directory (file-truename "/path/to/org-files/"))
-  :bind (("C-c n l" . org-roam-buffer-toggle)
-         ("C-c n f" . org-roam-node-find)
-         ("C-c n g" . org-roam-graph)
-         ("C-c n i" . org-roam-node-insert)
-         ("C-c n c" . org-roam-capture)
-         ;; Dailies
-         ("C-c n j" . org-roam-dailies-capture-today))
-  :config
-  (org-roam-db-autosync-mode)
-  ;; If using org-roam-protocol
-  (require 'org-roam-protocol))
-```
-
-Note that the `file-truename` function is only necessary when you use symbolic
-link to `org-roam-directory`. Org-roam won't automatically resolve symbolic link
-to the directory.
 </details>
 
 ### Using `straight.el`
@@ -177,9 +153,8 @@ dependencies. These include:
 - dash
 - f
 - s
-- org (9.4 is the minimal required version!)
+- org (9.6 is the minimum required version!)
 - emacsql
-- emacsql-sqlite
 - magit-section
 - filenotify-recursive
 
@@ -198,6 +173,33 @@ Org-roam also comes with `.texi` files to integrate with Emacs' built-in Info
 system. Read the manual to find more details for how to install them manually.
 </details>
 
+## Configuration
+
+Here's a very basic sample for configuration of `org-roam` using `use-package`:
+
+```emacs-lisp
+(use-package org-roam
+  :ensure t
+  :custom
+  (org-roam-directory (file-truename "/path/to/org-files/"))
+  :bind (("C-c n l" . org-roam-buffer-toggle)
+         ("C-c n f" . org-roam-node-find)
+         ("C-c n g" . org-roam-graph)
+         ("C-c n i" . org-roam-node-insert)
+         ("C-c n c" . org-roam-capture)
+         ;; Dailies
+         ("C-c n j" . org-roam-dailies-capture-today))
+  :config
+  ;; If you're using a vertical completion framework, you might want a more informative completion interface
+  (setq org-roam-node-display-template (concat "${title:*} " (propertize "${tags:10}" 'face 'org-tag)))
+  (org-roam-db-autosync-mode)
+  ;; If using org-roam-protocol
+  (require 'org-roam-protocol))
+```
+
+Note that the `file-truename` function is only necessary when you use symbolic
+link to `org-roam-directory`. Org-roam won't automatically resolve symbolic link
+to the directory.
 ## Getting Started
 
 [David Wilson](https://github.com/daviwil) of [System
@@ -225,8 +227,9 @@ it has not already been addressed on [GitHub][issues] or on
 
 - [Jethro Kuan](https://braindump.jethro.dev/)
   ([Source](https://github.com/jethrokuan/braindump/tree/master/org))
-- [Alexey Shmalko](https://braindump.rasen.dev/)
+- [Alexey Shmalko](https://www.alexeyshmalko.com/)
 - [Sidharth Arya](https://sidhartharya.github.io/braindump/index.html)
+- [Martin Edström](https://edstrom.dev/)
 
 ## Contributing
 

doc/org-roam.org

@@ -1,23 +1,23 @@
 #+title: Org-roam User Manual
 #+author: Jethro Kuan
 #+email: jethrokuan95@gmail.com
-#+date: 2020-2022
+#+date: 2020-2025
 #+language: en
 
 #+texinfo_deffn: t
 #+texinfo_dir_category: Emacs
 #+texinfo_dir_title: Org-roam: (org-roam).
 #+texinfo_dir_desc: Roam Research for Emacs.
-#+subtitle: for version 2.2.0
+#+subtitle: for version 2.3.1
 
 #+options: H:4 num:3 toc:nil creator:t ':t
 #+property: header-args :eval never
 #+texinfo: @noindent
 
-This manual is for Org-roam version 2.2.0.
+This manual is for Org-roam version 2.3.1.
 
 #+BEGIN_QUOTE
-Copyright (C) 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+Copyright (C) 2020-2025 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
@@ -134,7 +134,7 @@ A slip-box requires a method for quickly capturing ideas. These are called
 *fleeting notes*: they are simple reminders of information or ideas that will
 need to be processed later on, or trashed. This is typically accomplished using
 ~org-capture~ (see info:org#Capture), or using Org-roam's daily notes
-functionality (see [[*Org-roam Dailies][Org-roam Dailies]]). This provides a central inbox for collecting
+functionality (see [[*org-roam-dailies][org-roam-dailies]]). This provides a central inbox for collecting
 thoughts, to be processed later into permanent notes.
 
 *Permanent notes*
@@ -178,18 +178,7 @@ archives to =package-archives=:
 #+END_SRC
 
 Org-roam also depends on a recent version of Org, which can be obtained in Org's
-package repository (see info:org#Installation). To use Org's ELPA archive:
-
-#+BEGIN_SRC emacs-lisp
-(add-to-list 'package-archives '("org" . "https://orgmode.org/elpa/") 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
+package repository (see info:org#Installation).
 
 Once you have done that, you can install Org-roam and its dependencies
 using:
@@ -235,7 +224,6 @@ dependencies that it requires. These include:
 - s
 - org
 - emacsql
-- emacsql-sqlite
 - magit-section
 
 You can install this manually as well, or get the latest version from MELPA. You
@@ -279,40 +267,6 @@ file:
 install-info /path/to/my/info/files/org-roam.info /path/to/my/info/files/dir
 #+end_src
 
-** Installation Troubleshooting
-*** C Compiler
-Org-roam relies on an Emacs package called ~emacsql~ and ~emacsql-sqlite~ to
-work with the ~sqlite~ database. Both of them should be installed automatically
-in your Emacs environment as a prerequisite for Org-roam when you install it.
-
-~emacsql-sqlite~ requires a C compiler (e.g. ~gcc~ or ~clang~) to be present in
-your computer. How to install a C compiler depends on the OS that you use.
-
-**** C Compiler for Windows
-
-One of the easiest ways to install a C compiler in Windows is to use [[https://www.msys2.org/][MSYS2]] as at the time of this writing:
-
-1. Download and use the installer in the official MSYS2 website
-2. Run MSYS2 and in its terminal, type the following and answer "Y" to
-   proceed -- this will install ~gcc~ in your PC:
-
-   #+BEGIN_SRC bash
-     pacman -S gcc
-   #+END_SRC
-
-4. On Windows, add ~C:\msys64\usr\bin~ (command =where gcc= in MSYS2 terminal
-   can tell you the correct path) to ~PATH~ in your environmental variables
-
-5. Launch Emacs and call ~M-x org-roam-db-autosync-mode~ (launch Emacs after
-   defining the path, so that Emacs can recognize it)
-
-This will automatically start compiling ~emacsql-sqlite~; you should see a
-message in minibuffer. It may take a while until compilation completes. Once
-complete, you should see a new file ~emacsql-sqlite.exe~ created in a subfolder
-named ~sqlite~ under ~emacsql-sqlite~ installation folder. It's typically in
-your Emacs configuration folder like this:
-~/.config/emacs/elpa/emacsql-sqlite-20190727.1710/sqlite~
-
 * Getting Started
 ** The Org-roam Node
 
@@ -369,7 +323,12 @@ For this tutorial, create an empty directory, and set ~org-roam-directory~:
 #+END_SRC
 
 The ~file-truename~ function is only necessary when you use symbolic links
-inside ~org-roam-directory~: Org-roam does not resolve symbolic links.
+inside ~org-roam-directory~: Org-roam does not resolve symbolic links. One can
+however instruct Emacs to always resolve symlinks, at a performance cost:
+
+#+begin_src emacs-lisp
+  (setq find-file-visit-truename t)
+#+end_src
 
 Next, we setup Org-roam to run functions on file changes to maintain cache
 consistency. This is achieved by running ~M-x org-roam-db-autosync-mode~. To
@@ -413,51 +372,58 @@ brought through the node creation process.
 One can also conveniently insert links via the completion-at-point functions
 Org-roam provides (see [[*Completion][Completion]]).
 
+** Customizing Node Completions
+
+Node selection is achieved via the ~completing-read~ interface, typically
+through ~org-roam-node-read~. The presentation of these nodes are governed by
+~org-roam-node-display-template~.
+
+- Variable: org-roam-node-display-template
+
+  Configures display formatting for Org-roam node.
+
+  Patterns of form "${field-name:length}" are interpolated based
+  on the current node.
+
+  Each "field-name" is replaced with the return value of each
+  corresponding accessor function for org-roam-node, e.g.
+  "${title}" will be interpolated by the result of
+  org-roam-node-title. You can also define custom accessors using
+  cl-defmethod. For example, you can define:
+
+    (cl-defmethod org-roam-node-my-title ((node org-roam-node))
+      (concat "My " (org-roam-node-title node)))
+
+  and then reference it here or in the capture templates as
+  "${my-title}".
+
+  "length" is an optional specifier and declares how many
+  characters can be used to display the value of the corresponding
+  field. If it's not specified, the field will be inserted as is,
+  i.e. it won't be aligned nor trimmed. If it's an integer, the
+  field will be aligned accordingly and all the exceeding
+  characters will be trimmed out. If it's "*", the field will use
+  as many characters as possible and will be aligned accordingly.
+
+  A closure can also be assigned to this variable in which case the
+  closure is evaluated and the return value is used as the
+  template. The closure must evaluate to a valid template string.
+
+If you're using a vertical completion framework, such as Ivy and Selectrum,
+Org-roam supports the generation of an aligned, tabular completion interface.
+For example, to include a column for tags up to 10 character widths wide, one
+can set ~org-roam-node-display-template~ as such:
+
+#+begin_src emacs-lisp
+  (setq org-roam-node-display-template
+        (concat "${title:*} "
+                (propertize "${tags:10}" 'face 'org-tag)))
+#+end_src
+
 * Customizing Node Caching
 ** How to cache
-
-Org-roam uses a sqlite database to perform caching, but there are multiple Emacs
-libraries that can be used. The default used by Org-roam is ~emacs-sqlite~.
-Below the pros and cons of each package is used:
-
-[[https://github.com/skeeto/emacsql][**emacs-sqlite**]]
-
-The default option used by Org-roam. This library is the most mature and
-well-supported and is imported by default in Org-roam.
-
-One downside of using ~emacs-sqlite~ is that using it requires compilation and
-can cause issues in some environments (especially Windows). If you have issues
-producing the customized binary required by ~emacs-sqlite~, consider using
-~emacs-sqlite3~.
-
-[[https://github.com/cireu/emacsql-sqlite3][**emacs-sqlite3**]]
-
-~emacs-sqlite3~ uses the official sqlite3 binary that can be obtained from your
-system's package manager. This is useful if you have issues producing the
-~sqlite3~ binary required by the other packages. However, it is not recommended
-because it has some compatibility issues with Emacs, but should work for most
-regular cases. See [[https://nullprogram.com/blog/2014/02/06/][Chris Wellon's blog post]] for more information.
-
-To use ~emacsql-sqlite3~, ensure that the package is installed, and set:
-
-#+begin_src emacs-lisp
-  (setq org-roam-database-connector 'sqlite3)
-#+end_src
-
-[[https://github.com/emacscollective/emacsql-libsqlite3/][**emacsql-libsqlite3**]]
-
-~emacs-libsqlite3~ is a relatively young package which uses an Emacs module that
-exposes parts of the SQLite C API to Emacs Lisp, instead of using subprocess as
-~emacsql-sqlite~ does. It is expected to be a more performant drop-in
-replacement for ~emacs-sqlite~.
-
-At the moment it is experimental and does not work well with the SQL query load
-required by Org-roam, but you may still try it by ensuring the package is
-installed and setting:
-
-#+begin_src emacs-lisp
-  (setq org-roam-database-connector 'libsqlite3)
-#+end_src
+Org-roam uses a SQLite database to perform caching.  This integration is
+managed by the [[https://github.com/magit/emacsql][emacsql]] library.  It should "just work".
 
 ** What to cache
 
@@ -479,12 +445,41 @@ property to a non-nil value. For example:
 One can also set ~org-roam-db-node-include-function~. For example, to exclude
 all headlines with the ~ATTACH~ tag from the Org-roam database, one can set:
 
-#+begin_src org
+#+begin_src emacs-lisp
 (setq org-roam-db-node-include-function
       (lambda ()
         (not (member "ATTACH" (org-get-tags)))))
 #+end_src
 
+Org-roam relied on the obtained Org AST for the buffer to parse links. However,
+links appearing in some places (e.g. within property drawers) are not considered
+by the Org AST to be links. Therefore, Org-roam takes special care of
+additionally trying to process these links. Use
+~org-roam-db-extra-links-elements~ to specify which additional Org AST element
+types to consider.
+
+- Variable: org-roam-db-extra-links-elements
+
+  The list of Org element types to include for parsing by Org-roam.
+
+  By default, when parsing Org's AST, links within keywords and
+  property drawers are not parsed as links. Sometimes however, it
+  is desirable to parse and cache these links (e.g. hiding links in
+  a property drawer).
+
+Additionally, one may want to ignore certain keys from being excluded within
+property drawers. For example, we would not want ~ROAM_REFS~ links to be
+self-referential. Hence, to exclude specific keys, we use
+~org-roam-db-extra-links-exclude-keys~.
+
+- Variable: org-roam-db-extra-links-exclude-keys
+
+  Keys to ignore when mapping over links.
+
+  The car of the association list is the Org element type (e.g. keyword). The
+  cdr is a list of case-insensitive strings to exclude from being treated as
+  links.
+
 ** When to cache
 
 By default, Org-roam is eager in caching: each time an Org-roam file is modified
@@ -551,10 +546,10 @@ There are currently 3 provided widget types:
 - Unlinked references :: View nodes that contain text that match the nodes
   title/alias but are not linked
 
-To configure what sections are displayed in the buffer, set ~org-roam-mode-section-functions~.
+To configure what sections are displayed in the buffer, set ~org-roam-mode-sections~.
 
 #+begin_src emacs-lisp
-  (setq org-roam-mode-section-functions
+  (setq org-roam-mode-sections
         (list #'org-roam-backlinks-section
               #'org-roam-reflinks-section
               ;; #'org-roam-unlinked-references-section
@@ -563,6 +558,29 @@ To configure what sections are displayed in the buffer, set ~org-roam-mode-secti
 
 Note that computing unlinked references may be slow, and has not been added in by default.
 
+For each section function, you can pass args along to modify its behaviour. For
+example, if you want to render unique sources for backlinks (and also keep
+rendering reference links), set ~org-roam-mode-sections~ as follows:
+
+#+begin_src emacs-lisp
+  (setq org-roam-mode-sections
+        '((org-roam-backlinks-section :unique t)
+          org-roam-reflinks-section))
+#+end_src
+
+The backlinks section ~org-roam-backlinks-section~ also supports a
+predicate to filter backlinks, ~:show-backlink-p~.  This can be used
+as follows:
+
+#+begin_src emacs-lisp
+  (defun my-org-roam-show-backlink-p (backlink)
+    (not (member "daily" (org-roam-node-tags (org-roam-backlink-source-node backlink)))))
+
+  (setq org-roam-mode-sections
+        '((org-roam-backlinks-section :unique t :show-backlink-p my-org-roam-show-backlink-p)
+          org-roam-reflinks-section))
+#+end_src
+
 ** Configuring the Org-roam buffer display
 
 Org-roam does not control how the pop-up buffer is displayed: this is left to
@@ -670,7 +688,7 @@ With the above example, if another node links to https://www.google.com/, it
 will show up as a “reference backlink”.
 
 These keys also come in useful for when taking website notes, using the
- ~roam-ref~ protocol (see [[*Org-roam Protocol][Roam Protocol]]).
+ ~roam-ref~ protocol (see [[*org-roam-protocol][org-roam-protocol]]).
 
 You may assign multiple refs to a single node, for example when you want
 multiple papers in a series to share the same note, or an article has a citation
@@ -773,7 +791,7 @@ Similarly, the completion candidates are the titles and aliases for all Org-roam
 nodes, and upon choosing a candidate a ~roam:Title~ link will be inserted
 linking to the node of choice.
 
-This is disable by default. To enable it, set ~org-roam-completion-everywhere~
+This is disabled by default. To enable it, set ~org-roam-completion-everywhere~
 to ~t~:
 
 #+begin_src emacs-lisp
@@ -801,202 +819,6 @@ Note that the Org-roam database stores metadata information in plain-text
 (headline text, for example), so if this information is private to you then you
 should also ensure the database is encrypted.
 
-* Org-roam Protocol
-
-Org-roam provides extensions for capturing content from external applications
-such as the browser, via ~org-protocol~. Org-roam extends ~org-protocol~ with 2
-protocols: the ~roam-node~ and ~roam-ref~ protocols.
-
-** Installation
-
-To enable Org-roam's protocol extensions, simply add the following to your init
-file:
-
-#+BEGIN_SRC emacs-lisp
-(require 'org-roam-protocol)
-#+END_SRC
-
-We also need to set up ~org-protocol~: the instructions for setting up
-~org-protocol~ are reproduced below.
-
-*** Linux
-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.
-
-*** Mac OS
-For Mac OS, we need to create our own application.
-
-1. Launch Script Editor
-2. Use the following script, paying attention to the path to ~emacsclient~:
-
-#+begin_src emacs-lisp
-  on open location this_URL
-      set EC to "/usr/local/bin/emacsclient --no-wait "
-      set filePath to quoted form of this_URL
-      do shell script EC & filePath
-      tell application "Emacs" to activate
-  end open location
-#+end_src
-
-3. Save the script in ~/Applications/OrgProtocolClient.app~, changing the script type to
-   "Application", rather than "Script".
-4. Edit ~/Applications/OrgProtocolClient.app/Contents/Info.plist~, adding the
-   following before the last ~</dict>~ tag:
-
-#+begin_src text
-  <key>CFBundleURLTypes</key>
-  <array>
-    <dict>
-      <key>CFBundleURLName</key>
-      <string>org-protocol handler</string>
-      <key>CFBundleURLSchemes</key>
-      <array>
-        <string>org-protocol</string>
-      </array>
-    </dict>
-  </array>
-#+end_src
-
-5. Save the file, and run the ~OrgProtocolClient.app~ to register the 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:
-
-#+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.
-
-**** Testing org-protocol
-
-To test that you have the handler setup and registered properly from the command
-line you can run:
-
-#+begin_src bash
-  open org-protocol://roam-ref\?template=r\&ref=test\&title=this
-#+end_src
-
-If you get an error similar too this or the wrong handler is run:
-
-#+begin_quote
-No application knows how to open URL org-protocol://roam-ref?template=r&ref=test&title=this (Error Domain=NSOSStatusErrorDomain Code=-10814 "kLSApplicationNotFoundErr: E.g. no application claims the file" UserInfo={_LSLine=1489, _LSFunction=runEvaluator}).
-
-#+end_quote
-
-You may need to manually register your handler, like this:
-
-#+begin_src bash
-/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -R  -f /Applications/OrgProtocolClient.app
-#+end_src
-
-Here is a link to the lsregister command that is really useful: https://eclecticlight.co/2019/03/25/lsregister-a-valuable-undocumented-command-for-launchservices/
-*** Windows
-For Windows, create a temporary ~org-protocol.reg~ file:
-
-#+BEGIN_SRC text
-REGEDIT4
-
-[HKEY_CLASSES_ROOT\org-protocol]
-@="URL:Org Protocol"
-"URL Protocol"=""
-[HKEY_CLASSES_ROOT\org-protocol\shell]
-[HKEY_CLASSES_ROOT\org-protocol\shell\open]
-[HKEY_CLASSES_ROOT\org-protocol\shell\open\command]
-@="\"C:\\Windows\\System32\\wsl.exe\" emacsclient \"%1\""
-#+END_SRC
-
-The above will forward the protocol to WSL. If you run Emacs natively on
-Windows, replace the last line with:
-
-#+BEGIN_SRC text
-@="\"c:\\path\\to\\emacs\\bin\\emacsclientw.exe\"  \"%1\""
-#+END_SRC
-
-After executing the .reg file, the protocol is registered and you can delete the
-file.
-
-** The roam-node protocol
-
-The roam-node protocol opens the node with ID specified by the ~node~ key (e.g.
-~org-protocol://roam-node?node=node-id~). ~org-roam-graph~ uses this to make the
-graph navigable.
-
-** The roam-ref protocol
-
-This protocol finds or creates a new note with a given ~ROAM_REFS~:
-
-[[file:images/roam-ref.gif]]
-
-To use this, create the following [[https://en.wikipedia.org/wiki/Bookmarklet][bookmarklet]] in your browser:
-
-#+BEGIN_SRC javascript
-  javascript:location.href =
-      'org-protocol://roam-ref?template=r&ref='
-      + encodeURIComponent(location.href)
-      + '&title='
-      + encodeURIComponent(document.title)
-      + '&body='
-      + encodeURIComponent(window.getSelection())
-#+END_SRC
-
-or as a keybinding in ~qutebrowser~ in , using the ~config.py~ file (see
-[[https://github.com/qutebrowser/qutebrowser/blob/master/doc/help/configuring.asciidoc][Configuring qutebrowser]]):
-
-#+BEGIN_SRC python
-  config.bind("<Ctrl-r>", "open javascript: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]]).
-
 * The Templating System
 
 Org-roam extends the ~org-capture~ system, providing a smoother note-taking
@@ -1078,12 +900,232 @@ One can check the list of available keys for nodes by inspecting the
 
 This makes ~${file}~, ~${file-hash}~ etc. all valid substitutions.
 
