gstack/sync-gbrain/SKILL.md.tmpl

---
name: sync-gbrain
preamble-tier: 2
version: 1.0.0
description: |
  Keep gbrain current with this repo's code and refresh agent search
  guidance in CLAUDE.md. Wraps the gstack-gbrain-sync orchestrator with
  state probing, native code-surface registration, capability checks,
  and a verdict block. Re-runnable, idempotent. Use when: "sync gbrain",
  "refresh gbrain", "re-index this repo", "gbrain search isn't finding
  things". (gstack)
triggers:
  - sync gbrain
  - refresh gbrain
  - reindex repo
  - update gbrain
allowed-tools:
  - Bash
  - Read
  - Write
  - Edit
  - Glob
  - Grep
  - AskUserQuestion
---

{{PREAMBLE}}

# /sync-gbrain — Keep gbrain current and teach the agent to use it

You are running the canonical "keep this brain up to date" verb. /setup-gbrain
installs gbrain once; /sync-gbrain runs every time the user wants the brain
refreshed against this repo's current state, and refreshes the agent-side
guidance in CLAUDE.md so the coding agent knows when to prefer `gbrain`
search over Grep.

**Architecture (post-codex review):** This skill uses gbrain v0.20.0+'s
**native code surfaces** (`gbrain sources add`, `gbrain sync --strategy code`,
`gbrain reindex-code`, `gbrain code-def/code-refs/code-callers/code-callees`).
It does NOT use `gbrain import` (that path is for markdown directories).
It does NOT touch `~/.gstack/` indexing (the existing `gstack-gbrain-source-wireup`
owns that — never double-store).

## User-invocable

When the user types `/sync-gbrain`, run this skill. Argument modes (parsed by
the skill itself, not a dispatcher binary):

- `/sync-gbrain` — incremental sync (default; mtime fast-path; ~50ms steady-state)
- `/sync-gbrain --full` — full code reindex via `gbrain reindex-code` (~25-35 min on a big repo). Auto-builds the call graph (`gbrain dream`) **only when it was never built**.
- `/sync-gbrain --dream` — build this source's call graph (`gbrain code-callers`/`code-callees`) via a source-scoped `gbrain dream --source <id>` cycle; ~minutes; runs lock-free after the sync stages. Always forces, even if already built. Only produces a graph on a code-aware schema pack; otherwise the run reports a WARN explaining why the graph is still empty.
- `/sync-gbrain --no-dream` — skip the dream cycle that `--full` would otherwise auto-run.
- `/sync-gbrain --code-only` — only run the code stage; skip memory + brain-sync
- `/sync-gbrain --dry-run` — preview what would sync; no writes anywhere
- `/sync-gbrain --no-memory` / `--no-brain-sync` — selectively skip stages
- `/sync-gbrain --quiet` — suppress per-stage output
- `/sync-gbrain --refresh-cache` — force-rebuild brain-aware planning cache (v1.48; replaces /brain-refresh-context per D1 fold). Skips code + memory stages; routes to `gstack-brain-cache refresh --project <slug>`.
- `/sync-gbrain --audit` — emit summary of gstack-owned pages per project + sensitive-content audit (v1.48 / D10 lifecycle). Read-only.

Pass-through args go straight to the orchestrator at
`{{BIN_DIR}}/gstack-gbrain-sync.ts`.

**`--refresh-cache` short-circuit:** when this flag is present, the skill
runs ONLY the cache refresh (`gstack-brain-cache refresh --project <slug>`
for the current worktree's slug, plus a cross-project refresh of
user-profile if `gstack/user-profile/<user-slug>` exists). Code +
memory + brain-sync stages are skipped. Useful when the user knows the
brain has new info gstack should pick up before the next planning skill.

**`--audit` short-circuit:** when this flag is present, the skill runs
`gstack-brain-cache list --project <slug> --json`, summarizes by page
type, then scans for any cached salience entries that ended up outside
the SALIENCE_DEFAULT_ALLOWLIST (T17 / D9 leak check). Read-only; no
modifications to brain or cache.

---

## Step 1: State probe

Before doing anything, check that /setup-gbrain has been run on this Mac.

```bash
~/.claude/skills/gstack/bin/gstack-gbrain-detect 2>/dev/null
```

**Brain trust policy gate (v1.48 / Phase 1.5 / D4 — added by T13+T5c):**
If `gbrain_mcp_mode == "remote-http"` from the detect output AND the per-
endpoint policy is `unset`, the policy question MUST fire here before
the orchestrator runs. Local engines auto-set to `personal` silently per
the per-transport default table.

```bash
_HASH=$(~/.claude/skills/gstack/bin/gstack-config endpoint-hash 2>/dev/null)
_POLICY=$(~/.claude/skills/gstack/bin/gstack-config get brain_trust_policy@$_HASH 2>/dev/null || echo unset)
echo "BRAIN_TRUST_POLICY[$_HASH]: $_POLICY"
```

If `_POLICY == "unset"` AND `_HASH != "local"`, AskUserQuestion per the
Step 9.5 wording in `/setup-gbrain` (personal vs shared, with persistence
to `brain_trust_policy@<hash>` and conditional `artifacts_sync_mode=full`
flip for personal). Then continue.

