obsidian: support existing vaults and rename Concepts to Knowledge

modules/obsidian/README.md

@@ -1,9 +1,9 @@
 # obsidian
 
-A starter pack for a new Obsidian vault: settings (Catppuccin appearance,
-hotkeys, vimrc, CSS snippet, per-plugin settings), a folder layout, a root
-`AGENTS.md`, `Home.md`, and a `.gitignore`. After seeding, each vault owns
-its copy and is free to drift from this one.
+A starter pack for an Obsidian vault, new or existing: settings
+(Catppuccin appearance, hotkeys, vimrc, CSS snippet, per-plugin settings),
+a folder layout, a root `AGENTS.md`, `Home.md`, and a `.gitignore`. After
+seeding, each vault owns its copy and is free to drift from this one.
 
 The module is in no role. `./install` and `./provision.sh` skip it; run the
 script by hand.
@@ -14,18 +14,34 @@ script by hand.
 ~/.dotfiles/modules/obsidian/seed-vault ~/my-vault
 ```
 
-The script copies files without overwriting existing ones, creates the
-folders, and runs `git init` with no remote. Re-running it only fills in
-what is missing.
+Close Obsidian first; the script refuses to run while it is open, because
+Obsidian writes its in-memory settings back over the new files.
+
+The script:
+
+- resets the pack's settings files (`.obsidian/*.json`, the snippet,
+  per-plugin `data.json`, `.obsidian.vimrc`). A file that differs is
+  backed up to `~/.local/state/seed-vault/<vault>-<timestamp>/` first.
+  Settings the pack does not ship, such as `workspace.json` or other
+  plugins' folders, are left alone. `community-plugins.json` is replaced,
+  so plugins the vault had enabled that are not in the pack end up
+  disabled; re-enable them in Settings.
+- adds `AGENTS.md`, `Home.md` and `.gitignore` only when missing.
+- creates the folders and runs `git init` with no remote if there is no
+  repo yet.
+
+Re-running it on the same vault resets any settings changed since, again
+with a backup.
 
 ## Finish in Obsidian
 
 These steps are manual, or for an agent to walk through with the owner.
 
 1. Open the folder as a vault ("Open folder as vault").
 2. Settings → Community plugins: turn off Restricted mode, then Browse
-   and install each of these by name. The seeded settings are picked up
-   on install.
+   and install each of these by name. Plugin code is not part of the pack,
+   so until this step no plugin appears and vim bindings from the vimrc do
+   nothing. The seeded settings are picked up on install.
 
    | Search for     | Plugin id                 |
    |----------------|---------------------------|

modules/obsidian/config/app.json

@@ -22,7 +22,7 @@
   "spellcheck": false,
   "defaultViewMode": "source",
   "showUnsupportedFiles": true,
-  "attachmentFolderPath": "attachments",
+  "attachmentFolderPath": "./",
   "mobileToolbarCommands": [
     "command-palette:open",
     "editor:toggle-checklist-status",
@@ -52,7 +52,7 @@
   ],
   "propertiesInDocument": "hidden",
   "newFileLocation": "folder",
-  "newFileFolderPath": "_inbox",
+  "newFileFolderPath": "_Inbox",
   "openBehavior": "file:Home.md",
   "useTab": false
 }

modules/obsidian/config/plugins/templater-obsidian/data.json

@@ -1,6 +1,6 @@
 {
   "command_timeout": 5,
-  "templates_folder": "templates",
+  "templates_folder": "Templates",
   "templates_pairs": [
     [
       "",
@@ -31,4 +31,4 @@
   ],
   "intellisense_render": 1,
   "enable_ribbon_icon": true
-}
+}

modules/obsidian/config/vault/AGENTS.md

@@ -10,20 +10,18 @@ Obsidian knowledge vault. Start navigation at [[Home]].
 ## Structure
 