-* Graphing
+* Extensions
+** org-roam-protocol
+
+Org-roam provides extensions for capturing content from external applications
+such as the browser, via ~org-protocol~. Org-roam extends ~org-protocol~ with 2
+protocols: the ~roam-node~ and ~roam-ref~ protocols.
+
+*** Installation
+
+To enable Org-roam's protocol extensions, simply add the following to your init
+file:
+
+#+BEGIN_SRC emacs-lisp
+(require 'org-roam-protocol)
+#+END_SRC
+
+We also need to set up ~org-protocol~: the instructions for setting up
+~org-protocol~ are reproduced here.
+
+On a high-level, external calls are passed to Emacs via ~emacsclient~.
+~org-protocol~ intercepts these and runs custom actions based on the protocols
+registered. Hence, to use ~org-protocol~, once must:
+
+1. launch the ~emacsclient~ process
+2. Register ~org-protocol://~ as a valid scheme-handler
+
+The instructions for the latter for each operating system is detailed below.
+
+**** Linux
+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.
+
+**** Mac OS
+For Mac OS, we need to create our own application.
+
+1. Launch Script Editor
+2. Use the following script, paying attention to the path to ~emacsclient~:
+
+#+begin_src emacs-lisp
+  on open location this_URL
+      set EC to "/usr/local/bin/emacsclient --no-wait "
+      set filePath to quoted form of this_URL
+      do shell script EC & filePath & " &> /dev/null &"
+      tell application "Emacs" to activate
+  end open location
+#+end_src
+
+3. Save the script in ~/Applications/OrgProtocolClient.app~, changing the script type to
+   "Application", rather than "Script".
+4. Edit ~/Applications/OrgProtocolClient.app/Contents/Info.plist~, adding the
+   following before the last ~</dict>~ tag:
+
+#+begin_src text
+  <key>CFBundleURLTypes</key>
+  <array>
+    <dict>
+      <key>CFBundleURLName</key>
+      <string>org-protocol handler</string>
+      <key>CFBundleURLSchemes</key>
+      <array>
+        <string>org-protocol</string>
+      </array>
+    </dict>
+  </array>
+#+end_src
+
+5. Save the file, and run the ~OrgProtocolClient.app~ to register the 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:
+
+#+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.
+
+If you're using the [[https://formulae.brew.sh/formula/emacs][Emacs Homebrew formula]], you may need one of the following additional configurations:
+
+a) Add option `-c` to `emacsclient` in the script, and start emacs from command line with `emacs --daemon`
+
+#+begin_src emacs-lisp
+  on open location this_URL
+      set EC to "/usr/local/bin/emacsclient -c --no-wait "
+      set filePath to quoted form of this_URL
+      do shell script EC & filePath & " &> /dev/null &"
+      tell application "Emacs" to activate
+  end open location
+#+end_src
+
+b) Add `(server-start)` in .emacs (in this case you do not need option `-c` for `emacsclient` in the script, and you do not need to start emacs with `emacs --daemon`
+
+***** Testing org-protocol
+
+To test that you have the handler setup and registered properly from the command
+line you can run:
+
+#+begin_src bash
+  open org-protocol://roam-ref\?template=r\&ref=test\&title=this
+#+end_src
+
+If you get an error similar too this or the wrong handler is run:
+
+#+begin_quote
+No application knows how to open URL org-protocol://roam-ref?template=r&ref=test&title=this (Error Domain=NSOSStatusErrorDomain Code=-10814 "kLSApplicationNotFoundErr: E.g. no application claims the file" UserInfo={_LSLine=1489, _LSFunction=runEvaluator}).
+
+#+end_quote
+
+You may need to manually register your handler, like this:
+
+#+begin_src bash
+/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -R  -f /Applications/OrgProtocolClient.app
+#+end_src
+
+Here is a link to the lsregister command that is really useful: https://eclecticlight.co/2019/03/25/lsregister-a-valuable-undocumented-command-for-launchservices/
+**** Windows
+For Windows, create a temporary ~org-protocol.reg~ file:
+
+#+BEGIN_SRC text
+REGEDIT4
+
+[HKEY_CLASSES_ROOT\org-protocol]
+@="URL:Org Protocol"
+"URL Protocol"=""
+[HKEY_CLASSES_ROOT\org-protocol\shell]
+[HKEY_CLASSES_ROOT\org-protocol\shell\open]
+[HKEY_CLASSES_ROOT\org-protocol\shell\open\command]
+@="\"C:\\Windows\\System32\\wsl.exe\" emacsclient \"%1\""
+#+END_SRC
+
+The above will forward the protocol to WSL. If you run Emacs natively on
+Windows, replace the last line with:
+
+#+BEGIN_SRC text
+@="\"c:\\path\\to\\emacs\\bin\\emacsclientw.exe\"  \"%1\""
+#+END_SRC
+
+After executing the .reg file, the protocol is registered and you can delete the
+file.
+
+*** The roam-node protocol
+
+The roam-node protocol opens the node with ID specified by the ~node~ key (e.g.
+~org-protocol://roam-node?node=node-id~). ~org-roam-graph~ uses this to make the
+graph navigable.
+
+*** The roam-ref protocol
+
+This protocol finds or creates a new note with a given ~ROAM_REFS~:
+
+[[file:images/roam-ref.gif]]
+
+To use this, create the following [[https://en.wikipedia.org/wiki/Bookmarklet][bookmarklet]] in your browser:
+
+#+BEGIN_SRC javascript
+  javascript:location.href =
+      'org-protocol://roam-ref?template=r&ref='
+      + encodeURIComponent(location.href)
+      + '&title='
+      + encodeURIComponent(document.title)
+      + '&body='
+      + encodeURIComponent(window.getSelection())
+#+END_SRC
+
+or as a keybinding in ~qutebrowser~ in , using the ~config.py~ file (see
+[[https://github.com/qutebrowser/qutebrowser/blob/master/doc/help/configuring.asciidoc][Configuring qutebrowser]]):
+
+#+BEGIN_SRC python
+  config.bind("<Ctrl-r>", "open javascript: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]]).
+
+** org-roam-graph
 
 Org-roam provides basic graphing capabilities to explore interconnections
 between notes, in ~org-roam-graph~. This is done by performing SQL queries and
-generating images using [[https://graphviz.org/][Graphviz]]. The graph can also be navigated: see [[*Org-roam Protocol][Roam
-Protocol]].
+generating images using [[https://graphviz.org/][Graphviz]]. The graph can also be navigated: see [[*org-roam-protocol][org-roam-protocol]].
 
 The entry point to graph creation is ~org-roam-graph~.
 
@@ -1124,7 +1166,7 @@ ARG may be any of the following values:
           (org-roam-graph--open (concat "file://///wsl$/Ubuntu" file)))))
   #+END_SRC
 
-** Graph Options
+*** 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
@@ -1150,12 +1192,12 @@ for customizable options.
   Extra options for edges in the graphviz output (The "E" attributes).
   Example: ~'(("dir" . "back"))~
 
-* Org-roam Dailies
+** org-roam-dailies
 
 Org-roam provides journaling capabilities akin to
 Org-journal with ~org-roam-dailies~.
 
-** Configuration
+*** Configuration
 
 For ~org-roam-dailies~ to work, you need to define two variables:
 
@@ -1181,7 +1223,7 @@ Here is a sane default configuration:
 
 See [[*The Templating System][The Templating System]] for creating new templates.
 
-** Usage
+*** Usage
 
 ~org-roam-dailies~ provides these interactive functions:
 
@@ -1199,7 +1241,7 @@ There are variants of those commands for ~-yesterday~ and ~-tomorrow~:
 
 - Function: ~org-roam-dailies-capture-yesterday~ n &optional goto
 
-  Create an entry in the daily note for yesteday.
+  Create an entry in the daily note for yesterday.
 
   With numeric argument ~n~, use the daily note ~n~ days in the past.
 
@@ -1235,6 +1277,18 @@ There are also commands which allow you to use Emacs’s ~calendar~ to find the
 - Function: ~org-roam-dailies-goto-next-note~
 
   When in an daily-note, find the next one.
+** org-roam-export
+
+Because Org-roam files are plain org files, they can be exported easily using
+~org-export~ to a variety of formats, including ~html~ and ~pdf~. However,
+Org-roam relies heavily on ID links, which Org's html export has poor support
+of. To fix this, Org-roam provides a bunch of overrides to better support
+export. To use them, simply run:
+
+#+begin_src emacs-lisp
+  (require 'org-roam-export)
+#+end_src
+
 * Performance Optimization
 ** Garbage Collection
 
@@ -1308,7 +1362,7 @@ The Deft interface can slow down quickly when the number of files get huge.
 
 [[https://github.com/bastibe/org-journal][Org-journal]] provides journaling capabilities to Org-mode. A lot of its
 functionalities have been incorporated into Org-roam under the name
-[[*Org-roam Dailies][~org-roam-dailies~]]. It remains a good tool if you want to isolate your verbose
+[[*org-roam-dailies][~org-roam-dailies~]]. It remains a good tool if you want to isolate your verbose
 journal entries from the ideas you would write on a scratchpad.
 
 #+BEGIN_SRC emacs-lisp
@@ -1536,7 +1590,6 @@ to the publishing directory.  Example code follows:
                                          (kill-buffer (file-name-nondirectory svg))
                                          (setq my-publish-time 0)))))
 #+end_src
-
 * Developer's Guide to Org-roam
 ** Org-roam's Design Principle
 
@@ -1575,7 +1628,7 @@ queries on their Org files.
 ** Building Extensions and Advanced Customization of Org-roam
 
 Because Org-roam's core functionality is small, it is possible and sometimes
-desirable to build extensions on top of it. These extensions may one or more of
+desirable to build extensions on top of it. These extensions may use one or more of
 the following functionalities:
 
 - Access to Org-roam's database
@@ -1682,7 +1735,7 @@ When GOTO is non-nil, go the note without creating an entry."
 :END:
 
 #+BEGIN_QUOTE
-Copyright (C) 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+Copyright (C) 2020-2025 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

extensions/org-roam-dailies.el

@@ -1,14 +1,14 @@
 ;;; org-roam-dailies.el --- Daily-notes for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
 ;;;
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
 ;; Copyright © 2020 Leo Vivier <leo.vivier+dev@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;;      Leo Vivier <leo.vivier+dev@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org-roam "2.1"))
+;; Version: 2.3.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org-roam "2.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -34,10 +34,9 @@
 ;; each file named after certain date and stored in `org-roam-dailies-directory'.
 ;;
 ;; One can use dailies for various purposes, e.g. journaling, fleeting notes,
-;; scratch notes and whatever else you can came up with.
+;; scratch notes or whatever else you can think of.
 ;;
 ;;; Code:
-(require 'f)
 (require 'dash)
 (require 'org-roam)
 
@@ -140,72 +139,93 @@ In this case, interactive selection will be bypassed."
   (org-roam-dailies--capture (current-time) goto keys))
 
 ;;;###autoload
-(defun org-roam-dailies-goto-today ()
-  "Find the daily-note for today, creating it if necessary."
+(defun org-roam-dailies-goto-today (&optional keys)
+  "Find the daily-note for today, creating it if necessary.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
   (interactive)
-  (org-roam-dailies-capture-today t))
+  (org-roam-dailies-capture-today t keys))
 
 ;;;; Tomorrow
 ;;;###autoload
-(defun org-roam-dailies-capture-tomorrow (n &optional goto)
+(defun org-roam-dailies-capture-tomorrow (n &optional goto keys)
   "Create an entry in the daily-note for tomorrow.
 
 With numeric argument N, use the daily-note N days in the future.
 
 With a `C-u' prefix or when GOTO is non-nil, go the note without
-creating an entry."
+creating an entry.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
   (interactive "p")
-  (org-roam-dailies--capture (time-add (* n 86400) (current-time)) goto))
+  (org-roam-dailies--capture (time-add (* n 86400) (current-time)) goto keys))
 
 ;;;###autoload
-(defun org-roam-dailies-goto-tomorrow (n)
+(defun org-roam-dailies-goto-tomorrow (n &optional keys)
   "Find the daily-note for tomorrow, creating it if necessary.
 
 With numeric argument N, use the daily-note N days in the
-future."
+future.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
   (interactive "p")
-  (org-roam-dailies-capture-tomorrow n t))
+  (org-roam-dailies-capture-tomorrow n t keys))
 
 ;;;; Yesterday
 ;;;###autoload
-(defun org-roam-dailies-capture-yesterday (n &optional goto)
+(defun org-roam-dailies-capture-yesterday (n &optional goto keys)
   "Create an entry in the daily-note for yesteday.
 
 With numeric argument N, use the daily-note N days in the past.
 
-When GOTO is non-nil, go the note without creating an entry."
+When GOTO is non-nil, go the note without creating an entry.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
   (interactive "p")
-  (org-roam-dailies-capture-tomorrow (- n) goto))
+  (org-roam-dailies-capture-tomorrow (- n) goto keys))
 
 ;;;###autoload
-(defun org-roam-dailies-goto-yesterday (n)
+(defun org-roam-dailies-goto-yesterday (n &optional keys)
   "Find the daily-note for yesterday, creating it if necessary.
 
 With numeric argument N, use the daily-note N days in the
-future."
+future.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
   (interactive "p")
-  (org-roam-dailies-capture-tomorrow (- n) t))
+  (org-roam-dailies-capture-tomorrow (- n) t keys))
 
 ;;;; Date
 ;;;###autoload
-(defun org-roam-dailies-capture-date (&optional goto prefer-future)
+(defun org-roam-dailies-capture-date (&optional goto prefer-future keys)
   "Create an entry in the daily-note for a date using the calendar.
 Prefer past dates, unless PREFER-FUTURE is non-nil.
 With a `C-u' prefix or when GOTO is non-nil, go the note without
-creating an entry."
+creating an entry.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
   (interactive "P")
   (let ((time (let ((org-read-date-prefer-future prefer-future))
                 (org-read-date nil t nil (if goto
                                              "Find daily-note: "
                                            "Capture to daily-note: ")))))
-    (org-roam-dailies--capture time goto)))
+    (org-roam-dailies--capture time goto keys)))
 
 ;;;###autoload
-(defun org-roam-dailies-goto-date (&optional prefer-future)
+(defun org-roam-dailies-goto-date (&optional prefer-future keys)
   "Find the daily-note for a date using the calendar, creating it if necessary.
-Prefer past dates, unless PREFER-FUTURE is non-nil."
+Prefer past dates, unless PREFER-FUTURE is non-nil.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
   (interactive)
-  (org-roam-dailies-capture-date t prefer-future))
+  (org-roam-dailies-capture-date t prefer-future keys))
 
 ;;;; Navigation
 (defun org-roam-dailies-goto-next-note (&optional n)
@@ -269,7 +289,7 @@ If FILE is not specified, use the current buffer's file-path."
     (save-match-data
       (and
        (org-roam-file-p path)
-       (f-descendant-of-p path directory)))))
+       (org-roam-descendant-of-p path directory)))))
 
 ;;;###autoload
 (defun org-roam-dailies-find-directory ()
@@ -309,7 +329,8 @@ When GOTO is non-nil, go the note without creating an entry.
 