If `_POLICY == "unset"` AND `_HASH == "local"`, auto-set personal:

```bash
~/.claude/skills/gstack/bin/gstack-config set brain_trust_policy@$_HASH personal
```

**Split-engine model (v1.34.0.0+).** Code stage runs locally against the
per-machine gbrain engine (PGLite or whatever `gbrain config` points to),
with each worktree of a repo registered as its own source. **Memory stage
also runs locally** in local-stdio MCP mode — `gstack-memory-ingest` shells
out to `gbrain import` against the same local engine. In remote-http MCP
mode (Path 4), the memory stage instead persists staged markdown to
`~/.gstack/transcripts/<run-id>/` and the artifacts pipeline pushes it to
the brain admin's pull job (plan D11). Brain-sync (the `gstack-brain-sync`
push to git) is the one stage that never touches local engine and runs
regardless of mode.

Practically: local PGLite stays code-only on remote-http machines; the
remote brain holds everything else. Local-stdio machines mix code +
transcripts in one local engine, as they always have.

Also check the per-repo trust policy. If `gstack-gbrain-repo-policy get` for
this repo returns `deny`, STOP:

> "This repo's gbrain trust policy is `deny`. Run `/setup-gbrain --repo` to
> change it before syncing."

---

## Step 1.5: Local engine pre-flight (plan D12)

Read `gbrain_local_status` from the Step 1 detect output. Branch as follows
BEFORE invoking the orchestrator:

- **`ok`**: proceed to Step 2 normally.
- **`timeout`**: proceed to Step 2 — the engine is most likely healthy but
  slow (cold pooler connection, #1964). Tell the user in one line: "Engine
  probe timed out (>15s) — proceeding; raise `GSTACK_GBRAIN_PROBE_TIMEOUT_MS`
  if your pooler is slow." Do NOT treat this as a broken config.
- **`thin-client`**: proceed to Step 2 — this machine is a thin client of a
  remote-HTTP MCP brain (#2051): no local engine BY DESIGN, so the code,
  memory, and dream stages will SKIP with a thin-client reason (code indexing
  runs on the brain server; memory syncs via the remote brain's artifacts
  pull). Only the brain-sync push runs locally. Tell the user in one line:
  "Thin client of a remote brain — local stages skip by design; brain queries
  work via remote MCP (reachability is verified at use time, not probed
  here)." Do NOT route this into the broken-config remediation.
- **`engine-locked`**: STOP. "The local PGLite database is busy, usually
  because `gbrain serve` from a live Claude session owns it. Stop that process
  or run `/sync-gbrain` outside the live session, then retry. This identifies
  the conflict but does not remove PGLite's single-process limit."
- **`no-cli`**: STOP. "Local gbrain CLI not installed. Run `/setup-gbrain`
  first."
- **`missing-config`** AND `gbrain_mcp_mode == "remote-http"`: tell the user
  "Your brain queries (the `mcp__gbrain__*` tools) work via remote MCP, but
  symbol code search needs a local PGLite. Run `/setup-gbrain` and pick
  'Yes' at the new 'local code index' prompt (Step 4.5), or run
  `gbrain init --pglite --json --embedding-model voyage:voyage-code-3 --embedding-dimensions 1024`
  directly (drop the voyage flags if `VOYAGE_API_KEY` isn't set). Continuing
  without code stage."
  Then proceed to Step 2 — the orchestrator's `runCodeImport()` and
  `runMemoryIngest()` will return SKIP per plan D12; only `runBrainSyncPush()`
  will run. Do NOT abort.
- **`missing-config`** AND `gbrain_mcp_mode != "remote-http"`: STOP. "Local
  gbrain CLI is installed but no engine config. Run `/setup-gbrain` first."
- **`broken-config`** OR **`broken-db`**: STOP with a clear message:
  ```
  Local gbrain config at ~/.gbrain/config.json points at an unreachable
  engine (status: {gbrain_local_status}). Two options:
    1. Re-run /setup-gbrain — Step 1.5 offers Retry / Switch to PGLite /
       Switch brain mode / Quit (plan D4).
    2. Repair manually: mv ~/.gbrain/config.json ~/.gbrain/config.json.bak
       && gbrain init --pglite --json --embedding-model voyage:voyage-code-3 \
          --embedding-dimensions 1024   (drop voyage flags if VOYAGE_API_KEY unset)
  Re-run /sync-gbrain after.
  ```
  Do NOT continue — the orchestrator would skip code+memory and only run
  brain-sync, which is a degraded state the user should fix explicitly.

This pre-flight short-circuits the orchestrator before it spends ~80ms
probing the engine again. The orchestrator independently runs the same
classifier for defense-in-depth, but Step 1.5's STOP is where the user
gets the actionable remediation message.