 ```
-concepts/          # Ideas you synthesized: flat, evergreen, reusable
-projects/          # Things you work on, including their meetings and logs
-references/        # External information: people, teams, systems, processes
-  people/
-archive/           # Finished or historical material
-templates/         # Templater templates
-attachments/       # Pasted images and files
-_inbox/            # Default location for new notes; sort regularly
+Projects/          # Things you work on, finite or ongoing, with their meetings and logs
+Knowledge/         # What you worked out: ideas, mental models, lessons; flat and evergreen
+References/        # External information: people, teams, systems, processes
+Archive/           # Finished or historical material
+Templates/         # Templater templates
+_Inbox/            # Default location for new notes; sort regularly
 .claude/           # Claude Code skills, hooks, and settings for this vault
 ```
 
-- Boundary test: "Did I author this insight?" → `concepts/`. "Am I recording external info?" → `references/`. "Am I working on it?" → `projects/`.
-- Folders describe domain, not status. Completed projects stay in `projects/` with `status: complete`.
-- New notes land in `_inbox/`. Move a note to its folder once its home is clear; `Home.md` lists what is waiting.
+- Filing test: "Am I working on it?" → `Projects/`. "Did I work this out myself?" → `Knowledge/`. "Am I recording information from outside?" → `References/`. Group related references in subfolders (`References/People/`) as they accumulate.
+- Folders describe domain, not status. Completed projects stay in `Projects/` with `status: complete`.
+- New notes land in `_Inbox/`. Move a note to its folder once its home is clear; `Home.md` lists what is waiting.
 - Add an `AGENTS.md` to a folder when it gains conventions of its own. This file is authoritative at the root; folder files add local rules.
 
 ## Properties (frontmatter)
@@ -44,7 +42,7 @@ _inbox/            # Default location for new notes; sort regularly
 
 ## Templates
 
-Templater reads `templates/`. Templates have frontmatter and no H1; use `<% tp.date.now("YYYY-MM-DD") %>` for dates. When an agent creates a note from a template, it writes the expanded values (such as today's date) instead of the `<% %>` tags.
+Templater reads `Templates/`. Templates have frontmatter and no H1; use `<% tp.date.now("YYYY-MM-DD") %>` for dates. When an agent creates a note from a template, it writes the expanded values (such as today's date) instead of the `<% %>` tags.
 
 ## Keys
 

modules/obsidian/config/vault/Home.md

@@ -13,11 +13,11 @@ SORT status ASC, file.mtime DESC
 
 ## Inbox
 
-New notes land in `_inbox/`. Move each one to its folder once it has a home.
+New notes land in `_Inbox/`. Move each one to its folder once it has a home.
 
 ```dataview
 LIST
-FROM "_inbox"
+FROM "_Inbox"
 SORT file.ctime DESC
 ```
 

modules/obsidian/seed-vault

@@ -7,11 +7,17 @@
 #
 # usage: seed-vault <vault-path>
 #
-# Run by hand, once per vault; no role lists this module, so ./install and
-# ./provision.sh never touch it. Files are copied rather than linked because
-# Obsidian rewrites its JSON whenever a setting changes, and a vault's tweaks
-# should stay in that vault. An existing file is never overwritten, so a
-# re-run only fills in what is missing.
+# Run by hand; no role lists this module, so ./install and ./provision.sh
+# never touch it. Files are copied rather than linked because Obsidian
+# rewrites its JSON whenever a setting changes, and a vault's tweaks should
+# stay in that vault.
+#
+# Settings (.obsidian/ files from the pack and .obsidian.vimrc) are reset to
+# the pack's: an existing file that differs is backed up under
+# $XDG_STATE_HOME/seed-vault/ and replaced. Settings the pack does not ship
+# (workspace, other plugins) are left alone. Starter content (AGENTS.md,
+# Home.md, .gitignore) is never overwritten. Obsidian must be closed, or it
+# writes its in-memory settings back over the new files.
 #
 # Plugin code, the Catppuccin theme, and fonts are not shipped here; see
 # README.md for the steps that finish the vault inside Obsidian.
@@ -37,21 +43,44 @@ place() {
   fi
 }
 
+# usage: place_setting <src> <dest> - copy, backing up a differing dest.
+place_setting() {
+  local rel="${2#"$VAULT"/}"
+  if [ -e "$2" ] && cmp -s "$1" "$2"; then
+    skip "$rel up to date"
+    return
+  fi
+  if [ -e "$2" ]; then
+    mkdir -p "$(dirname "$BACKUP/$rel")"
+    cp -p "$2" "$BACKUP/$rel"
+    note "replaced $rel (old copy in $BACKUP)"
+  else
+    mkdir -p "$(dirname "$2")"
+    note "added $rel"
+  fi
+  cp "$1" "$2"
+}
+
+if pgrep -x obsidian >/dev/null 2>&1; then
+  die "Obsidian is running; close it first, or it overwrites the new settings"
+fi
+
 log "seeding $VAULT"
 mkdir -p "$VAULT"
 VAULT="$(cd "$VAULT" && pwd)"
+BACKUP="${XDG_STATE_HOME:-$HOME/.local/state}/seed-vault/$(basename "$VAULT")-$(date +%Y%m%dT%H%M%S)"
 
-for d in concepts projects references/people archive templates attachments _inbox .claude/skills; do
+for d in Projects Knowledge References Archive Templates _Inbox .claude/skills; do
   mkdir -p "$VAULT/$d"
 done
 
 # Obsidian settings: everything under config/ except the vimrc (which lives
 # at the vault root) and vault/ (starter content).
 while IFS= read -r -d '' f; do
   rel="${f#"$CONFIG"/}"
-  place "$f" "$VAULT/.obsidian/$rel"
+  place_setting "$f" "$VAULT/.obsidian/$rel"
 done < <(find "$CONFIG" -path "$CONFIG/vault" -prune -o -type f ! -name vimrc -print0)
-place "$CONFIG/vimrc" "$VAULT/.obsidian.vimrc"
+place_setting "$CONFIG/vimrc" "$VAULT/.obsidian.vimrc"
 
 # Starter content. gitignore is stored without its dot so it does not apply
 # to this repo.