 ELisp programs can set KEYS to a string associated with a template.
 In this case, interactive selection will be bypassed."
-  (let ((org-roam-directory (expand-file-name org-roam-dailies-directory org-roam-directory)))
+  (let ((org-roam-directory (expand-file-name org-roam-dailies-directory org-roam-directory))
+        (org-roam-dailies-directory "./"))
     (org-roam-capture- :goto (when goto '(4))
                        :keys keys
                        :node (org-roam-node-create)

extensions/org-roam-export.el

@@ -0,0 +1,75 @@
+;;; org-roam-export.el --- Org-roam org-export tweaks -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.3.1
+;; Package-Requires: ((emacs "26.1") (org "9.6") (org-roam "2.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This package provides the necessary changes required to make org-export work out-of-the-box.
+;;
+;; To enable it, run:
+;;
+;;    (require 'org-roam-export)
+;;
+;; The key issue Org's export-to-html functionality has is that it does not respect the ID property, which
+;; Org-roam relies heavily on. This patches the necessary function in ox-html to export ID links correctly,
+;; pointing to the correct place.
+;;
+;;; Code:
+(require 'ox-html)
+
+(defun org-roam-export--org-html--reference (datum info &optional named-only)
+  "Org-roam's patch for `org-html--reference' to support ID link export.
+See `org-html--reference' for DATUM, INFO and NAMED-ONLY."
+  (let* ((type (org-element-type datum))
+         (user-label
+          (org-element-property
+           (pcase type
+             ((or `headline `inlinetask) :CUSTOM_ID)
+             ((or `radio-target `target) :value)
+             (_ :name))
+           datum))
+         (user-label
+          (or user-label
+              (when-let ((path (org-element-property :ID datum)))
+                ;; see `org-html-link' for why we use "ID-"
+                ;; (search for "ID-" in ox-html.el)
+                (concat "ID-" path)))))
+    (cond
+     ((and user-label
+           (or (plist-get info :html-prefer-user-labels)
+               (memq type '(headline inlinetask))))
+      user-label)
+     ((and named-only
+           (not (memq type '(headline inlinetask radio-target target)))
+           (not user-label))
+      nil)
+     (t
+      (org-export-get-reference datum info)))))
+
+(advice-add 'org-html--reference :override #'org-roam-export--org-html--reference)
+
+(provide 'org-roam-export)
+;;; org-roam-export.el ends here

extensions/org-roam-graph.el

@@ -1,12 +1,12 @@
 ;;; org-roam-graph.el --- Basic graphing functionality for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.0
-;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))
+;; Version: 2.3.1
+;; Package-Requires: ((emacs "26.1") (org "9.6") (org-roam "2.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -266,7 +266,7 @@ Handles both Org-roam nodes, and string nodes (e.g. urls)."
                 (org-roam-quote-string
                  (pcase org-roam-graph-shorten-titles
                    (`truncate (truncate-string-to-width title org-roam-graph-max-title-length nil nil "..."))
-                   (`wrap (s-word-wrap org-roam-graph-max-title-length title))
+                   (`wrap (org-roam-word-wrap org-roam-graph-max-title-length title))
                    (_ title)))))
           (setq node-id (org-roam-node-id node)
                 node-properties `(("label"   . ,shortened-title)

extensions/org-roam-overlay.el

@@ -1,12 +1,12 @@
 ;;; org-roam-overlay.el --- Link overlay for [id:] links to Org-roam nodes -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.0
-;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))
+;; Version: 2.3.1
+;; Package-Requires: ((emacs "26.1") (org "9.6") (org-roam "2.1"))
 
 ;; This file is NOT part of GNU Emacs.
 

extensions/org-roam-protocol.el

@@ -1,11 +1,11 @@
 ;;; org-roam-protocol.el --- Protocol handler for roam:// links  -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.0
-;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))
+;; Version: 2.3.1
+;; Package-Requires: ((emacs "26.1") (org "9.6") (org-roam "2.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -169,25 +169,6 @@ org-protocol://roam-node?node=uuid"
 (push '("org-roam-node"  :protocol "roam-node"   :function org-roam-protocol-open-node)
       org-protocol-protocol-alist)
 
-;;; Capture implementation
-(add-hook 'org-roam-capture-preface-hook #'org-roam-protocol--try-capture-to-ref-h)
-(defun org-roam-protocol--try-capture-to-ref-h ()
-  "Try to capture to an existing node that match the ref."
-  (when-let ((node (and (plist-get org-roam-capture--info :ref)
-                        (org-roam-node-from-ref
-                         (plist-get org-roam-capture--info :ref)))))
-    (set-buffer (org-capture-target-buffer (org-roam-node-file node)))
-    (goto-char (org-roam-node-point node))
-    (widen)
-    (org-roam-node-id node)))
-
-(add-hook 'org-roam-capture-new-node-hook #'org-roam-protocol--insert-captured-ref-h)
-(defun org-roam-protocol--insert-captured-ref-h ()
-  "Insert the ref if any."
-  (when-let ((ref (plist-get org-roam-capture--info :ref)))
-    (org-roam-ref-add ref)))
-
-
 (provide 'org-roam-protocol)
 
 ;;; org-roam-protocol.el ends here

github-eldev

@@ -0,0 +1,11 @@
+#! /bin/sh
+set -e
+
+ELDEV_BIN_DIR=~/.local/bin
+
+# `$GITHUB_PATH' is a magic file which contents is translated to environment variable `$PATH'.
+echo "$ELDEV_BIN_DIR" >> $GITHUB_PATH
+
+mkdir -p $ELDEV_BIN_DIR
+curl -fsSL https://raw.githubusercontent.com/doublep/eldev/f111d19cda305e5e8fcb70a5675b87173041cb68/bin/eldev > $ELDEV_BIN_DIR/eldev
+chmod a+x $ELDEV_BIN_DIR/eldev

org-roam-capture.el

@@ -1,12 +1,12 @@
 ;;; org-roam-capture.el --- Capture functionality -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
+;; Version: 2.3.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (emacsql "4.1.0") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -407,6 +407,8 @@ TEMPLATES is a list of org-roam templates."
           (mapcar (lambda (template)
                     (org-roam-capture--convert-template template props))
                   (or templates org-roam-capture-templates)))
+         (_ (setf (org-roam-node-id node) (or (org-roam-node-id node)
+                                              (org-id-new))))
          (org-roam-capture--node node)
          (org-roam-capture--info info))
     (when (and (not keys)
@@ -503,7 +505,7 @@ Return the ID of the location."
        (set-buffer (org-capture-target-buffer path))
        (when new-file-p
          (org-roam-capture--put :new-file path)
-         (insert (org-roam-capture--fill-template head t)))
+         (insert (org-roam-capture--fill-template head 'ensure-newline)))
        (widen)
        (setq p (goto-char (point-min))))
       (`(file+head+olp ,path ,head ,olp)
@@ -513,7 +515,7 @@ Return the ID of the location."
        (widen)
        (when new-file-p
          (org-roam-capture--put :new-file path)
-         (insert (org-roam-capture--fill-template head t)))
+         (insert (org-roam-capture--fill-template head 'ensure-newline)))
        (setq p (point-min))
        (let ((m (org-roam-capture-find-or-create-olp olp)))
          (goto-char m)))
@@ -572,11 +574,11 @@ Return the ID of the location."
     ;; caller.
     (save-excursion
       (goto-char p)
-      (when-let* ((node org-roam-capture--node)
-                  (id (org-roam-node-id node)))
-        (org-entry-put p "ID" id))
+      (if-let ((id (org-entry-get p "ID")))
+          (setf (org-roam-node-id org-roam-capture--node) id)
+        (org-entry-put p "ID" (org-roam-node-id org-roam-capture--node)))
       (prog1
-          (org-id-get-create)
+          (org-id-get)
         (run-hooks 'org-roam-capture-new-node-hook)))))
 
 (defun org-roam-capture--get-target ()
@@ -589,8 +591,9 @@ Return the ID of the location."
 PATH is a string that can optionally contain templated text in
 it."
   (or (org-roam-node-file org-roam-capture--node)
-      (thread-first path
-        (org-roam-capture--fill-template t)
+      (thread-first
+        path
+        (org-roam-capture--fill-template)
         (string-trim)
         (expand-file-name org-roam-directory))))
 
@@ -615,7 +618,7 @@ you can catch it with `condition-case'."
     (org-with-wide-buffer
      (goto-char start)
      (dolist (heading olp)
-       (setq heading (org-roam-capture--fill-template heading t))
+       (setq heading (org-roam-capture--fill-template heading))
        (let ((re (format org-complex-heading-regexp-format
                          (regexp-quote heading)))
              (cnt 0))
@@ -677,6 +680,24 @@ the current value of `point'."
             (goto-char (org-entry-end-position))))))))
   (point))
 
+;;; Capture implementation
+(add-hook 'org-roam-capture-preface-hook #'org-roam-capture--try-capture-to-ref-h)
+(defun org-roam-capture--try-capture-to-ref-h ()
+  "Try to capture to an existing node that match the ref."
+  (when-let ((node (and (plist-get org-roam-capture--info :ref)
+                        (org-roam-node-from-ref
+                         (plist-get org-roam-capture--info :ref)))))
+    (set-buffer (org-capture-target-buffer (org-roam-node-file node)))
+    (goto-char (org-roam-node-point node))
+    (widen)
+    (org-roam-node-id node)))
+
+(add-hook 'org-roam-capture-new-node-hook #'org-roam-capture--insert-captured-ref-h)
+(defun org-roam-capture--insert-captured-ref-h ()
+  "Insert the ref if any."
+  (when-let ((ref (plist-get org-roam-capture--info :ref)))
+    (org-roam-ref-add ref)))
+
 ;;;; Finalizers
 (add-hook 'org-capture-prepare-finalize-hook #'org-roam-capture--install-finalize-h)
 (defun org-roam-capture--install-finalize-h ()
@@ -686,14 +707,15 @@ the current value of `point'."
 
 (defun org-roam-capture--finalize ()
   "Finalize the `org-roam-capture' process."
-  (when-let ((region (org-roam-capture--get :region)))
-    (org-roam-unshield-region (car region) (cdr region)))
   (if org-note-abort
-      (when-let ((new-file (org-roam-capture--get :new-file)))
-        (org-roam-message "Deleting file for aborted capture %s" new-file)
+      (when-let ((new-file (org-roam-capture--get :new-file))
+                 (_ (yes-or-no-p "Delete file for aborted capture?")))
         (when (find-buffer-visiting new-file)
           (kill-buffer (find-buffer-visiting new-file)))
         (delete-file new-file))
+    (when-let* ((buffer (plist-get org-capture-plist :buffer))
+                (file (buffer-file-name buffer)))
+      (org-id-add-location (org-roam-capture--get :id) file))
     (when-let* ((finalize (org-roam-capture--get :finalize))
                 (org-roam-finalize-fn (intern (concat "org-roam-capture--finalize-"
                                                       (symbol-name finalize)))))
@@ -716,52 +738,59 @@ This function is to be called in the Org-capture finalization process."
               (buf (marker-buffer mkr)))
     (with-current-buffer buf
       (when-let ((region (org-roam-capture--get :region)))
-        (org-roam-unshield-region (car region) (cdr region))
         (delete-region (car region) (cdr region))
         (set-marker (car region) nil)
         (set-marker (cdr region) nil))
-      (org-with-point-at mkr
-        (insert (org-link-make-string (concat "id:" (org-roam-capture--get :id))
-                                      (org-roam-capture--get :link-description)))))))
+      (let* ((id (org-roam-capture--get :id))
+             (description (org-roam-capture--get :link-description))
+             (link (org-link-make-string (concat "id:" id)
+                                         description)))
+        (if (eq (point) (marker-position mkr))
+            (insert link)
+          (org-with-point-at mkr
+            (insert link)))
+        (run-hook-with-args 'org-roam-post-node-insert-hook
+                            id
+                            description)))))
 
 ;;;; Processing of the capture templates
-(defun org-roam-capture--fill-template (template &optional org-capture-p newline)
+(defun org-roam-capture--fill-template (template &optional ensure-newline)
   "Expand TEMPLATE and return it.
-It expands ${var} occurrences in TEMPLATE. When ORG-CAPTURE-P,
-also run Org-capture's template expansion.
-If NEWLINE, ensure that the template returned ends with a newline."
-  (setq template (org-roam-format-template
-                  template
-                  (lambda (key default-val)
-                    (let ((fn (intern key))
-                          (node-fn (intern (concat "org-roam-node-" key)))
-                          (ksym (intern (concat ":" key))))
-                      (cond
-                       ((fboundp fn)
-                        (funcall fn org-roam-capture--node))
-                       ((fboundp node-fn)
-                        (funcall node-fn org-roam-capture--node))
-                       ((plist-get org-roam-capture--info ksym)
-                        (plist-get org-roam-capture--info ksym))
-                       (t (let ((r (read-from-minibuffer (format "%s: " key) default-val)))
-                            (plist-put org-roam-capture--info ksym r)
-                            r)))))))
-  ;; WARNING:
-  ;; `org-capture-fill-template' fills the template, but post-processes whitespace such that the resultant
-  ;; template does not start with any whitespace, and only ends with a single newline
-  ;;
-  ;; In most cases where we rely on `org-capture-fill-template' to populate non-org-capture-related templates,
-  ;; (e.g. in OLPs), we strip the final newline, obtaining a template that seems to be string-trimmed.
-  ;;
-  ;; This means that if the original passed template has newlines, and ORG-CAPTURE-P is true, then the extra
-  ;; whitespace specified in the template will be ignored.
-  (when org-capture-p
+It expands ${var} occurrences in TEMPLATE, and then runs
+org-capture's template expansion.
+When ENSURE-NEWLINE, always ensure there's a newline behind."
+  (let* ((template (if (functionp template)
+                       (funcall template)
+                     template))
+         (template-whitespace-content (org-roam-whitespace-content template)))
     (setq template
-          (replace-regexp-in-string "\n$" "" (org-capture-fill-template template))))
-  (when (and newline
-             (not (string-suffix-p "\n" template)))
-    (setq template (concat template "\n")))
-  template)
+          (org-roam-format-template
+           template
+           (lambda (key default-val)
+             (let ((fn (intern key))
+                   (node-fn (intern (concat "org-roam-node-" key)))
+                   (ksym (intern (concat ":" key))))
+               (cond
+                ((fboundp fn)
+                 (funcall fn org-roam-capture--node))
+                ((fboundp node-fn)
+                 (funcall node-fn org-roam-capture--node))
+                ((plist-get org-roam-capture--info ksym)
+                 (plist-get org-roam-capture--info ksym))
+                (t (let ((r (read-from-minibuffer (format "%s: " key) default-val)))
+                     (plist-put org-roam-capture--info ksym r)
+                     r)))))))
+    ;; WARNING:
+    ;; `org-capture-fill-template' fills the template, but post-processes whitespace such that the resultant
+    ;; template does not start with any whitespace, and only ends with a single newline
+    ;;
+    ;; Instead, we restore the whitespace in the original template.
+    (setq template (replace-regexp-in-string "[\n]*\\'" "" (org-capture-fill-template template)))
+    (when (and ensure-newline
+               (string-equal template-whitespace-content ""))
+      (setq template-whitespace-content "\n"))
+    (setq template (concat template template-whitespace-content))
+    template))
 
 (defun org-roam-capture--convert-template (template &optional props)
   "Convert TEMPLATE from Org-roam syntax to `org-capture-templates' syntax.

org-roam-compat.el

@@ -1,11 +1,11 @@
 ;;; org-roam-compat.el --- Backward compatibility code -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.0
+;; Version: 2.3.1
 ;; Package-Requires: ((emacs "26.1"))
 
 ;; This file is NOT part of GNU Emacs.
@@ -229,6 +229,10 @@ nodes." org-id-locations-file)
   'org-roam-remove-property
   'org-roam-property-remove "org-roam 2.1")
 
+(define-obsolete-variable-alias
+  'org-roam-mode-section-functions
+  'org-roam-mode-sections "org-roam 2.2.0")
+
 ;;; Obsolete functions
 (make-obsolete 'org-roam-get-keyword 'org-collect-keywords "org-roam 2.0")
 

org-roam-db.el

@@ -1,12 +1,12 @@
 ;;; org-roam-db.el --- Org-roam database API -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
+;; Version: 2.3.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (emacsql "4.1.0") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -31,29 +31,11 @@
 ;;
 ;;; Code:
 (require 'org-roam)
+(require 'url-parse)
+(require 'ol)
 (defvar org-outline-path-cache)
 
 ;;; Options
-(defcustom org-roam-database-connector 'sqlite
-  "The database connector used by Org-roam.
-This must be set before `org-roam' is loaded. To use an
-alternative connector you must install the respective package
-explicitly. When `sqlite', then use the `emacsql-sqlite' library
-that is being maintained in the same repository as `emacsql'
-itself. When `libsqlite3', then use the `emacsql-libsqlite3'
-library, which itself uses a module provided by the `sqlite3'
-package. This is still experimental. When `sqlite3', then use the
-`emacsql-sqlite3' library, which uses the official `sqlite3' cli
-tool, which is not recommended because it is not suitable to be
-used like this, but has the advantage that you likely don't need
-a compiler. See https://nullprogram.com/blog/2014/02/06/."
-  :package-version '(org-roam . "2.2.0")
-  :group 'org-roam
-  :type '(choice (const sqlite)
-                 (const libsqlite3)
-                 (const sqlite3)
-                 (symbol :tag "other")))
-
 (defcustom org-roam-db-location (locate-user-emacs-file "org-roam.db")
   "The path to file where the Org-roam database is stored.
 
@@ -98,8 +80,35 @@ slow."
   :type 'boolean
   :group 'org-roam)
 
+(defcustom org-roam-db-extra-links-elements '(node-property keyword)
+  "The list of Org element types to include for parsing by Org-roam.
+
+By default, when parsing Org's AST, links within keywords and
+property drawers are not parsed as links. Sometimes however, it
+is desirable to parse and cache these links (e.g. hiding links in
+a property drawer)."
+  :package-version '(org-roam . "2.2.0")
+  :group 'org-roam
+  :type '(set
+          (const :tag "keywords" keyword)
+          (const :tag "property drawers" node-property)))
+
+(defcustom org-roam-db-extra-links-exclude-keys '((node-property . ("ROAM_REFS"))
+                                                  (keyword . ("transclude")))
+  "Keys to ignore when mapping over links.
+
+The car of the association list is the Org element type (e.g.
+keyword). The cdr is a list of case-insensitive strings to
+exclude from being treated as links.
+
+For example, we use this to prevent self-referential links in
+ROAM_REFS."
+  :package-version '(org-roam . "2.2.0")
+  :group 'org-roam
+  :type '(alist))
+
 ;;; Variables
-(defconst org-roam-db-version 18)
+(defconst org-roam-db-version 20)
 
 (defvar org-roam-db--connection (make-hash-table :test #'equal)
   "Database connection to Org-roam database.")
@@ -110,26 +119,6 @@ slow."
   (gethash (expand-file-name (file-name-as-directory org-roam-directory))
            org-roam-db--connection))
 
-(declare-function emacsql-sqlite "ext:emacsql-sqlite")
-(declare-function emacsql-libsqlite3 "ext:emacsql-libsqlite3")
-(declare-function emacsql-sqlite3 "ext:emacsql-sqlite3")
-
-(defun org-roam-db--conn-fn ()
-  "Return the function for creating the database connection."
-  (cl-case org-roam-database-connector
-    (sqlite
-     (progn
-       (require 'emacsql-sqlite)
-       #'emacsql-sqlite))
-    (libsqlite3
-     (progn
-       (require 'emacsql-libsqlite3)
-       #'emacsql-libsqlite3))
-    (sqlite3
-     (progn
-       (require 'emacsql-sqlite3)
-       #'emacsql-sqlite3))))
-
 (defun org-roam-db ()
   "Entrypoint to the Org-roam sqlite database.
 Initializes and stores the database, and the database connection.
@@ -138,10 +127,7 @@ Performs a database upgrade when required."
                (emacsql-live-p (org-roam-db--get-connection)))
     (let ((init-db (not (file-exists-p org-roam-db-location))))
       (make-directory (file-name-directory org-roam-db-location) t)
-      (let ((conn (funcall (org-roam-db--conn-fn) org-roam-db-location)))
-        (emacsql conn [:pragma (= foreign_keys ON)])
-        (when-let ((process (emacsql-process conn)))
-          (set-process-query-on-exit-flag process nil))
+      (let ((conn (emacsql-sqlite-open org-roam-db-location)))
         (puthash (expand-file-name (file-name-as-directory org-roam-directory))
                  conn
                  org-roam-db--connection)
@@ -153,7 +139,7 @@ Performs a database upgrade when required."
            ((> version org-roam-db-version)
             (emacsql-close conn)
             (user-error
-             "The Org-roam database was created with a newer Org-roam version.  "
+             "The Org-roam database was created with a newer Org-roam version.  %s"
              "You need to update the Org-roam package"))
            ((< version org-roam-db-version)
             (emacsql-close conn)
@@ -295,20 +281,21 @@ If FILE is nil, clear the current buffer."
 If there is no title, return the file name relative to
 `org-roam-directory'."
   (org-link-display-format
-   (or (cadr (assoc "TITLE" (org-collect-keywords '("title"))))
+   (or (string-join (cdr (assoc "TITLE" (org-collect-keywords '("title")))) " ")
        (file-name-sans-extension (file-relative-name
                                   (buffer-file-name (buffer-base-buffer))
                                   org-roam-directory)))))
 
-(defun org-roam-db-insert-file ()
+(defun org-roam-db-insert-file (&optional hash)
   "Update the files table for the current buffer.
-If UPDATE-P is non-nil, first remove the file in the database."
+If UPDATE-P is non-nil, first remove the file in the database.
+If HASH is non-nil, use that as the file's hash without recalculating it."
   (let* ((file (buffer-file-name))
          (file-title (org-roam-db--file-title))
          (attr (file-attributes file))
          (atime (file-attribute-access-time attr))
          (mtime (file-attribute-modification-time attr))
-         (hash (org-roam-db--file-hash)))
+         (hash (or hash (org-roam-db--file-hash file))))
     (org-roam-db-query
      [:insert :into files
       :values $v1]
@@ -317,12 +304,12 @@ If UPDATE-P is non-nil, first remove the file in the database."
 (defun org-roam-db-get-scheduled-time ()
   "Return the scheduled time at point in ISO8601 format."
   (when-let ((time (org-get-scheduled-time (point))))
-    (org-format-time-string "%FT%T%z" time)))
+    (format-time-string "%FT%T" time)))
 
 (defun org-roam-db-get-deadline-time ()
   "Return the deadline time at point in ISO8601 format."
   (when-let ((time (org-get-deadline-time (point))))
-    (org-format-time-string "%FT%T%z" time)))
+    (format-time-string "%FT%T" time)))
 
 (defun org-roam-db-node-p ()
   "Return t if headline at point is an Org-roam node, else return nil."
@@ -332,12 +319,13 @@ If UPDATE-P is non-nil, first remove the file in the database."
 
