Brain setup

Template: ${CLAUDE_PLUGIN_ROOT}/vault-template. If that still reads as a literal ${...}, the template is ../../vault-template relative to this skill's base directory. Set TPL to that absolute path in every command; the Bash environment does not carry CLAUDE_PLUGIN_ROOT.

Config directory: C="${CLAUDE_CONFIG_DIR:-$HOME/.claude}". Edit $C/CLAUDE.md and $C/settings.json in place (they may be symlinks), never through mv or a full rewrite.

1. Ask for the path and pick the mode

Ask for the vault's absolute path (expand ~). Reject a path that holds ', ", $, a backtick, \ or a newline and ask again; set V and TPL in single quotes in every command. If $C/CLAUDE.md already has a Brain vault: line with another path, show it and ask which one to keep. If the user picks the new path, remember the old one for the report.

• Path missing or an empty directory: new vault.
• Path non-empty: ask whether to connect an existing vault. If not, stop; never copy into a non-empty directory.

2a. New vault

TPL='/abs/path/to/plugin/vault-template'; V='/abs/path/to/vault'
mkdir -p "$V" && cp -R "$TPL/." "$V/"

2b. Connect an existing vault

Add only what is missing; never overwrite, move or delete a file. Do not copy the example notes. The .gitignore lines are added only to a vault that is a git repository or already has a .gitignore.

TPL='/abs/path/to/plugin/vault-template'; V='/abs/path/to/vault'
for d in DEV INFRA PROJECTS QA TOOLS _archive _inbox _reports _views templates; do mkdir -p "$V/$d"; done
(cd "$TPL" && for f in _views/*.base templates/note.md; do [ -e "$V/$f" ] || cp "$f" "$V/$f"; done)
if [ -e "$V/.git" ] || [ -e "$V/.gitignore" ]; then
  touch "$V/.gitignore"
  while IFS= read -r l; do case "$l" in ''|'#'*) continue;; esac; grep -qxF "$l" "$V/.gitignore" || printf '%s\n' "$l" >> "$V/.gitignore"; done < "$TPL/.gitignore"
fi

.obsidian/types.json: add only the keys from the template's file that are absent; never change an existing value. If the file is missing, copy the template's. Show the change and apply it after approval, written back with cat new > file as in step 3 (set TPL and V in the same Bash call; existing values win: jq -s '.[0] * {types: (.[1].types + .[0].types)}' "$V/.obsidian/types.json" "$TPL/.obsidian/types.json"); ask the user to close Obsidian first, because it rewrites the file while open. Without jq, tell the user to set the property types in Obsidian's properties panel.

3. Point Claude Code at the vault

Show the edits as a diff and apply them only after the user approves:

• $C/CLAUDE.md: append Brain vault: <V> (skip if the line is already there). Tell the user the plugin's optional brain_vault option (/config or the plugin dialog) wins over this line when set, so a later move changes both or clears the option.
• $C/settings.json: add <V> to permissions.additionalDirectories (skip if present).
• Recommended, asked as a separate yes/no: $C/settings.json: "autoMemoryEnabled": false (skip if already false). Say why in one line: Claude Code's auto memory keeps a second, unreviewed store per project and machine, and developer-os keeps long-term knowledge in the vault (D24). Ask it before building the preview and set AM=true on a yes, AM=false on a no (or when it is already false); if the answer changes after the preview, build the preview again before applying.

Bash calls do not keep variables: set C, S and V at the top of each call. Preview:

C="${CLAUDE_CONFIG_DIR:-$HOME/.claude}"; S="$C/settings.json"; V='/abs/path/to/vault'; AM=true
{ cat "$S" 2>/dev/null || echo '{}'; } | jq --arg p "$V" --argjson am "$AM" '.permissions.additionalDirectories //= [] | if any(.permissions.additionalDirectories[]; . == $p) then . else .permissions.additionalDirectories += [$p] end | if $am then .autoMemoryEnabled = false else . end' > "$S.brain-setup" && diff -N "$S" "$S.brain-setup"

After approval, in a new call:

C="${CLAUDE_CONFIG_DIR:-$HOME/.claude}"; S="$C/settings.json"; V='/abs/path/to/vault'
cat "$S.brain-setup" > "$S" && rm "$S.brain-setup"
# replace an existing Brain vault: line (the user chose the new path in step 1), else append
if grep -q '^Brain vault:' "$C/CLAUDE.md" 2>/dev/null; then t=$(mktemp); V="$V" awk '/^Brain vault:/ { print "Brain vault: " ENVIRON["V"]; next } 1' "$C/CLAUDE.md" > "$t" && cat "$t" > "$C/CLAUDE.md"; rm -f "$t"; else printf '\nBrain vault: %s\n' "$V" >> "$C/CLAUDE.md"; fi

On decline: rm "$S.brain-setup".

If jq is missing or settings.json is not valid JSON, remove $S.brain-setup, change nothing else, and show the user the key to add by hand.

4. Smoke test

Run the developer-os:brain-search skill and give it the vault path <V> explicitly (the line just written is not in this session's context): in a new vault search for "webhooks" (it must find _inbox/process-webhooks-once-per-event-id.md); in a connected vault search for the topic of one existing note. Then tell the user to open the vault in Obsidian and enable the Bases and Templates core plugins, with templates as the Templates folder. If "$C"/projects/*/memory/ (or a configured autoMemoryDirectory) holds .md files, give the count per project and offer the developer-os:brain-import-memory skill to move them into the vault; turning auto memory off does not delete them. Tell them too that vault upkeep does not run on its own: they run brain-review weekly and brain-garden monthly, and a one-line notice at the start of a new session reminds them when either is due (DEVELOPER_OS_NOTICES=off turns it off).

Stop point

Stop after the smoke test. Report the mode, the vault path, what was created or appended, which config edits were applied or declined (auto memory on or off), the old vault path still in permissions.additionalDirectories (if the path changed; the user removes it by hand), the smoke-test result, and the upkeep cadence.

Never

• Copy into a non-empty directory in new-vault mode, or overwrite any existing file in the vault (.obsidian/, notes, .gitignore, .base views).
• Edit CLAUDE.md or settings.json before the user approves the diff, rewrite settings.json by hand, or replace either file with mv.
• Search the disk for vaults or read notes beyond the smoke test.