 (defun org-roam-db-map-nodes (fns)
   "Run FNS over all nodes in the current buffer."
-  (org-map-region
-   (lambda ()
-     (when (org-roam-db-node-p)
-       (dolist (fn fns)
-         (funcall fn))))
-   (point-min) (point-max)))
+  (org-with-wide-buffer
+   (org-map-region
+    (lambda ()
+      (when (org-roam-db-node-p)
+        (dolist (fn fns)
+          (funcall fn))))
+    (point-min) (point-max))))
 
 (defun org-roam-db-map-links (fns)
   "Run FNS over all links in the current buffer."
@@ -346,30 +334,23 @@ If UPDATE-P is non-nil, first remove the file in the database."
       ;; `re-search-forward' let the cursor one character after the link, we need to go backward one char to
       ;; make the point be on the link.
       (backward-char)
-      (let* ((element (org-element-context))
+      (let* ((begin (match-beginning 0))
+             (element (org-element-context))
              (type (org-element-type element))
-             link bounds)
+             link)
         (cond
          ;; Links correctly recognized by Org Mode
          ((eq type 'link)
           (setq link element))
-         ;; Prevent self-referencing links in ROAM_REFS
-         ((and (eq type 'node-property)
-               (org-roam-string-equal (org-element-property :key element) "ROAM_REFS"))
-          nil)
          ;; Links in property drawers and lines starting with #+. Recall that, as for Org Mode v9.4.4, the
          ;; org-element-type of links within properties drawers is "node-property" and for lines starting with
          ;; #+ is "keyword".
-         ((and (or (eq type 'node-property)
-                   (eq type 'keyword))
-               (setq bounds (org-in-regexp org-link-any-re))
-               (setq link (buffer-substring-no-properties
-                           (car bounds)
-                           (cdr bounds))))
-          (with-temp-buffer
-            (delay-mode-hooks (org-mode))
-            (insert link)
-            (setq link (org-element-context)))))
+         ((and (member type org-roam-db-extra-links-elements)
+               (not (member-ignore-case (org-element-property :key element)
+                                        (cdr (assoc type org-roam-db-extra-links-exclude-keys))))
+               (setq link (save-excursion
+                            (goto-char begin)
+                            (save-match-data (org-element-link-parser)))))))
         (when link
           (dolist (fn fns)
             (funcall fn link)))))))
@@ -493,9 +474,14 @@ INFO is the org-element parsed buffer."
                 (;; https://google.com, cite:citeKey
                  ;; Note: we use string-match here because it matches any link: e.g. [[cite:abc][abc]]
                  ;; But this form of matching is loose, and can accept invalid links e.g. [[cite:abc]
-                 (string-match org-link-plain-re ref)
-                 (let ((link-type (match-string 1 ref))
-                       (path (match-string 2 ref)))
+                 (string-match org-link-any-re (org-link-encode ref '(#x20)))
+                 (setq ref (org-link-encode ref '(#x20)))
+                 (let ((ref-url (url-generic-parse-url (or (match-string 2 ref) (match-string 0 ref))))
+                       (link-type ()) ;; clear url-type for backward compatible.
+                       (path ()))
+                   (setq link-type (url-type ref-url))
+                   (setf (url-type ref-url) nil)
+                   (setq path (org-link-decode (url-recreate-url ref-url)))
                    (if (and (boundp 'org-ref-cite-types)
                             (or (assoc link-type org-ref-cite-types)
                                 (member link-type org-ref-cite-types)))
@@ -514,12 +500,18 @@ INFO is the org-element parsed buffer."
   "Insert link data for LINK at current point into the Org-roam cache."
   (save-excursion
     (goto-char (org-element-property :begin link))
-    (let ((type (org-element-property :type link))
-          (path (org-element-property :path link))
-          (source (org-roam-id-at-point))
-          (properties (list :outline (ignore-errors
-                                       ;; This can error if link is not under any headline
-                                       (org-get-outline-path 'with-self 'use-cache)))))
+    (let* ((type (org-element-property :type link))
+           (path (org-element-property :path link))
+           (option (and (string-match "::\\(.*\\)\\'" path)
+                        (match-string 1 path)))
+           (path (if (not option) path
+                   (substring path 0 (match-beginning 0))))
+           (source (org-roam-id-at-point))
+           (properties (list :outline (ignore-errors
+                                        ;; This can error if link is not under any headline
+                                        (org-get-outline-path 'with-self 'use-cache))))
+           (properties (if option (plist-put properties :search-option option)
+                         properties)))
       ;; For Org-ref links, we need to split the path into the cite keys
       (when (and source path)
         (if (and (boundp 'org-ref-cite-types)
@@ -559,19 +551,12 @@ INFO is the org-element parsed buffer."
       (puthash (car row) (cadr row) ht))
     ht))
 
-(defun org-roam-db--file-hash (&optional file-path)
-  "Compute the hash of FILE-PATH, a file or current buffer."
-  ;; If it is a GPG encrypted file, we always want to compute the hash
-  ;; for the GPG encrypted file (undecrypted)
-  (when (and (not file-path) (equal "gpg" (file-name-extension (buffer-file-name))))
-    (setq file-path (buffer-file-name)))
-  (if file-path
-      (with-temp-buffer
-        (set-buffer-multibyte nil)
-        (insert-file-contents-literally file-path)
-        (secure-hash 'sha1 (current-buffer)))
-    (org-with-wide-buffer
-     (secure-hash 'sha1 (current-buffer)))))
+(defun org-roam-db--file-hash (file-path)
+  "Compute the hash of FILE-PATH."
+  (with-temp-buffer
+    (set-buffer-multibyte nil)
+    (insert-file-contents-literally file-path)
+    (secure-hash 'sha1 (current-buffer))))
 
 ;;;; Synchronization
 (defun org-roam-db-update-file (&optional file-path no-require)
@@ -594,27 +579,28 @@ in `org-roam-db-sync'."
         (org-roam-require '(org-ref oc)))
       (org-roam-with-file file-path nil
         (emacsql-with-transaction (org-roam-db)
-          (save-excursion
-            (org-set-regexps-and-options 'tags-only)
-            (org-refresh-category-properties)
-            (org-roam-db-clear-file)
-            (org-roam-db-insert-file)
-            (org-roam-db-insert-file-node)
-            (setq org-outline-path-cache nil)
-            (org-roam-db-map-nodes
-             (list #'org-roam-db-insert-node-data
-                   #'org-roam-db-insert-aliases
-                   #'org-roam-db-insert-tags
-                   #'org-roam-db-insert-refs))
-            (setq org-outline-path-cache nil)
-            (setq info (org-element-parse-buffer))
-            (org-roam-db-map-links
-             (list #'org-roam-db-insert-link))
-            (when (fboundp 'org-cite-insert)
-              (require 'oc)             ;ensure feature is loaded
-              (org-roam-db-map-citations
-               info
-               (list #'org-roam-db-insert-citation)))))))))
+          (org-with-wide-buffer
+           (org-set-regexps-and-options 'tags-only)
+           ;; Org doesn't use this anymore, so we probably should stop too.
+           ;; (org-refresh-category-properties)
+           (org-roam-db-clear-file)
+           (org-roam-db-insert-file content-hash)
+           (org-roam-db-insert-file-node)
+           (setq org-outline-path-cache nil)
+           (org-roam-db-map-nodes
+            (list #'org-roam-db-insert-node-data
+                  #'org-roam-db-insert-aliases
+                  #'org-roam-db-insert-tags
+                  #'org-roam-db-insert-refs))
+           (setq org-outline-path-cache nil)
+           (setq info (org-element-parse-buffer))
+           (org-roam-db-map-links
+            (list #'org-roam-db-insert-link))
+           (when (fboundp 'org-cite-insert)
+             (require 'oc)             ;ensure feature is loaded
+             (org-roam-db-map-citations
+              info
+              (list #'org-roam-db-insert-citation)))))))))
 
 ;;;###autoload
 (defun org-roam-db-sync (&optional force)
@@ -669,12 +655,14 @@ database, see `org-roam-db-sync' command."
       (add-hook 'kill-emacs-hook #'org-roam-db--close-all)
       (advice-add #'rename-file :after  #'org-roam-db-autosync--rename-file-a)
       (advice-add #'delete-file :before #'org-roam-db-autosync--delete-file-a)
+      (advice-add #'vc-delete-file :around #'org-roam-db-autosync--vc-delete-file-a)
       (org-roam-db-sync))
      (t
       (remove-hook 'find-file-hook  #'org-roam-db-autosync--setup-file-h)
       (remove-hook 'kill-emacs-hook #'org-roam-db--close-all)
       (advice-remove #'rename-file #'org-roam-db-autosync--rename-file-a)
       (advice-remove #'delete-file #'org-roam-db-autosync--delete-file-a)
+      (advice-remove #'vc-delete-file #'org-roam-db-autosync--vc-delete-file-a)
       (org-roam-db--close-all)
       ;; Disable local hooks for all org-roam buffers
       (dolist (buf (org-roam-buffer-list))
@@ -702,6 +690,17 @@ FILE is removed from the database."
              (org-roam-file-p file))
     (org-roam-db-clear-file (expand-file-name file))))
 
+(defun org-roam-db-autosync--vc-delete-file-a (fun file)
+  "Maintain cache consistency on file deletion by FUN.
+FILE is removed from the database."
+  (let ((org-roam-file-p (and (not (auto-save-file-name-p file))
+                              (not (backup-file-name-p file))
+                              (org-roam-file-p file))))
+    (apply fun `(,file))
+    (when (and org-roam-file-p
+               (not (file-exists-p file)))
+      (org-roam-db-clear-file (expand-file-name file)))))
+
 (defun org-roam-db-autosync--rename-file-a (old-file new-file-or-dir &rest _args)
   "Maintain cache consistency of file rename.
 OLD-FILE is cleared from the database, and NEW-FILE-OR-DIR is added."

org-roam-id.el

@@ -0,0 +1,94 @@
+;;; org-roam-id.el --- ID-related utilities for Org-roam -*- lexical-binding: t; -*-
+
+;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.3.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (magit-section "3.0.0"))
+
+;; 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 module provides ID-related facilities using the Org-roam database.
+;;
+;;; Code:
+(require 'org-id)
+
+(defun org-roam-id-at-point ()
+  "Return the ID at point, if any.
+Recursively traverses up the headline tree to find the
+first encapsulating ID."
+  (org-with-wide-buffer
+   (org-back-to-heading-or-point-min t)
+   (while (and (not (org-roam-db-node-p))
+               (not (bobp)))
+     (org-roam-up-heading-or-point-min))
+   (when (org-roam-db-node-p)
+     (org-id-get))))
+
+(defun org-roam-id-find (id &optional markerp)
+  "Return the location of the entry with the id ID using the Org-roam db.
+The return value is a cons cell (file-name . position), or nil
+if there is no entry with that ID.
+With optional argument MARKERP, return the position as a new marker."
+  (cond
+   ((symbolp id) (setq id (symbol-name id)))
+   ((numberp id) (setq id (number-to-string id))))
+  (let ((node (org-roam-populate (org-roam-node-create :id id))))
+    (when-let ((file (org-roam-node-file node)))
+      (if markerp
+          (let ((buffer (or (find-buffer-visiting file)
+                            (find-file-noselect file))))
+            (with-current-buffer buffer
+              (move-marker (make-marker) (org-roam-node-point node) buffer)))
+        (cons (org-roam-node-file node)
+              (org-roam-node-point node))))))
+
+(defalias 'org-roam-id-open 'org-id-open
+  "Obsolete alias - use `org-id-open' directly.")
+
+(advice-add 'org-id-find :before-until #'org-roam-id-find)
+
+;;;###autoload
+(defun org-roam-update-org-id-locations (&rest directories)
+  "Scan Org-roam files to update `org-id' related state.
+This is like `org-id-update-id-locations', but will automatically
+use the currently bound `org-directory' and `org-roam-directory'
+along with DIRECTORIES (if any), where the lookup for files in
+these directories will be always recursive.
+
+Note: Org-roam doesn't have hard dependency on
+`org-id-locations-file' to lookup IDs for nodes that are stored
+in the database, but it still tries to properly integrates with
+`org-id'. This allows the user to cross-reference IDs outside of
+the current `org-roam-directory', and also link with \"id:\"
+links to headings/files within the current `org-roam-directory'
+that are excluded from identification in Org-roam as
+`org-roam-node's, e.g. with \"ROAM_EXCLUDE\" property."
+  (interactive)
+  (cl-loop for dir in (cons org-roam-directory directories)
+           for org-roam-directory = dir
+           nconc (org-roam-list-files) into files
+           finally (org-id-update-id-locations files org-roam-verbose)))
+
+(provide 'org-roam-id)
+
+;;; org-roam-id.el ends here

org-roam-log.el

@@ -0,0 +1,53 @@
+;;; org-roam-log.el --- Integrations with Org-log -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2022-2025 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.3.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (emacsql "4.1.0") (magit-section "3.0.0"))
+
+;; 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 module provides integrations with Org-log.
+;;
+;;; Code:
+(require 'org-roam)
+
+(defcustom org-roam-log-setup-hook nil
+  "Hook run when a log for an Org-roam file is setup."
+  :group 'org-roam
+  :type 'hook)
+
+(defun org-roam-log-p ()
+  "Return t if the log buffer is for an Org-roam file, nil otherwise."
+  (and org-log-note-marker
+       (org-roam-file-p (buffer-file-name (marker-buffer org-log-note-marker)))))
+
+(defun org-roam-log--setup ()
+  "Run hooks in `org-roam-log-setup-hook'."
+  (run-hooks 'org-roam-log-setup-hook))
+
+(add-hook 'org-roam-log-setup-hook #'org-roam--register-completion-functions-h)
+(add-hook 'org-log-buffer-setup-hook #'org-roam-log--setup)
+
+(provide 'org-roam-log)
+;;; org-roam-log.el ends here

org-roam-migrate.el

@@ -1,12 +1,12 @@
 ;;; org-roam-migrate.el --- Migration utilities from v1 to v2 -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
+;; Version: 2.3.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (emacsql "4.1.0") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 

org-roam-mode.el

@@ -1,12 +1,12 @@
 ;;; org-roam-mode.el --- Major mode for special Org-roam buffers -*- lexical-binding: t -*-
 
-;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
+;; Version: 2.3.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (emacsql "4.1.0") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -39,14 +39,28 @@
 (defvar org-ref-buffer-hacked)
 
 ;;; Options
-(defcustom org-roam-mode-section-functions (list #'org-roam-backlinks-section
-                                                 #'org-roam-reflinks-section)
-  "Functions that insert sections in the `org-roam-mode' based buffers.
-Each function is called with one argument, which is an
-`org-roam-node' for which the buffer will be constructed for.
-Normally this node is `org-roam-buffer-current-node'."
+(defcustom org-roam-mode-sections (list #'org-roam-backlinks-section
+                                        #'org-roam-reflinks-section)
+  "A list of sections for the `org-roam-mode' based buffers.
+Each section is a function that is passed the `org-roam-node'
+for which the section will be constructed as the first
+argument. Normally this node is `org-roam-buffer-current-node'.
+The function may also accept other optional arguments. Each item
+in the list is either:
+
+1. A function, which is called only with the `org-roam-node' as the argument
+2. A list, containing the function and the optional arguments.
+
+For example, one can add
+
+    (org-roam-backlinks-section :unique t)
+
+to the list to pass :unique t to the section-rendering function."
   :group 'org-roam
-  :type 'hook)
+  :type `(repeat (choice (symbol :tag "Function")
+                         (list :tag "Function with arguments"
+                               (symbol :tag "Function")
+                               (repeat :tag "Arguments" :inline t (sexp :tag "Arg"))))))
 
 (defcustom org-roam-buffer-postrender-functions (list)
   "Functions to run after the Org-roam buffer is rendered.
@@ -168,7 +182,7 @@ This mode is used by special Org-roam buffers, such as persistent
 `org-roam-buffer' and dedicated Org-roam buffers
 \(`org-roam-buffer-display-dedicated'), which render the
 information in a section-like manner (see
-`org-roam-mode-section-functions'), with which the user can
+`org-roam-mode-sections'), with which the user can
 interact with."
   :group 'org-roam
   (face-remap-add-relative 'header-line 'org-roam-header-line))
@@ -228,7 +242,14 @@ buffer."
      (org-roam-node-title org-roam-buffer-current-node))
     (magit-insert-section (org-roam)
       (magit-insert-heading)
-      (run-hook-with-args 'org-roam-mode-section-functions org-roam-buffer-current-node))
+      (dolist (section org-roam-mode-sections)
+        (pcase section
+          ((pred functionp)
+           (funcall section org-roam-buffer-current-node))
+          (`(,fn . ,args)
+           (apply fn (cons org-roam-buffer-current-node args)))
+          (_
+           (user-error "Invalid `org-roam-mode-sections' specification")))))
     (run-hooks 'org-roam-buffer-postrender-functions)
     (goto-char 0)))
 
@@ -289,7 +310,7 @@ To toggle its display use `org-roam-buffer-toggle' command.")
   (pcase (org-roam-buffer--visibility)
     ('visible
      (progn
-       (delete-window (get-buffer-window org-roam-buffer))
+       (quit-window nil (get-buffer-window org-roam-buffer))
        (remove-hook 'post-command-hook #'org-roam-buffer--redisplay-h)))
     ((or 'exists 'none)
      (progn
@@ -298,7 +319,7 @@ To toggle its display use `org-roam-buffer-toggle' command.")
 
 (define-inline org-roam-buffer--visibility ()
   "Return the current visibility state of the persistent `org-roam-buffer'.
-Valid states are 'visible, 'exists and 'none."
+Valid states are `visible', `exists' and `none'."
   (declare (side-effect-free t))
   (inline-quote
    (cond
@@ -318,7 +339,7 @@ Has no effect when there's no `org-roam-node-at-point'."
         (add-hook 'kill-buffer-hook #'org-roam-buffer--persistent-cleanup-h nil t)))))
 
 (defun org-roam-buffer--persistent-cleanup-h ()
-  "Clean-up global state thats dedicated for the persistent `org-roam-buffer'."
+  "Clean-up global state that's dedicated for the persistent `org-roam-buffer'."
   (setq-default org-roam-buffer-current-node nil
                 org-roam-buffer-current-directory nil))
 
@@ -420,7 +441,7 @@ In interactive calls OTHER-WINDOW is set with
     (with-current-buffer buf
       (widen)
       (goto-char point))
-    (when (org-invisible-p) (org-show-context))
+    (when (org-invisible-p) (org-fold-show-context))
     buf))
 
 (defun org-roam-preview-default-function ()
@@ -428,10 +449,12 @@ In interactive calls OTHER-WINDOW is set with
 
 This function returns the all contents under the current
 headline, up to the next headline."
-  (let ((beg (progn (org-roam-end-of-meta-data t)
-                    (point)))
-        (end (progn (org-next-visible-heading 1)
-                    (point))))
+  (let ((beg (save-excursion
+               (org-roam-end-of-meta-data t)
+               (point)))
+        (end (save-excursion
+               (org-next-visible-heading 1)
+               (point))))
     (string-trim (buffer-substring-no-properties beg end))))
 
 (defun org-roam-preview-get-contents (file pt)
@@ -459,14 +482,23 @@ headline, up to the next headline."
         (org-roam-populate (org-roam-backlink-target-node backlink)))
   backlink)
 
-(defun org-roam-backlinks-get (node)
-  "Return the backlinks for NODE."
-  (let ((backlinks (org-roam-db-query
-                    [:select [source dest pos properties]
-                     :from links
-                     :where (= dest $s1)
-                     :and (= type "id")]
-                    (org-roam-node-id node))))
+(cl-defun org-roam-backlinks-get (node &key unique)
+  "Return the backlinks for NODE.
+
+ When UNIQUE is nil, show all positions where references are found.
+ When UNIQUE is t, limit to unique sources."
+  (let* ((sql (if unique
+                  [:select :distinct [source dest pos properties]
+                   :from links
+                   :where (= dest $s1)
+                   :and (= type "id")
+                   :group :by source
+                   :having (funcall min pos)]
+                [:select [source dest pos properties]
+                 :from links
+                 :where (= dest $s1)
+                 :and (= type "id")]))
+         (backlinks (org-roam-db-query sql (org-roam-node-id node))))
     (cl-loop for backlink in backlinks
              collect (pcase-let ((`(,source-id ,dest-id ,pos ,properties) backlink))
                        (org-roam-populate
@@ -482,16 +514,28 @@ Sorts by title."
   (string< (org-roam-node-title (org-roam-backlink-source-node a))
            (org-roam-node-title (org-roam-backlink-source-node b))))
 
-(defun org-roam-backlinks-section (node)
-  "The backlinks section for NODE."
-  (when-let ((backlinks (seq-sort #'org-roam-backlinks-sort (org-roam-backlinks-get node))))
+(cl-defun org-roam-backlinks-section (node &key (unique nil) (show-backlink-p nil)
+                                           (section-heading "Backlinks:"))
+  "The backlinks section for NODE.
+
+When UNIQUE is nil, show all positions where references are found.
+When UNIQUE is t, limit to unique sources.
+
+When SHOW-BACKLINK-P is not null, only show backlinks for which
+this predicate is not nil.
+
+SECTION-HEADING is the string used as a heading for the backlink section."
+  (when-let ((backlinks (seq-sort #'org-roam-backlinks-sort (org-roam-backlinks-get node :unique unique))))
     (magit-insert-section (org-roam-backlinks)
-      (magit-insert-heading "Backlinks:")
+      (magit-insert-heading section-heading)
       (dolist (backlink backlinks)
-        (org-roam-node-insert-section
-         :source-node (org-roam-backlink-source-node backlink)
-         :point (org-roam-backlink-point backlink)
-         :properties (org-roam-backlink-properties backlink)))
+        (when (or (null show-backlink-p)
+                  (and (not (null show-backlink-p))
+                       (funcall show-backlink-p backlink)))
+          (org-roam-node-insert-section
+           :source-node (org-roam-backlink-source-node backlink)
+           :point (org-roam-backlink-point backlink)
+           :properties (org-roam-backlink-properties backlink))))
       (insert ?\n))))
 
 ;;;; Reflinks
@@ -586,7 +630,7 @@ instead."
         (forward-line (1- row)))
       (when col
         (forward-char (1- col))))
-    (when (org-invisible-p) (org-show-context))
+    (when (org-invisible-p) (org-fold-show-context))
     buf))
 
 ;;;; Unlinked references
@@ -614,49 +658,69 @@ This is the ROW within FILE."
        (end-of-line)
        (point)))))
 
+(defun org-roam-unlinked-references--rg-command (titles temp-file)
+  "Return the ripgrep command searching for TITLES using TEMP-FILE for pattern.
+This avoids shell escaping issues by writing the pattern to a file instead
+of passing it directly through the shell command line."
+  ;; Write pattern to temp file to avoid shell escaping issues with quotes,
+  ;; spaces, and other special characters in titles
+  (with-temp-file temp-file
+    (insert "\\[([^[]]++|(?R))*\\]"
+            (mapconcat (lambda (title)
+                         ;; Use regexp-quote instead of shell-quote-argument
+                         ;; since we're writing a regex pattern, not a shell argument
+                         (format "|(\\b%s\\b)" (regexp-quote title)))
+                       titles "")))
+
+  (concat "rg --follow --only-matching --vimgrep --pcre2 --ignore-case "
+          (mapconcat (lambda (glob) (concat "--glob " glob))
+                     (org-roam--list-files-search-globs org-roam-file-extensions)
+                     " ")
+          " --file " (shell-quote-argument temp-file) " "
+          (shell-quote-argument (expand-file-name org-roam-directory))))
+
 (defun org-roam-unlinked-references-section (node)
   "The unlinked references section for NODE.
 References from FILE are excluded."
   (when (and (executable-find "rg")
+             (org-roam-node-title node)
              (not (string-match "PCRE2 is not available"
                                 (shell-command-to-string "rg --pcre2-version"))))
     (let* ((titles (cons (org-roam-node-title node)
                          (org-roam-node-aliases node)))
-           (rg-command (concat "rg -o --vimgrep -P -i "
-                               (mapconcat (lambda (glob) (concat "-g " glob))
-                                          (org-roam--list-files-search-globs org-roam-file-extensions)
-                                          " ")
-                               (format " '\\[([^[]]++|(?R))*\\]%s' "
-                                       (mapconcat (lambda (title)
-                                                    (format "|(\\b%s\\b)" (shell-quote-argument title)))
-                                                  titles ""))
-                               org-roam-directory))
-           (results (split-string (shell-command-to-string rg-command) "\n"))
-           f row col match)
-      (magit-insert-section (unlinked-references)
-        (magit-insert-heading "Unlinked References:")
-        (dolist (line results)
-          (save-match-data
-            (when (string-match org-roam-unlinked-references-result-re line)
-              (setq f (match-string 1 line)
-                    row (string-to-number (match-string 2 line))
-                    col (string-to-number (match-string 3 line))
-                    match (match-string 4 line))
-              (when (and match
-                         (not (f-equal-p (org-roam-node-file node) f))
-                         (member (downcase match) (mapcar #'downcase titles)))
-                (magit-insert-section section (org-roam-grep-section)
-                  (oset section file f)
-                  (oset section row row)
-                  (oset section col col)
-                  (insert (propertize (format "%s:%s:%s"
-                                              (truncate-string-to-width (file-name-base f) 15 nil nil t)
-                                              row col) 'font-lock-face 'org-roam-dim)
-                          " "
-                          (org-roam-fontify-like-in-org-mode
-                           (org-roam-unlinked-references-preview-line f row))
-                          "\n"))))))
-        (insert ?\n)))))
+           ;; Create temp file for the regex pattern
+           (temp-file (make-temp-file "org-roam-rg-pattern-"))
+           (rg-command (org-roam-unlinked-references--rg-command titles temp-file)))
+      ;; Use unwind-protect to ensure temp file cleanup even if errors occur
+      (unwind-protect
+          (let* ((results (split-string (shell-command-to-string rg-command) "\n"))
+                 f row col match)
+            (magit-insert-section (unlinked-references)
+              (magit-insert-heading "Unlinked References:")
+              (dolist (line results)
+                (save-match-data
+                  (when (string-match org-roam-unlinked-references-result-re line)
+                    (setq f (match-string 1 line)
+                          row (string-to-number (match-string 2 line))
+                          col (string-to-number (match-string 3 line))
+                          match (match-string 4 line))
+                    (when (and match
+                               (not (file-equal-p (org-roam-node-file node) f))
+                               (member (downcase match) (mapcar #'downcase titles)))
+                      (magit-insert-section section (org-roam-grep-section)
+                        (oset section file f)
+                        (oset section row row)
+                        (oset section col col)
+                        (insert (propertize (format "%s:%s:%s"
+                                                    (truncate-string-to-width (file-name-base f) 15 nil nil t)
+                                                    row col) 'font-lock-face 'org-roam-dim)
+                                " "
+                                (org-roam-fontify-like-in-org-mode
+                                 (org-roam-unlinked-references-preview-line f row))
+                                "\n"))))))
+              (insert ?\n)))
+        ;; Clean up temp file - this runs even if an error occurs above
+        (delete-file temp-file)))))
 
 (provide 'org-roam-mode)
 ;;; org-roam-mode.el ends here

org-roam-node.el

@@ -1,12 +1,12 @@
 ;;; org-roam-node.el --- Interfacing and interacting with nodes -*- lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (magit-section "3.0.0"))
+;; Version: 2.3.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -32,13 +32,23 @@
 ;; interactively.
 ;;
 ;;; Code:
+(require 'crm)
 (require 'org-roam)
 
 ;;; Options
 ;;;; Completing-read
-(defcustom org-roam-node-display-template
-  (concat "${title:*} " (propertize "${tags:10}" 'face 'org-tag))
+(defcustom org-roam-node-display-template "${title}"
   "Configures display formatting for Org-roam node.
+
+If it is a function, it will be called to format a node.
+Its result is expected to be a string (potentially with
+embedded properties).
+
+If it is a string and it will be used as described in org-roam
+ (see org-roam-node-display-template)
+
+When it is a string, the following processing is done:
+
 Patterns of form \"${field-name:length}\" are interpolated based
 on the current node.
 
@@ -64,9 +74,23 @@ as many characters as possible and will be aligned accordingly.
 
 A closure can also be assigned to this variable in which case the
 closure is evaluated and the return value is used as the
-template. The closure must evaluate to a valid template string."
+template. The closure must evaluate to a valid template string.
+
+When org-roam-node-display-template is a function, the function is
+expected to return a string, potentially propertized. For example, the
+following function shows the title and base filename of the node:
+
+\(defun my--org-roam-format (node)
+  \"formats the node\"
+  (format \"%-40s %s\"
+          (if (org-roam-node-title node)
+              (propertize (org-roam-node-title node) 'face 'org-todo)
+            \"\")
+          (file-name-nondirectory (org-roam-node-file node))))
+
+\q(setq org-roam-node-display-template 'my--org-roam-format)"
   :group 'org-roam
-  :type  '(string function))
+  :type  '(choice string function))
 
 (defcustom org-roam-node-annotation-function #'org-roam-node-read--annotation
   "This function used to attach annotations for `org-roam-node-read'.
@@ -90,7 +114,7 @@ argument, an `org-roam-node', and return a string.
 If a string is provided, it is a template string expanded by
 `org-roam-node--format-entry'."
   :group 'org-roam
-  :type '(string function))
+  :type '(choice string function))
 
 (defcustom org-roam-node-template-prefixes
   '(("tags" . "#")
@@ -113,6 +137,12 @@ It takes a single argument REF, which is a propertized string."
   :group 'org-roam
   :type  '(function))
 
+(defcustom org-roam-ref-prompt-function nil
+  "Function to prompt for ref strings in `org-roam-ref-add'.
+Should take no arguments, prompt the user, and return a string."
+  :group 'org-roam
+  :type 'function)
+
 ;;;; Completion-at-point
 (defcustom org-roam-completion-everywhere nil
   "When non-nil, provide link completion matching outside of Org links."
@@ -132,10 +162,15 @@ It takes a single argument REF, which is a propertized string."
   :type 'boolean)
 
 (defcustom org-roam-extract-new-file-path "%<%Y%m%d%H%M%S>-${slug}.org"
-  "The file path to use when a node is extracted to its own file."
+  "The file path template to use when a node is extracted to its own file.
+This path is relative to `org-roam-directory'."
   :group 'org-roam
   :type 'string)
 
+(defvar org-roam-link-type "roam"
+  "Link type for org-roam nodes.
+Replaced by `id' automatically when `org-roam-link-auto-replace' is non-nil.")
+
 (defvar org-roam-node-history nil
   "Minibuffer history of nodes.")
 
@@ -144,6 +179,11 @@ It takes a single argument REF, which is a propertized string."
 
 ;;; Definition
 (cl-defstruct (org-roam-node (:constructor org-roam-node-create)
+                             (:constructor org-roam-node-create-from-db
+                                           (title aliases                    ; 2
+                                                  id file file-title level todo     ; 5
+                                                  point priority scheduled deadline properties ;;5
+                                                  olp file-atime file-mtime tags refs)) ;;5
                              (:copier nil))
   "A heading or top level file with an assigned ID property."
   file file-title file-hash file-atime file-mtime
@@ -175,6 +215,7 @@ It takes a single argument REF, which is a propertized string."
                            776 ; U+0308 COMBINING DIAERESIS
                            777 ; U+0309 COMBINING HOOK ABOVE
                            778 ; U+030A COMBINING RING ABOVE
+                           779 ; U+030B COMBINING DOUBLE ACUTE ACCENT
                            780 ; U+030C COMBINING CARON
                            795 ; U+031B COMBINING HORN
                            803 ; U+0323 COMBINING DOT BELOW
@@ -186,14 +227,12 @@ It takes a single argument REF, which is a propertized string."
                            816 ; U+0330 COMBINING TILDE BELOW
                            817 ; U+0331 COMBINING MACRON BELOW
                            )))
-    (cl-flet* ((nonspacing-mark-p (char)
-                                  (memq char slug-trim-chars))
-               (strip-nonspacing-marks (s)
-                                       (string-glyph-compose
-                                        (apply #'string (seq-remove #'nonspacing-mark-p
-                                                                    (string-glyph-decompose s)))))
-               (cl-replace (title pair)
-                           (replace-regexp-in-string (car pair) (cdr pair) title)))
+    (cl-flet* ((nonspacing-mark-p (char) (memq char slug-trim-chars))
+               (strip-nonspacing-marks (s) (string-glyph-compose
+                                            (apply #'string
+                                                   (seq-remove #'nonspacing-mark-p
+                                                               (string-glyph-decompose 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
@@ -211,6 +250,10 @@ It takes a single argument REF, which is a propertized string."
     (_
      (org-roam-node-title node))))
 
+(cl-defmethod org-roam-node-category ((node org-roam-node))
+  "Return the category for NODE."
+  (cdr (assoc-string "CATEGORY" (org-roam-node-properties node))))
+
 ;;; Nodes
 ;;;; Getters
 (defun org-roam-node-at-point (&optional assert)
@@ -225,9 +268,12 @@ populated."
                                     (magit-section-up)
                                     (org-roam-node-at-point)))
         (t (org-with-wide-buffer
-            (org-back-to-heading-or-point-min t)
-            (while (and (not (org-roam-db-node-p))
-                        (not (bobp)))
+            (while (not (or (org-roam-db-node-p)
+                            (bobp)
+                            (eq (funcall outline-level)
+                                (save-excursion
+                                  (org-roam-up-heading-or-point-min)
+                                  (funcall outline-level)))))
               (org-roam-up-heading-or-point-min))
             (when-let ((id (org-id-get)))
               (org-roam-populate
@@ -244,17 +290,21 @@ Return nil if a node with ID does not exist."
                                     id)) 0)
     (org-roam-populate (org-roam-node-create :id id))))
 
-(defun org-roam-node-from-title-or-alias (s)
+(defun org-roam-node-from-title-or-alias (s &optional nocase)
   "Return an `org-roam-node' for the node with title or alias S.
 Return nil if the node does not exist.
-Throw an error if multiple choices exist."
+Throw an error if multiple choices exist.
+
+If NOCASE is non-nil, the query is case insensitive.  It is case sensitive otherwise."
   (let ((matches (seq-uniq
                   (append
-                   (org-roam-db-query [:select [id] :from nodes
-                                       :where (= title $s1)]
+                   (org-roam-db-query (vconcat [:select [id] :from nodes
+                                                :where (= title $s1)]
+                                               (if nocase [ :collate NOCASE ]))
                                       s)
-                   (org-roam-db-query [:select [node-id] :from aliases
-                                       :where (= alias $s1)]
+                   (org-roam-db-query (vconcat [:select [node-id] :from aliases
+                                                :where (= alias $s1)]
+                                               (if nocase [ :collate NOCASE ]))
                                       s)))))
     (cond
      ((seq-empty-p matches)
@@ -293,7 +343,8 @@ Return nil if there's no node with such REF."
 Uses the ID, and fetches remaining details from the database.
 This can be quite costly: avoid, unless dealing with very few
 nodes."
-  (when-let ((node-info (car (org-roam-db-query [:select [file level pos todo priority
+  (when-let ((node-info (car (org-roam-db-query [:select [
+                                                          file level pos todo priority
                                                           scheduled deadline title properties olp]
                                                  :from nodes
                                                  :where (= id $s1)
@@ -334,23 +385,27 @@ nodes."
 (defun org-roam-node-list ()
   "Return all nodes stored in the database as a list of `org-roam-node's."
   (let ((rows (org-roam-db-query
-               "SELECT
+               "
+SELECT
+  title,
+  aliases,
+
   id,
   file,
   filetitle,
   \"level\",
   todo,
+
   pos,
   priority ,
   scheduled ,
   deadline ,
-  title,
   properties ,
+
   olp,
   atime,
   mtime,
   '(' || group_concat(tags, ' ') || ')' as tags,
-  aliases,
   refs
 FROM
   (
@@ -399,46 +454,56 @@ FROM
     LEFT JOIN refs ON refs.node_id = nodes.id
     GROUP BY nodes.id, tags.tag, aliases.alias )
   GROUP BY id, tags )
-GROUP BY id")))
-    (cl-loop for row in rows
-             append (pcase-let* ((`(,id ,file ,file-title ,level ,todo ,pos ,priority ,scheduled ,deadline
-                                        ,title ,properties ,olp ,atime ,mtime ,tags ,aliases ,refs)
-                                  row)
-                                 (all-titles (cons title aliases)))
-                      (mapcar (lambda (temp-title)
-                                (org-roam-node-create :id id
-                                                      :file file
-                                                      :file-title file-title
-                                                      :file-atime atime
-                                                      :file-mtime mtime
-                                                      :level level
-                                                      :point pos
-                                                      :todo todo
-                                                      :priority priority
-                                                      :scheduled scheduled
-                                                      :deadline deadline
-                                                      :title temp-title
-                                                      :aliases aliases
-                                                      :properties properties
-                                                      :olp olp
-                                                      :tags tags
-                                                      :refs refs))
-                              all-titles)))))
+GROUP BY id
+")))
+    (mapcan
+     (lambda (row)
+       (let (
+             (all-titles (cons (car row) (nth 1 row)))
+             )
+         (mapcar (lambda (temp-title)
+                   (apply 'org-roam-node-create-from-db (cons temp-title (cdr row))))
+                 all-titles)
+         ))
+     rows)
+    )
+  )
 
 ;;;; Finders
-(defun org-roam-node-find-noselect (node &optional force)
-  "Navigate to the point for NODE, and return the buffer.
-If NODE is already visited, this won't automatically move the
-point to the beginning of the NODE, unless FORCE is non-nil."
-  (unless (org-roam-node-file node)
-    (user-error "Node does not have corresponding file"))
-  (let ((buf (find-file-noselect (org-roam-node-file node))))
-    (with-current-buffer buf
-      (when (or force
-                (not (equal (org-roam-node-id node)
-                            (org-roam-id-at-point))))
-        (goto-char (org-roam-node-point node))))
-    buf))
+(defun org-roam-node-marker (node)
+  "Get the marker for NODE."
+  (let* ((file (org-roam-node-file node))
+         (buffer (or (find-buffer-visiting file)
+                     (find-file-noselect file))))
+    (with-current-buffer buffer
+      (move-marker (make-marker) (org-roam-node-point node) buffer))))
+
+(defun org-roam-node-open (node &optional cmd force)
+  "Go to the node NODE.
+CMD is the command used to display the buffer. If not provided,
+`org-link-frame-setup' is respected. Assumes that the node is
+fully populated, with file and point. If NODE is already visited,
+this won't automatically move the point to the beginning of the
+NODE, unless FORCE is non-nil."
+  (interactive (list (org-roam-node-at-point) current-prefix-arg))
+  (org-mark-ring-push)
+  (let ((m (org-roam-node-marker node))
+        (cmd (or cmd
+                 (cdr
+                  (assq
+                   (cdr (assq 'file org-link-frame-setup))
+                   '((find-file . switch-to-buffer)
+                     (find-file-other-window . switch-to-buffer-other-window)
+                     (find-file-other-frame . switch-to-buffer-other-frame))))
+                 'switch-to-buffer-other-window)))
+    (if (not (equal (current-buffer) (marker-buffer m)))
+        (funcall cmd (marker-buffer m)))
+    (when (or force
+              (not (equal (org-roam-node-id node)
+                          (org-roam-id-at-point))))
+      (goto-char m))
+    (move-marker m nil))
+  (org-fold-show-context))
 
 (defun org-roam-node-visit (node &optional other-window force)
   "From the current buffer, visit NODE. Return the visited buffer.
@@ -450,16 +515,13 @@ If NODE is already visited, this won't automatically move the
 point to the beginning of the NODE, unless FORCE is non-nil. In
 interactive calls FORCE always set to t."
   (interactive (list (org-roam-node-at-point t) current-prefix-arg t))
-  (let ((buf (org-roam-node-find-noselect node force))
-        (display-buffer-fn (if other-window
+  (org-roam-node-open node (if other-window
                                #'switch-to-buffer-other-window
-                             #'pop-to-buffer-same-window)))
-    (funcall display-buffer-fn buf)
-    (when (org-invisible-p) (org-show-context))
-    buf))
+                             #'pop-to-buffer-same-window)
+                      force))
 
 ;;;###autoload
-(cl-defun org-roam-node-find (&optional other-window initial-input filter-fn &key templates)
+(cl-defun org-roam-node-find (&optional other-window initial-input filter-fn pred &key templates)
   "Find and open an Org-roam node by its title or alias.
 INITIAL-INPUT is the initial input for the prompt.
 FILTER-FN is a function to filter out nodes: it takes an `org-roam-node',
@@ -468,7 +530,7 @@ If OTHER-WINDOW, visit the NODE in another window.
 The TEMPLATES, if provided, override the list of capture templates (see
 `org-roam-capture-'.)"
   (interactive current-prefix-arg)
-  (let ((node (org-roam-node-read initial-input filter-fn)))
+  (let ((node (org-roam-node-read initial-input filter-fn pred)))
     (if (org-roam-node-file node)
         (org-roam-node-visit node other-window)
       (org-roam-capture-
@@ -477,16 +539,16 @@ The TEMPLATES, if provided, override the list of capture templates (see
        :props '(:finalize find-file)))))
 
 ;;;###autoload
-(defun org-roam-node-random (&optional other-window)
+(defun org-roam-node-random (&optional other-window filter-fn)
   "Find and open a random Org-roam node.
 With prefix argument OTHER-WINDOW, visit the node in another
-window instead."
+window instead.
+FILTER-FN is a function to filter out nodes: it takes an `org-roam-node',
+and when nil is returned the node will be filtered out."
   (interactive current-prefix-arg)
-  (let ((random-row (seq-random-elt (org-roam-db-query [:select [id file pos] :from nodes]))))
-    (org-roam-node-visit (org-roam-node-create :id (nth 0 random-row)
-                                               :file (nth 1 random-row)
-                                               :point (nth 2 random-row))
-                         other-window)))
+  (org-roam-node-visit
+   (cdr (seq-random-elt (org-roam-node-read--completions filter-fn)))
+   other-window))
 
 ;;;; Completing-read interface
 (defun org-roam-node-read (&optional initial-input filter-fn sort-fn require-match prompt)
@@ -498,17 +560,7 @@ SORT-FN is a function to sort nodes. See `org-roam-node-read-sort-by-file-mtime'
 for an example sort function.
 If REQUIRE-MATCH, the minibuffer prompt will require a match.
 PROMPT is a string to show at the beginning of the mini-buffer, defaulting to \"Node: \""
-  (let* ((nodes (org-roam-node-read--completions))
-         (nodes (if filter-fn
-                    (cl-remove-if-not
-                     (lambda (n) (funcall filter-fn (cdr n)))
-                     nodes)
-                  nodes))
-         (sort-fn (or sort-fn
-                      (when org-roam-node-default-sort
-                        (intern (concat "org-roam-node-read-sort-by-"
-                                        (symbol-name org-roam-node-default-sort))))))
-         (_ (when sort-fn (setq nodes (seq-sort sort-fn nodes))))
+  (let* ((nodes (org-roam-node-read--completions filter-fn sort-fn))
          (prompt (or prompt "Node: "))
          (node (completing-read
                 prompt
@@ -529,15 +581,52 @@ PROMPT is a string to show at the beginning of the mini-buffer, defaulting to \"
     (or (cdr (assoc node nodes))
         (org-roam-node-create :title node))))
 
-(defun org-roam-node-read--completions ()
+(defun org-roam--format-nodes-using-template (nodes)
+  "Formats NODES using org-roam template features.
+Uses org-roam--node-display-template."
+  (let  (
+         (wTemplate (org-roam-node--process-display-format org-roam-node-display-template))
+         )
+    (mapcar (lambda (node)
+              (org-roam-node-read--to-candidate node wTemplate)) nodes))
+  )
+
+(defun org-roam--format-nodes-using-function (nodes)
+  "Formats NODES using the function org-roam-node-display-template."
+  (mapcar (lambda (node)
+            (cons
+             (propertize (funcall org-roam-node-display-template node) 'node node)
+             node))
+          nodes)
+  )
+
+(defun org-roam-node-read--completions (&optional filter-fn sort-fn)
   "Return an alist for node completion.
 The car is the displayed title or alias for the node, and the cdr
 is the `org-roam-node'.
+FILTER-FN is a function to filter out nodes: it takes an `org-roam-node',
+and when nil is returned the node will be filtered out.
+SORT-FN is a function to sort nodes. See `org-roam-node-read-sort-by-file-mtime'
+for an example sort function.
 The displayed title is formatted according to `org-roam-node-display-template'."
-  (let ((template (org-roam-node--process-display-format org-roam-node-display-template))
-        (nodes (org-roam-node-list)))
-    (mapcar (lambda (node)
-              (org-roam-node-read--to-candidate node template)) nodes)))
+  (let* (
+         (nodes (org-roam-node-list))
+         (nodes (if filter-fn
+                    (cl-remove-if-not
+                     (lambda (n) (funcall filter-fn n))
+                     nodes)
+                  nodes))
+         (nodes (if (functionp org-roam-node-display-template)
+                    (org-roam--format-nodes-using-function nodes)
+                  (org-roam--format-nodes-using-template nodes)))
+
+         (sort-fn (or sort-fn
+                      (when org-roam-node-default-sort
+                        (intern (concat "org-roam-node-read-sort-by-"
+                                        (symbol-name org-roam-node-default-sort))))))
+         (nodes (if sort-fn (seq-sort sort-fn nodes)
+                  nodes)))
+    nodes))
 
 (defun org-roam-node-read--to-candidate (node template)
   "Return a minibuffer completion candidate given NODE.
@@ -545,7 +634,8 @@ TEMPLATE is the processed template used to format the entry."
   (let ((candidate-main (org-roam-node--format-entry
                          template
                          node
-                         (1- (frame-width)))))
+                         (1- (if (bufferp (current-buffer))
+                                 (window-width) (frame-width))))))
     (cons (propertize candidate-main 'node node) node)))
 
 (defun org-roam-node--format-entry (template node &optional width)
@@ -663,9 +753,13 @@ The INFO, if provided, is passed to the underlying `org-roam-capture-'."
                   (delete-region beg end)
                   (set-marker beg nil)
                   (set-marker end nil))
-                (insert (org-link-make-string
-                         (concat "id:" (org-roam-node-id node))
-                         description)))
+                (let ((id (org-roam-node-id node)))
+                  (insert (org-link-make-string
+                           (concat "id:" id)
+                           description))
+                  (run-hook-with-args 'org-roam-post-node-insert-hook
+                                      id
+                                      description)))
             (org-roam-capture-
              :node node
              :info info
@@ -673,33 +767,12 @@ The INFO, if provided, is passed to the underlying `org-roam-capture-'."
              :props (append
                      (when (and beg end)
                        (list :region (cons beg end)))
-                     (list :insert-at (point-marker)
-                           :link-description description
+                     (list :link-description description
                            :finalize 'insert-link))))))
     (deactivate-mark)))
 
-(add-hook 'org-roam-find-file-hook #'org-roam-open-id-with-org-roam-db-h)
-(defun org-roam-open-id-with-org-roam-db-h ()
-  "Try to open \"id:\" links at point by querying them to the database."
-  (add-hook 'org-open-at-point-functions #'org-roam-open-id-at-point nil t))
-
-(defun org-roam-open-id-at-point ()
-  "Navigate to \"id:\" link at point using the Org-roam database."
-  (when (org-in-regexp org-link-any-re)
-    (let ((link (match-string 2))
-          id)
-      (when (string-prefix-p "id:" link)
-        (setq id (substring-no-properties link 3))
-        (let ((node (org-roam-populate (org-roam-node-create :id id))))
-          (cond
-           ((org-roam-node-file node)
-            (org-mark-ring-push)
-            (org-roam-node-visit node nil 'force)
-            t)
-           (t nil)))))))
-
 ;;;;; [roam:] link
-(org-link-set-parameters "roam" :follow #'org-roam-link-follow-link)
+(org-link-set-parameters org-roam-link-type :follow #'org-roam-link-follow-link)
 (defun org-roam-link-follow-link (title-or-alias)
   "Navigate \"roam:\" link to find and open the node with TITLE-OR-ALIAS.
 Assumes that the cursor was put where the link is."
@@ -728,7 +801,7 @@ Assumes that the cursor was put where the link is."
              node)
         (goto-char (org-element-property :begin link))
         (when (and (org-in-regexp org-link-any-re 1)
-                   (string-equal type "roam")
+                   (string-equal type org-roam-link-type)
                    (setq node (save-match-data (org-roam-node-from-title-or-alias path))))
           (replace-match (org-link-make-string
                           (concat "id:" (org-roam-node-id node))
@@ -738,7 +811,7 @@ Assumes that the cursor was put where the link is."
   "Replace all \"roam:\" links in buffer with \"id:\" links."
   (interactive)
   (org-with-point-at 1
-    (while (re-search-forward org-link-bracket-re nil t)
+    (while (search-forward (concat "[[" org-roam-link-type ":") nil t)
       (org-roam-link-replace-at-point))))
 
 (add-hook 'org-roam-find-file-hook #'org-roam--replace-roam-links-on-save-h)
@@ -758,7 +831,8 @@ We use this as a substitute for `org-link-bracket-re', because
   "Complete \"roam:\" link at point to an existing Org-roam node."
   (let (roam-p start end)
     (when (org-in-regexp org-roam-bracket-completion-re 1)
-      (setq roam-p (not (string-blank-p (match-string 1)))
+      (setq roam-p (not (or (org-in-src-block-p)
+                            (string-blank-p (match-string 1))))
             start (match-beginning 2)
             end (match-end 2))
       (list start end
@@ -780,6 +854,7 @@ outside of the bracket syntax for links (i.e. \"[[roam:|]]\"),
 hence \"everywhere\"."
   (when (and org-roam-completion-everywhere
              (thing-at-point 'word)
+             (not (org-in-src-block-p))
              (not (save-match-data (org-in-regexp org-link-any-re))))
     (let ((bounds (bounds-of-thing-at-point 'word)))
       (list (car bounds) (cdr bounds)
@@ -794,6 +869,8 @@ hence \"everywhere\"."
             :exclusive 'no))))
 
 (add-hook 'org-roam-find-file-hook #'org-roam--register-completion-functions-h)
+(add-hook 'org-roam-indirect-buffer-hook #'org-roam--register-completion-functions-h)
+
 (defun org-roam--register-completion-functions-h ()
   "Setup `org-roam-completion-functions' for `completion-at-point'."
   (dolist (f org-roam-completion-functions)
@@ -811,7 +888,8 @@ Any tags declared on #+FILETAGS: are transferred to tags on the new top heading.
 Any top level properties drawers are incorporated into the new heading."
   (interactive)
   (org-with-point-at 1
-    (org-map-entries 'org-do-demote)
+    (org-map-region #'org-do-demote
+                    (point-min) (point-max))
     (insert "* "
             (org-roam--get-keyword "title")
             "\n")
@@ -820,31 +898,52 @@ Any top level properties drawers are incorporated into the new heading."
     (org-roam-erase-keyword "title")
     (org-roam-erase-keyword "filetags")))
 
+(defun org-roam--h1-count ()
+  "Count level-1 headings in the current file."
+  (let ((h1-count 0))
+    (org-with-wide-buffer
+     (org-map-region (lambda ()
+                       (if (= (org-current-level) 1)
+                           (cl-incf h1-count)))
+                     (point-min) (point-max))
+     h1-count)))
+
+(defun org-roam--buffer-promoteable-p ()
+  "Verify that this buffer is promoteable:
+There is a single level-1 heading
+and no extra content before the first heading."
+  (and
+   (= (org-roam--h1-count) 1)
+   (org-with-point-at 1 (org-at-heading-p))))
+
 (defun org-roam-promote-entire-buffer ()
   "Promote the current buffer.
-Converts a file containing a headline node at the top to a file
+Converts a file containing a single level-1 headline node to a file
 node."
   (interactive)
+  (unless (org-roam--buffer-promoteable-p)
+    (user-error "Cannot promote: multiple root headings or there is extra file-level text"))
   (org-with-point-at 1
-    (org-map-entries (lambda ()
-                       (when (> (org-outline-level) 1)
-                         (org-do-promote))))
     (let ((title (nth 4 (org-heading-components)))
-          (tags (nth 5 (org-heading-components))))
-      (beginning-of-line)
-      (kill-line 1)
-      (org-roam-set-keyword "title" title)
-      (when tags (org-roam-set-keyword "filetags" tags)))))
+          (tags (org-get-tags)))
+      (org-fold-show-all)
+      (kill-whole-line)
+      (org-roam-end-of-meta-data t)
+      (insert "#+title: " title "\n")
+      (when tags (org-roam-tag-add tags))
+      (org-map-region #'org-promote (point-min) (point-max))
+      (org-roam-db-update-file))))
 
 ;;;###autoload
-(defun org-roam-refile ()
-  "Refile node at point to an Org-roam node.
+(defun org-roam-refile (node)
+  "Refile node at point to an org-roam NODE.
+
 If region is active, then use it instead of the node at point."
-  (interactive)
+  (interactive
+   (list (org-roam-node-read nil nil nil 'require-match)))
   (let* ((regionp (org-region-active-p))
          (region-start (and regionp (region-beginning)))
          (region-end (and regionp (region-end)))
-         (node (org-roam-node-read nil nil nil 'require-match))
          (file (org-roam-node-file node))
          (nbuf (or (find-buffer-visiting file)
                    (find-file-noselect file)))
@@ -888,7 +987,7 @@ If region is active, then use it instead of the node at point."
         (if (buffer-file-name)
             (delete-file (buffer-file-name)))
         (set-buffer-modified-p nil)
-        ;; In this was done during capture, abort the capture process.
+        ;; If this was done during capture, abort the capture process.
         (when (and org-capture-mode
                    (buffer-base-buffer (current-buffer)))
           (org-capture-kill))
@@ -920,53 +1019,22 @@ If region is active, then use it instead of the node at point."
                            (t (let ((r (read-from-minibuffer (format "%s: " key) default-val)))
                                 (plist-put template-info ksym r)
                                 r)))))))
-           (file-path (read-file-name "Extract node to: "
-                                      (file-name-as-directory org-roam-directory) template nil template)))
+           (file-path
+            (expand-file-name
+             (read-file-name "Extract node to: "
+                             (file-name-as-directory org-roam-directory) template nil template)
+             org-roam-directory)))
       (when (file-exists-p file-path)
         (user-error "%s exists. Aborting" file-path))
       (org-cut-subtree)
       (save-buffer)
       (with-current-buffer (find-file-noselect file-path)
         (org-paste-subtree)
+        (while (> (org-current-level) 1) (org-promote-subtree))
+        (save-buffer)
         (org-roam-promote-entire-buffer)
         (save-buffer)))))
 
-;;; IDs
-;;;; Getters
-(defun org-roam-id-at-point ()
-  "Return the ID at point, if any.
-Recursively traverses up the headline tree to find the
-first encapsulating ID."
-  (org-with-wide-buffer
-   (org-back-to-heading-or-point-min t)
-   (while (and (not (org-roam-db-node-p))
-               (not (bobp)))
-     (org-roam-up-heading-or-point-min))
-   (when (org-roam-db-node-p)
-     (org-id-get))))
-
-;;;###autoload
-(defun org-roam-update-org-id-locations (&rest directories)
-  "Scan Org-roam files to update `org-id' related state.
-This is like `org-id-update-id-locations', but will automatically
-use the currently bound `org-directory' and `org-roam-directory'
-along with DIRECTORIES (if any), where the lookup for files in
-these directories will be always recursive.
-
-Note: Org-roam doesn't have hard dependency on
-`org-id-locations-file' to lookup IDs for nodes that are stored
-in the database, but it still tries to properly integrates with
-`org-id'. This allows the user to cross-reference IDs outside of
-the current `org-roam-directory', and also link with \"id:\"
-links to headings/files within the current `org-roam-directory'
-that are excluded from identification in Org-roam as
-`org-roam-node's, e.g. with \"ROAM_EXCLUDE\" property."
-  (interactive)
-  (cl-loop for dir in (cons org-roam-directory directories)
-           for org-roam-directory = dir
-           nconc (org-roam-list-files) into files
-           finally (org-id-update-id-locations files org-roam-verbose)))
-
 ;;; Refs
 ;;;; Completing-read interface
 (defun org-roam-ref-read (&optional initial-input filter-fn)
@@ -1003,8 +1071,10 @@ The car is the ref, and the cdr is the corresponding node for the ref."
                                                               :file file
                                                               :point pos
                                                               :title title)))
-                       (cons (propertize ref 'node node 'type type)
-                             node)))))
+                       (cons
+                        (concat (propertize ref 'node node 'type type)
+                                (propertize id 'invisible t))
+                        node)))))
 
 (defun org-roam-ref-read--annotation (ref)
   "Return the annotation for REF, which assumed to be a propertized string."
@@ -1027,11 +1097,15 @@ and when nil is returned the node will be filtered out."
 ;;;; Editing
 (defun org-roam-ref-add (ref)
   "Add REF to the node at point."
-  (interactive "sRef: ")
+  (interactive `(,(if org-roam-ref-prompt-function
+                      (funcall org-roam-ref-prompt-function)
+                    (read-string "Ref: "))))
   (let ((node (org-roam-node-at-point 'assert)))
     (save-excursion
       (goto-char (org-roam-node-point node))
-      (org-roam-property-add "ROAM_REFS" ref))))
+      (org-roam-property-add "ROAM_REFS" (if (member " " (string-to-list ref))
+                                             (concat "\"" ref "\"")
+                                           ref)))))
 
 (defun org-roam-ref-remove (&optional ref)
   "Remove a REF from the node at point."
@@ -1059,7 +1133,8 @@ and when nil is returned the node will be filtered out."
 (defun org-roam-tag-add (tags)
   "Add TAGS to the node at point."
   (interactive
-   (list (completing-read-multiple "Tag: " (org-roam-tag-completions))))
+   (list (let ((crm-separator "[ 	]*:[ 	]*"))
+           (completing-read-multiple "Tag: " (org-roam-tag-completions)))))
   (let ((node (org-roam-node-at-point 'assert)))
     (save-excursion
       (goto-char (org-roam-node-point node))

org-roam-utils.el

@@ -1,12 +1,12 @@
 ;;; org-roam-utils.el --- Utilities for Org-roam -*- lexical-binding: t; -*-
 
-;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4"))
+;; Version: 2.3.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -52,6 +52,16 @@
        (org-roam-replace-string "\\" "\\\\")
        (org-roam-replace-string "\"" "\\\"")))
 
+(defun org-roam-word-wrap (len s)
+  "If S is longer than LEN, wrap the words with newlines."
+  (declare (side-effect-free t))
+  (save-match-data
+    (with-temp-buffer
+      (insert s)
+      (let ((fill-column len))
+        (fill-region (point-min) (point-max)))
+      (buffer-substring (point-min) (point-max)))))
+
 (defun org-roam-string-equal (s1 s2)
   "Return t if S1 and S2 are equal.
 Like `string-equal', but case-insensitive."
@@ -59,6 +69,14 @@ Like `string-equal', but case-insensitive."
        (or (string-equal s1 s2)
            (string-equal (downcase s1) (downcase s2)))))
 
+(defun org-roam-whitespace-content (s)
+  "Return the whitespace content at the end of S."
+  (with-temp-buffer
+    (insert s)
+    (skip-chars-backward " \t\n")
+    (buffer-substring-no-properties
+     (point) (point-max))))
+
 (defun org-roam-strip-comments (s)
   "Strip Org comments from string S."
   (with-temp-buffer
@@ -66,7 +84,8 @@ Like `string-equal', but case-insensitive."
     (goto-char (point-min))
     (while (not (eobp))
       (if (org-at-comment-p)
-          (delete-region (point-at-bol) (progn (forward-line) (point)))
+          (delete-region (line-beginning-position)
+                         (progn (forward-line) (point)))
         (forward-line)))
     (buffer-string)))
 
@@ -99,6 +118,12 @@ SPEC is a list, as per `dolist'."
     `(dolist ,spec ,@body)))
 
 ;;; File utilities
+(defun org-roam-descendant-of-p (a b)
+  "Return t if A is descendant of B."
+  (unless (and a b (equal (file-truename a) (file-truename b)))
+    (string-prefix-p (replace-regexp-in-string "^\\([A-Za-z]\\):" 'downcase (expand-file-name b) t t)
+                     (replace-regexp-in-string "^\\([A-Za-z]\\):" 'downcase (expand-file-name a) t t))))
+
 (defmacro org-roam-with-file (file keep-buf-p &rest body)
   "Execute BODY within FILE.
 If FILE is nil, execute BODY in the current buffer.
@@ -138,7 +163,8 @@ If FILE, set `default-directory' to FILE's directory and insert its contents."
   (let ((current-org-roam-directory (make-symbol "current-org-roam-directory")))
     `(let ((,current-org-roam-directory org-roam-directory))
        (with-temp-buffer
-         (let ((org-roam-directory ,current-org-roam-directory))
+         (let ((org-roam-directory ,current-org-roam-directory)
+               (org-inhibit-startup t))
            (delay-mode-hooks (org-mode))
            (when ,file
              (insert-file-contents ,file)
@@ -204,36 +230,10 @@ Like `org-fontify-like-in-org-mode', but supports `org-ref'."
     (insert s)
     (let ((org-ref-buffer-hacked t))
       (org-mode)
-      (org-font-lock-ensure)
+      (setq-local org-fold-core-style 'overlays)
+      (font-lock-ensure)
       (buffer-string))))
 
-;;;; Shielding regions
-(defface org-roam-shielded
-  '((t :inherit (warning)))
-  "Face for regions that are shielded (marked as read-only).
-This face is used on the region target by org-roam-insertion
-during an `org-roam-capture'."
-  :group 'org-roam-faces)
-
-(defun org-roam-shield-region (beg end)
-  "Shield region against modifications.
-BEG and END are markers for the beginning and end regions.
-REGION must be a cons-cell containing the marker to the region
-beginning and maximum values."
-  (add-text-properties beg end
-                       '(font-lock-face org-roam-shielded
-                                        read-only t)
-                       (marker-buffer beg)))
-
-(defun org-roam-unshield-region (beg end)
-  "Unshield the shielded REGION.
-BEG and END are markers for the beginning and end regions."
-  (let ((inhibit-read-only t))
-    (remove-text-properties beg end
-                            '(font-lock-face org-roam-shielded
-                                             read-only t)
-                            (marker-buffer beg))))
-
 ;;; Org-mode utilities
 ;;;; Motions
 (defun org-roam-up-heading-or-point-min ()
@@ -339,26 +339,14 @@ If the property is already set, it's value is replaced."
 (defun org-roam-add-property (val prop)
   "Add VAL value to PROP property for the node at point.
 Both, VAL and PROP are strings."
-  (let* ((p (org-entry-get (point) prop))
-         (lst (when p (split-string-and-unquote p)))
-         (lst (if (memq val lst) lst (cons val lst)))
-         (lst (seq-uniq lst)))
-    (org-set-property prop (combine-and-quote-strings lst))
-    val))
+  (org-roam-property-add prop val))
 
 (defun org-roam-remove-property (prop &optional val)
   "Remove VAL value from PROP property for the node at point.
 Both VAL and PROP are strings.
 
 If VAL is not specified, user is prompted to select a value."
-  (let* ((p (org-entry-get (point) prop))
-         (lst (when p (split-string-and-unquote p)))
-         (prop-to-remove (or val (completing-read "Remove: " lst)))
-         (lst (delete prop-to-remove lst)))
-    (if lst
-        (org-set-property prop (combine-and-quote-strings lst))
-      (org-delete-property prop))
-    prop-to-remove))
+  (org-roam-property-remove prop val))
 
 (defun org-roam-property-add (prop val)
   "Add VAL value to PROP property for the node at point.
@@ -461,8 +449,11 @@ See <https://github.com/raxod502/straight.el/issues/520>."
                                          '("Doom" "Spacemacs" "N/A" "I don't know"))
                       (quit "N/A"))))
     (insert (format "- Org: %s\n" (org-version nil 'full)))
-    (insert (format "- Org-roam: %s" (org-roam-version)))))
-
+    (insert (format "- Org-roam: %s" (org-roam-version)))
+    (insert (format "- sqlite-connector: %s"
+                    (if-let ((conn (org-roam-db--get-connection)))
+                        (eieio-object-class conn)
+                      "not connected")))))
 
 (provide 'org-roam-utils)
 ;;; org-roam-utils.el ends here

org-roam.el

@@ -1,12 +1,12 @@
 ;;; org-roam.el --- A database abstraction layer for Org-mode -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
+;; Version: 2.3.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (emacsql "4.1.0") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -71,7 +71,6 @@
 ;; majority of them can be found at https://github.com/org-roam and MELPA.
 ;;
 ;;; Code:
-(require 'f)
 (require 'dash)
 
 (require 'rx)
@@ -81,9 +80,13 @@
 (require 'magit-section)
 
 (require 'emacsql)
+;; REVIEW: is this require needed?
+;; emacsql-sqlite provides a common interface to an emacsql SQLite backend (e.g. emacs-sqlite-builtin)
+;; not to be confused with a backend itself named emacsql-sqlite that existed in emacsql < 4.0.
 (require 'emacsql-sqlite)
 
 (require 'org)
+(require 'org-attach)                   ; To set `org-attach-id-dir'
 (require 'org-id)
 (require 'ol)
 (require 'org-element)
@@ -123,6 +126,12 @@ All Org files, at any level of nesting, are considered part of the Org-roam."
   :group 'org-roam
   :type 'hook)
 
+(defcustom org-roam-post-node-insert-hook nil
+  "Hook run when an Org-roam node is inserted as an Org link.
+Each function takes two arguments: the id of the node, and the link description."
+  :group 'org-roam
+  :type 'hook)
+
 (defcustom org-roam-file-extensions '("org")
   "List of file extensions to be included by Org-Roam.
 While a file extension different from \".org\" may be used, the
@@ -131,9 +140,11 @@ responsibility to ensure that."
   :type '(repeat string)
   :group 'org-roam)
 
-(defcustom org-roam-file-exclude-regexp nil
-  "Files matching this regular expression are excluded from the Org-roam."
+(defcustom org-roam-file-exclude-regexp (list org-attach-id-dir)
+  "Files matching this regular expression or list of regular expressions are excluded from the Org-roam."
   :type '(choice
+          (repeat
+           (string :tag "Regular expression matching files to ignore"))
           (string :tag "Regular expression matching files to ignore")
           (const :tag "Include everything" nil))
   :group 'org-roam)
@@ -144,36 +155,46 @@ responsibility to ensure that."
     '(find fd fdfind rg))
   "Commands that will be used to find Org-roam files.
 
-It should be a list of symbols or cons cells representing any of the following
-supported file search methods.
+It should be a list of symbols or cons cells representing any of
+the following supported file search methods.
 
-The commands will be tried in order until an executable for a command is found.
-The Elisp implementation is used if no command in the list is found.
+The commands will be tried in order until an executable for a
+command is found. The Elisp implementation is used if no command
+in the list is found.
 
   `find'
+
     Use find as the file search method.
     Example command:
-    find /path/to/dir -type f \( -name \"*.org\" -o -name \"*.org.gpg\" \)
+      find /path/to/dir -type f \
+        \( -name \"*.org\" -o -name \"*.org.gpg\" -name \"*.org.age\" \)
 
   `fd'
+
     Use fd as the file search method.
-    Example command: fd /path/to/dir/ --type file -e \".org\" -e \".org.gpg\"
+    Example command:
+      fd /path/to/dir/ --type file -e \".org\" -e \".org.gpg\" -e \".org.age\"
 
   `fdfind'
+
     Same as `fd'. It's an alias that used in some OSes (e.g. Debian, Ubuntu)
 
   `rg'
-    Use ripgrep as the file search method.
-    Example command: rg /path/to/dir/ --files -g \"*.org\" -g \"*.org.gpg\"
 
-By default, `executable-find' will be used to look up the path to the
-executable. If a custom path is required, it can be specified together with the
-method symbol as a cons cell. For example: '(find (rg . \"/path/to/rg\"))."
-  :type '(set (const :tag "find" find)
-              (const :tag "fd" fd)
-              (const :tag "fdfind" fdfind)
-              (const :tag "rg" rg)
-              (const :tag "elisp" nil)))
+    Use ripgrep as the file search method.
+    Example command:
+       rg /path/to/dir/ --files -g \"*.org\" -g \"*.org.gpg\" -g \"*.org.age\"
+
+By default, `executable-find' will be used to look up the path to
+the executable. If a custom path is required, it can be specified
+together with the method symbol as a cons cell. For example:
+\\='(find (rg . \"/path/to/rg\"))."
+  :type '(set
+          (const :tag "find" find)
+          (const :tag "fd" fd)
+          (const :tag "fdfind" fdfind)
+          (const :tag "rg" rg)
+          (const :tag "elisp" nil)))
 
 ;;; Library
 (defun org-roam-file-p (&optional file)
@@ -184,19 +205,34 @@ FILE is an Org-roam file if:
 - It's located somewhere under `org-roam-directory'
 - It has a matching file extension (`org-roam-file-extensions')
 - It doesn't match excluded regexp (`org-roam-file-exclude-regexp')"
-  (let* ((path (or file (buffer-file-name (buffer-base-buffer))))
-         (ext (when path (org-roam--file-name-extension path)))
-         (ext (if (string= ext "gpg")
-                  (org-roam--file-name-extension (file-name-sans-extension path))
-                ext)))
-    (save-match-data
-      (and
-       path
-       (member ext org-roam-file-extensions)
-       (not (and org-roam-file-exclude-regexp
-                 (string-match-p org-roam-file-exclude-regexp path)))
-       (f-descendant-of-p path (expand-file-name org-roam-directory))))))
+  (when (or file (buffer-file-name (buffer-base-buffer)))
+    (let* ((path (or file (buffer-file-name (buffer-base-buffer))))
+           (relative-path (file-relative-name path org-roam-directory))
+           (ext (org-roam--file-name-extension path))
+           (ext (if (or (string= ext "gpg")
+                        (string= ext "age"))
+                    (org-roam--file-name-extension (file-name-sans-extension path))
+                  ext))
+           (org-roam-dir-p (org-roam-descendant-of-p path org-roam-directory))
+           (valid-file-ext-p (member ext org-roam-file-extensions))
+           (match-exclude-regexp-p
+            (cond
+             ((not org-roam-file-exclude-regexp) nil)
+             ((stringp org-roam-file-exclude-regexp)
+              (string-match-p org-roam-file-exclude-regexp relative-path))
+             ((listp org-roam-file-exclude-regexp)
+              (let (is-match)
+                (dolist (exclude-re org-roam-file-exclude-regexp)
+                  (setq is-match (or is-match (string-match-p exclude-re relative-path))))
+                is-match)))))
+      (save-match-data
+        (and
+         path
+         org-roam-dir-p
+         valid-file-ext-p
+         (not match-exclude-regexp-p))))))
 
+;;;###autoload
 (defun org-roam-list-files ()
   "Return a list of all Org-roam files under `org-roam-directory'.
 See `org-roam-file-p' for how each file is determined to be as
@@ -260,14 +296,16 @@ If no files are found, an empty list is returned."
        (shell-command-to-string it)
        (ansi-color-filter-apply it)
        (split-string it "\n")
-       (seq-filter #'s-present? it)))
+       (seq-filter (lambda (s)
+                     (not (or (null s) (string= "" s)))) it)))
 
 (defun org-roam--list-files-search-globs (exts)
   "Given EXTS, return a list of search globs.
 E.g. (\".org\") => (\"*.org\" \"*.org.gpg\")"
   (cl-loop for e in exts
            append (list (format "\"*.%s\"" e)
-                        (format "\"*.%s.gpg\"" e))))
+                        (format "\"*.%s.gpg\"" e)
+                        (format "\"*.%s.age\"" e))))
 
 (defun org-roam--list-files-find (executable dir)
   "Return all Org-roam files under DIR, using \"find\", provided as EXECUTABLE."
@@ -288,8 +326,9 @@ E.g. (\".org\") => (\"*.org\" \"*.org.gpg\")"
 (defun org-roam--list-files-rg (executable dir)
   "Return all Org-roam files under DIR, using \"rg\", provided as EXECUTABLE."
   (let* ((globs (org-roam--list-files-search-globs org-roam-file-extensions))
-         (command (string-join `(,executable "-L" ,dir "--files"
-                                             ,@(mapcar (lambda (glob) (concat "-g " glob)) globs)) " ")))
+         (command (string-join `(
+                                 ,executable "-L" ,dir "--files"
+                                 ,@(mapcar (lambda (glob) (concat "-g " glob)) globs)) " ")))
     (org-roam--shell-command-files command)))
 
 (declare-function org-roam--directory-files-recursively "org-roam-compat")
@@ -298,7 +337,7 @@ E.g. (\".org\") => (\"*.org\" \"*.org.gpg\")"
   "Return all Org-roam files under DIR, using Elisp based implementation."
   (let ((regex (concat "\\.\\(?:"(mapconcat
                                   #'regexp-quote org-roam-file-extensions
-                                  "\\|" )"\\)\\(?:\\.gpg\\)?\\'"))
+                                  "\\|" )"\\)\\(?:\\.gpg\\|\\.age\\)?\\'"))
         result)
     (dolist (file (org-roam--directory-files-recursively dir regex nil nil t) result)
       (when (and (file-readable-p file)
@@ -313,8 +352,10 @@ E.g. (\".org\") => (\"*.org\" \"*.org.gpg\")"
   (require 'org-roam-utils)
   (require 'org-roam-db)
   (require 'org-roam-node)
+  (require 'org-roam-id)
   (require 'org-roam-capture)
   (require 'org-roam-mode)
+  (require 'org-roam-log)
   (require 'org-roam-migrate))
 
 ;;; org-roam.el ends here

tests/roam-files/demoteable.org

@@ -0,0 +1,8 @@
+:PROPERTIES:
+:ID: 97bf31cf-dfee-45d8-87a5-2ae0dabc4734
+:END:
+#+title: Demoteable
+
+* Demoteable h1
+
+** Demoteable child

tests/roam-files/family.org

@@ -0,0 +1,19 @@
+:PROPERTIES:
+:ID: 998b2341-b7fe-434d-848c-5282c0727870
+:END:
+#+title: Family
+
+* Grand-Parent
+:PROPERTIES:
+:ID: 77a90980-1994-464e-901f-7e3d3df07fd3
+:END:
+
+** Parent
+:PROPERTIES:
+:ID: 0fa5bb3e-3d8c-4966-8bc9-78d32e505d69
+:END:
+
+*** Child
+:PROPERTIES:
+:ID: 5fb4fdc5-b6d2-4f75-8d54-e60053e467ec
+:END:

tests/roam-files/promoteable.org

@@ -0,0 +1,3 @@
+* Promoteable h1
+
+** Promoteable child

tests/roam-files/ref_with_space.org

@@ -0,0 +1,7 @@
+:PROPERTIES:
+:ROAM_REFS: "http://site.net/docs/01. introduction - hello world.html"
+:ID: 5b9a7400-f59c-4ef9-acbb-045b69af98f1
+:END:
+#+title: ref with space
+* Note
+hello

tests/roam-files/with-alias.org

@@ -0,0 +1,5 @@
+:PROPERTIES:
+:ID: 57ff3ce7-5bda-4825-8fca-c09f523e87ba
+:ROAM_ALIASES: Batman
+:END:
+#+title: Bruce Wayne

tests/roam-files/with-times.org

@@ -0,0 +1,16 @@
+:PROPERTIES:
+:ID: 9a20ca6c-5555-41c9-a039-ac38bf59c7a9
+:END:
+#+title: With Times
+
+* Scheduled heading
+SCHEDULED: <2024-07-16 Tue>
+:PROPERTIES:
+:ID: a523c198-4cb4-44d2-909c-a0e3258089cd
+:END:
+
+* Deadline heading
+DEADLINE: <2024-07-17 Tue>
+:PROPERTIES:
+:ID: 3ab84701-d1c1-463f-b5c6-715e6ff5a0bf
+:END:

tests/test-org-roam-capture.el

@@ -0,0 +1,63 @@
+;;; test-org-roam-capture.el --- Tests for Org-roam -*- lexical-binding: t; -*-
+
+;; Copyright (C) 2020 Jethro Kuan
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; Package-Requires: ((buttercup))
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation, either version 3 of the License, or
+;; (at your option) any later version.
+
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+
+;; You should have received a copy of the GNU General Public License
+;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+;;; Commentary:
+;;; Code:
+
+(require 'buttercup)
+(require 'org-roam)
+
+(describe "org-roam-capture--fill-template"
+  (it "fills template without newline"
+    (expect
+     (org-roam-capture--fill-template "foo")
+     :to-equal "foo"))
+
+  (it "fills template ensuring newline"
+    (expect
+     (org-roam-capture--fill-template "foo" 'ensure-newline)
+     :to-equal "foo\n"))
+
+  (it "fills template with newline"
+    (expect
+     (org-roam-capture--fill-template "foo\n")
+     :to-equal "foo\n"))
+
+  (it "fills template with two newlines"
+    (expect
+     (org-roam-capture--fill-template "foo\n\n")
+     :to-equal "foo\n\n")
+    (expect
+     (org-roam-capture--fill-template "foo\n\t\n")
+     :to-equal "foo\n\t\n"))
+
+  (it "fills template without deleting newlines in its body"
+    (expect
+     (org-roam-capture--fill-template "foo\n\n\nbar\n\n")
+     :to-equal "foo\n\n\nbar\n\n"))
+
+  (it "expands templates when it's a function"
+    (expect
+     (org-roam-capture--fill-template (lambda () "foo"))
+     :to-equal "foo")))
+
+(provide 'test-org-roam-capture)
+
+;;; test-org-roam-capture.el ends here

tests/test-org-roam-db.el

@@ -0,0 +1,120 @@
+;;; test-org-roam-db.el --- Tests for Org-roam -*- lexical-binding: t; -*-
+
+;; Copyright (C) 2020 Jethro Kuan
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; Package-Requires: ((buttercup))
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation, either version 3 of the License, or
+;; (at your option) any later version.
+
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+
+;; You should have received a copy of the GNU General Public License
+;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+;;; Commentary:
+;;; Code:
+
+(require 'buttercup)
+(require 'org-roam)
+
+(defvar root-directory default-directory)
+
+(describe "org-roam-db-get-scheduled-time"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location)
+    (cd root-directory))
+
+  (it "should get scheduled time for current heading node"
+    (org-roam-id-open "a523c198-4cb4-44d2-909c-a0e3258089cd" nil)
+    (expect (org-roam-db-get-scheduled-time) :to-equal "2024-07-16T00:00:00")))
+
+(describe "org-roam-db-get-deadline-time"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location)
+    (cd root-directory))
+
+  (it "should get deadline time for current heading node"
+    (org-roam-id-open "3ab84701-d1c1-463f-b5c6-715e6ff5a0bf" nil)
+    (expect (org-roam-db-get-deadline-time) :to-equal "2024-07-17T00:00:00")))
+
+(describe "org-roam-db--file-hash"
+  (it "computes the SHA1 of file"
+    (expect (org-roam-db--file-hash "tests/roam-files/family.org")
+            :to-equal
+            "c4ebf8918c1533df72e4d182cbf1bbd90f776b3b")))
+
+(describe "org-roam-db-sync"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location))
+
+  (it "has the correct number of files"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from files]))
+            :to-equal
+            9))
+
+  (it "has the correct number of nodes"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from nodes]))
+            :to-equal
+            12))
+
+  (it "has the correct number of links"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links]))
+            :to-equal
+            1))
+
+  (it "respects ROAM_EXCLUDE"
+    ;; The excluded node has ID "53fadc75-f48e-461e-be06-44a1e88b2abe"
+    (expect (mapcar #'car (org-roam-db-query [:select id :from nodes]))
+            :to-have-same-items-as
+            '("884b2341-b7fe-434d-848c-5282c0727861"
+              "440795d0-70c1-4165-993d-aebd5eef7a24"
+              "5b9a7400-f59c-4ef9-acbb-045b69af98f1"
+              "0fa5bb3e-3d8c-4966-8bc9-78d32e505d69"
+              "5fb4fdc5-b6d2-4f75-8d54-e60053e467ec"
+              "77a90980-1994-464e-901f-7e3d3df07fd3"
+              "57ff3ce7-5bda-4825-8fca-c09f523e87ba"
+              "998b2341-b7fe-434d-848c-5282c0727870"
+              "a523c198-4cb4-44d2-909c-a0e3258089cd"
+              "3ab84701-d1c1-463f-b5c6-715e6ff5a0bf"
+              "9a20ca6c-5555-41c9-a039-ac38bf59c7a9"
+              "97bf31cf-dfee-45d8-87a5-2ae0dabc4734")))
+
+  (it "reads ref in quotes correctly"
+    (expect (mapcar #'car (org-roam-db-query [:select [ref] :from refs]))
+            :to-have-same-items-as
+            '("//site.net/docs/01. introduction - hello world.html"))))
+
+(provide 'test-org-roam-db)
+
+;;; test-org-roam-db.el ends here

tests/test-org-roam-id.el

@@ -0,0 +1,79 @@
+;;; test-org-roam-id.el --- Tests for Org-roam -*- lexical-binding: t; -*-
+
+;; Copyright (C) 2020 Jethro Kuan
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; Package-Requires: ((buttercup))
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation, either version 3 of the License, or
+;; (at your option) any later version.
+
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+
+;; You should have received a copy of the GNU General Public License
+;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+;;; Commentary:
+;;; Code:
+
+(require 'buttercup)
+(require 'org-roam)
+
+(defvar root-directory default-directory)
+
+(describe "org-roam-id-at-point"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location)
+    (cd root-directory))
+
+  (it "returns the correct node ids"
+    (find-file "tests/roam-files/family.org" nil)
+    (expect (org-roam-id-at-point) :to-equal "998b2341-b7fe-434d-848c-5282c0727870")
+
+    (search-forward "Grand")
+    (expect (org-roam-id-at-point) :to-equal "77a90980-1994-464e-901f-7e3d3df07fd3")
+
+    (search-forward "Child")
+    (expect (org-roam-id-at-point) :to-equal "5fb4fdc5-b6d2-4f75-8d54-e60053e467ec")))
+
+(describe "org-roam-id-find"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location))
+
+  (it "finds nothing for non-existing node"
+    (expect (org-roam-id-find "non-existing") :to-equal nil))
+
+  (it "finds the correct file node"
+    (let ((location (org-roam-id-find "884b2341-b7fe-434d-848c-5282c0727861")))
+      (expect (car location) :to-match ".*/tests/roam-files/foo.org")
+      (expect (cdr location) :to-equal 1)))
+
+  (it "finds the correct heading node"
+    (let ((location (org-roam-id-find "0fa5bb3e-3d8c-4966-8bc9-78d32e505d69")))
+      (expect (car location) :to-match ".*/tests/roam-files/family.org")
+      (expect (cdr location) :to-equal 156))))
+
+(provide 'test-org-roam-id)
+
+;;; test-org-roam-id.el ends here

tests/test-org-roam-mode.el

@@ -0,0 +1,39 @@
+;;; test-org-roam-mode.el --- Tests for Org-roam -*- lexical-binding: t; -*-
+
+;; Copyright (C) 2020 Jethro Kuan
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; Package-Requires: ((buttercup))
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation, either version 3 of the License, or
+;; (at your option) any later version.
+
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+
+;; You should have received a copy of the GNU General Public License
+;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+;;; Commentary:
+;;; Code:
+
+(require 'buttercup)
+(require 'org-roam)
+
+(describe "org-roam-unlinked-references--rg-command"
+  (before-each
+    ;; the space in the directory is on purpose
+    (setq org-roam-directory "/tmp/org roam"))
+
+  (it "returns the correct rg command for unlinked references"
+    (expect (org-roam-unlinked-references--rg-command '("foo" "bar") "/tmp/regex")
+            :to-equal
+            "rg --follow --only-matching --vimgrep --pcre2 --ignore-case --glob \"*.org\" --glob \"*.org.gpg\" --glob \"*.org.age\" --file /tmp/regex /tmp/org\\ roam")))
+
+(provide 'test-org-roam-mode)
+
+;;; test-org-roam-mode.el ends here

tests/test-org-roam-node.el

@@ -0,0 +1,164 @@
+;;; test-org-roam-node.el --- Tests for Org-roam -*- lexical-binding: t; -*-
+
+;; Copyright (C) 2020 Jethro Kuan
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; Package-Requires: ((buttercup))
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation, either version 3 of the License, or
+;; (at your option) any later version.
+
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+
+;; You should have received a copy of the GNU General Public License
+;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+;;; Commentary:
+;;; Code:
+
+(require 'buttercup)
+(require 'org-roam)
+
+(defvar root-directory default-directory)
+
+(describe "org-roam-node-from-id"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location))
+
+  (it "returns nil for unknown id"
+    (expect (org-roam-node-from-id "non-existing") :to-equal nil))
+
+  (it "returns correct node from id"
+    (let ((node (org-roam-node-from-id "884b2341-b7fe-434d-848c-5282c0727861")))
+      (expect (org-roam-node-title node) :to-equal "Foo"))))
+
+(describe "org-roam-node-from-title-or-alias"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location))
+
+  (it "returns nil for unknown title"
+    (expect (org-roam-node-from-title-or-alias "non-existing") :to-equal nil))
+
+  (it "returns correct node from title"
+    (let ((node (org-roam-node-from-title-or-alias "Foo")))
+      (expect (org-roam-node-title node) :to-equal "Foo")))
+
+  (it "returns correct node from alias"
+    (let ((node (org-roam-node-from-title-or-alias "Batman")))
+      (expect (org-roam-node-title node) :to-equal "Bruce Wayne")))
+
+  (it "returns correct node from alias with nocase"
+    (let ((node (org-roam-node-from-title-or-alias "batman" t)))
+      (expect (org-roam-node-title node) :to-equal "Bruce Wayne"))))
+
+(describe "org-roam-demote-entire-buffer"
+  (after-each
+    (cd root-directory))
+
+  (it "demotes an entire org buffer"
+    (find-file "tests/roam-files/demoteable.org" nil)
+    (org-roam-demote-entire-buffer)
+    (expect (buffer-substring-no-properties (point) (point-max))
+            :to-equal "* Demoteable\n:PROPERTIES:\n:ID: 97bf31cf-dfee-45d8-87a5-2ae0dabc4734\n:END:\n\n** Demoteable h1\n\n*** Demoteable child\n")))
+
+(describe "org-roam--h1-count"
+  (after-each
+    (cd root-directory))
+
+  (it "returns the correct number of level-1 headings"
+    (find-file "tests/roam-files/foo.org" nil)
+    (expect (org-roam--h1-count) :to-equal 0)
+
+    (cd root-directory)
+
+    (find-file "tests/roam-files/family.org" nil)
+    (expect (org-roam--h1-count) :to-equal 1)))
+
+(describe "org-roam--buffer-promoteable-p"
+  (after-each
+    (cd root-directory))
+
+  (it "should check if buffer is promoteable"
+    (find-file "tests/roam-files/foo.org" nil)
+    (expect (org-roam--buffer-promoteable-p) :to-equal nil)
+
+    (cd root-directory)
+
+    (find-file "tests/roam-files/family.org" nil)
+    (expect (org-roam--buffer-promoteable-p) :to-equal nil)
+
+    (cd root-directory)
+
+    (find-file "tests/roam-files/promoteable.org" nil)
+    (expect (org-roam--buffer-promoteable-p) :to-equal t)))
+
+(describe "org-roam--get-titles"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location))
+
+  (it "returns the list of titles and aliases"
+    (expect (org-roam--get-titles)
+            :to-have-same-items-as
+            `("Bar" "Batman" "Bruce Wayne" "Child" "Deadline heading" "Demoteable" "Family"
+              "Foo" "Grand-Parent" "Parent" "ref with space" "Scheduled heading" "With Times"))))
+
+
+(describe "org-roam-alias"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location)
+    (cd root-directory))
+
+  (it "adds an alias to a node"
+    (cd root-directory)
+    (find-file "tests/roam-files/foo.org" nil)
+    (org-roam-alias-add "qux")
+    (expect (buffer-substring-no-properties (point) (point-max))
+            :to-equal ":PROPERTIES:\n:ID:       884b2341-b7fe-434d-848c-5282c0727861\n:ROAM_ALIASES: qux\n:END:\n#+title: Foo\n"))
+
+  (it "removes an alias from a node"
+    (cd root-directory)
+    (find-file "tests/roam-files/with-alias.org" nil)
+    (org-roam-alias-remove "Batman")
+    (expect (buffer-substring-no-properties (point) (point-max))
+            :to-equal ":PROPERTIES:\n:ID: 57ff3ce7-5bda-4825-8fca-c09f523e87ba\n:END:\n#+title: Bruce Wayne\n")))
+
+(provide 'test-org-roam-node)
+
+;;; test-org-roam-node.el ends here

tests/test-org-roam-utils.el

@@ -0,0 +1,64 @@
+;;; test-org-roam-utils.el --- Tests for Org-roam -*- lexical-binding: t; -*-
+
+;; Copyright (C) 2020 Jethro Kuan
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; Package-Requires: ((buttercup))
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation, either version 3 of the License, or
+;; (at your option) any later version.
+
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+
+;; You should have received a copy of the GNU General Public License
+;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+;;; Commentary:
+;;; Code:
+
+(require 'buttercup)
+(require 'org-roam)
+
+(describe "org-roam-whitespace-content"
+  (it "extracts whitespace correctly"
+    (expect
+     (org-roam-whitespace-content "foo")
+     :to-equal "")
+    (expect
+     (org-roam-whitespace-content "foo\n")
+     :to-equal "\n")
+    (expect
+     (org-roam-whitespace-content "foo\n\t\n")
+     :to-equal "\n\t\n")))
+
+(describe "org-roam-db--file-title"
+  (it "supports normal titles"
+    (expect
+     (with-temp-buffer
+       (insert "#+title:normal title")
+       (org-roam-db--file-title))
+     :to-equal "normal title"))
+  (it "supports multi-line titles"
+    (expect
+     (with-temp-buffer
+       (insert "#+title: title:\n#+title: separated by newline")
+       (org-roam-db--file-title))
+     :to-equal "title: separated by newline"))
+  (it "supports file-name based titles"
+    (progn
+      (setq org-roam-directory temporary-file-directory
+            org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+            org-roam-file-extensions '("org"))
+      (with-temp-buffer
+        (write-file (expand-file-name "test file.org" org-roam-directory))
+        (org-roam-db--file-title)))
+    :to-equal "test file"))
+
+(provide 'test-org-roam-utils)
+
+;;; test-org-roam-utils.el ends here

tests/test-org-roam.el

@@ -24,6 +24,28 @@
 (require 'buttercup)
 (require 'org-roam)
 
+(defvar root-directory default-directory)
+
+(describe "org-roam-file-p"
+  (it "checks if given file respects criteria"
+    (setq org-roam-directory "/non-existent")
+    (expect (org-roam-file-p "tests/roam-files/family.org") :to-equal nil)
+
+    (setq org-roam-directory (expand-file-name "tests/roam-files"))
+    (expect (org-roam-file-p "tests/roam-files/family.org") :to-equal t)
+    (expect (org-roam-file-p "tests/roam-files/markdown.md") :to-equal nil)
+
+    (setq org-roam-file-exclude-regexp (regexp-quote "family.org"))
+    (expect (org-roam-file-p "tests/roam-files/family.org") :to-equal nil)))
+
+(describe "org-roam-buffer-p"
+  (it "checks if current buffer respects criteria"
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-file-exclude-regexp nil)
+    (find-file "tests/roam-files/family.org" nil)
+    (expect (org-roam-buffer-p) :to-equal t)
+    (cd root-directory)))
+
 (describe "org-roam-list-files"
   (before-each
     (setq org-roam-directory (expand-file-name "tests/roam-files")
@@ -31,52 +53,29 @@
           org-roam-file-extensions '("org")
           org-roam-file-exclude-regexp nil))
 
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location))
+
   (it "gets files correctly"
-    (expect (length (org-roam-list-files))
-            :to-equal 3))
+    (expect (length (org-roam-list-files)) :to-equal 9))
 
   (it "respects org-roam-file-extensions"
     (setq org-roam-file-extensions '("md"))
     (expect (length (org-roam-list-files)) :to-equal 1)
     (setq org-roam-file-extensions '("org" "md"))
-    (expect (length (org-roam-list-files)) :to-equal 4))
+    (expect (length (org-roam-list-files)) :to-equal 10))
 
   (it "respects org-roam-file-exclude-regexp"
     (setq org-roam-file-exclude-regexp (regexp-quote "foo.org"))
-    (expect (length (org-roam-list-files)) :to-equal 2)))
+    (expect (length (org-roam-list-files)) :to-equal 8)))
 
-(describe "org-roam-db-sync"
-  (before-all
-    (setq org-roam-directory (expand-file-name "tests/roam-files")
-          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
-          org-roam-file-extensions '("org")
-          org-roam-file-exclude-regexp nil)
-    (org-roam-db-sync))
+(describe "org-roam--list-files-search-globs"
 
-  (after-all
-    (org-roam-db--close)
-    (delete-file org-roam-db-location))
-
-  (it "has the correct number of files"
-    (expect (caar (org-roam-db-query [:select (funcall count) :from files]))
-            :to-equal
-            3))
-
-  (it "has the correct number of nodes"
-    (expect (caar (org-roam-db-query [:select (funcall count) :from nodes]))
-            :to-equal
-            2))
-
-  (it "has the correct number of links"
-    (expect (caar (org-roam-db-query [:select (funcall count) :from links]))
-            :to-equal
-            1))
-
-  (it "respects ROAM_EXCLUDE"
-    ;; The excluded node has ID "53fadc75-f48e-461e-be06-44a1e88b2abe"
-    (expect (mapcar #'car (org-roam-db-query [:select id :from nodes]))
+  (it "returns the correct list of globs"
+    (expect (org-roam--list-files-search-globs org-roam-file-extensions)
             :to-have-same-items-as
-            '("884b2341-b7fe-434d-848c-5282c0727861" "440795d0-70c1-4165-993d-aebd5eef7a24"))))
+            '("\"*.org\"" "\"*.org.gpg\"" "\"*.org.age\""))))
 
 (provide 'test-org-roam)