---

## Step 2: Run the orchestrator

Pass user args to the orchestrator. Do not paraphrase them — pass through
as-is.

```bash
bun run ~/.claude/skills/gstack/bin/gstack-gbrain-sync.ts <user-args>
```

The orchestrator runs three stages: code → memory → brain-sync (per the
plan's storage tiering). Each stage failure is non-fatal; subsequent stages
still run. State is persisted to `~/.gstack/.gbrain-sync-state.json` via
tmp-file + atomic rename. Concurrent runs are blocked by a lock file at
`~/.gstack/.sync-gbrain.lock` (5-min stale-takeover).

---

## Step 3: Code-index health check

After the sync run, verify the cwd source registration and its page count:

```bash
SOURCE_JSON=$(bun run ~/.claude/skills/gstack/bin/gstack-gbrain-read-capability.ts --source-only 2>/dev/null)
SOURCE_ID=$(printf '%s' "$SOURCE_JSON" | jq -er 'if .status=="source" then .source_id else empty end' 2>/dev/null)
PAGES=$(printf '%s' "$SOURCE_JSON" | jq -er 'if .status=="source" and (.page_count | type)=="number" then .page_count else empty end' 2>/dev/null)
echo "cwd source: $SOURCE_ID, page_count: $PAGES"
```

`--source-only` validates the pretty state schema, writer, successful code stage,
real worktree path, `.gbrain-source` pin, and gbrain's registration path before
returning its safe integer page count. It does not read any page. An empty source
or page count is **unknown**, not zero: report WARN and do not offer a full
reindex on that evidence. If `PAGES` is proven `0` AND the user did NOT
pass `--no-code` AND mode was not `--full`, AskUserQuestion via the format in
the preamble:

> D1 — This repo has 0 indexed pages in gbrain. Run a full code reindex now?
>
> ELI10: gbrain hasn't indexed this repo's code yet. The semantic search
> tools (`gbrain search`, `code-def`, `code-refs`) will return nothing
> until we run a full pass. Takes ~25-35 minutes on a big Mac.
>
> Recommendation: A — the brain is unusable for code search until indexed,
> and Step 2 of this skill already verified gbrain is configured correctly.
>
> Note: options differ in kind, not coverage — no completeness score.
>
> A) Run /sync-gbrain --full now (recommended)
> B) Skip — I'll run it later

If A: re-invoke the orchestrator with `--full --code-only`.
If B: continue to Step 4 with the empty-corpus state recorded.

---

## Step 3.5: Call-graph health check (offer `--dream`)

`gbrain code-callers` / `code-callees` (who-calls-this / what-this-calls) return
`count: 0` until a `gbrain dream` cycle runs the `resolve_symbol_edges` phase for
this source — not done by the code import in Step 2.

**One hard prerequisite:** building a call graph requires this source's active
**schema pack to extract code symbols** (the `extract_atoms` phase). On a pack
that doesn't declare it (e.g. `gbrain-base` / `gbrain-base-v2`), a `dream` cycle
completes but `resolve_symbol_edges` matches nothing — the graph stays empty no
matter how many times you run it. So "build the call graph" is only meaningful on
a code-aware pack. The `--dream` stage detects this and reports it honestly
(a WARN row) rather than claiming a build that didn't happen. gbrain exposes pack
capability only at cycle runtime (no pre-flight query as of 0.41.x), so we can't
detect it before running. `code-def` / `code-refs` need the same symbol
extraction; they are NOT free "direct lookups" on a non-code-aware pack.

Detect whether this source's call graph is built via doctor's `cycle_freshness`
check, matching the cwd `SOURCE_ID` literally:

```bash
SOURCE_JSON=$(bun run ~/.claude/skills/gstack/bin/gstack-gbrain-read-capability.ts --source-only 2>/dev/null)
SOURCE_ID=$(printf '%s' "$SOURCE_JSON" | jq -er 'if .status=="source" then .source_id else empty end' 2>/dev/null)
CYCLE=unknown
if [ -n "$SOURCE_ID" ]; then
  CYCLE=$(gbrain doctor --json --fast 2>/dev/null \
    | jq -er --arg id "$SOURCE_ID" '
        if type=="object" and has("error") then empty
        else (.checks[]? | select(.name=="cycle_freshness")) as $c
          | if $c.status=="ok" then "completed"
            elif (($c.message // "") | index($id)) then "never"
            else "unknown" end end' 2>/dev/null || echo unknown)
fi
# index($id) = literal substring (NOT test() regex), matching the lib reader in
# cycleCompleted(). A fail/warn that doesn't name this source → "unknown" (don't
# mask other-source failures).
echo "call graph for $SOURCE_ID: $CYCLE"
```

If `CYCLE == never` AND the user did NOT pass `--dream`/`--full` AND Step 3
`PAGES > 0`, AskUserQuestion via the format in the preamble:

> D2 — This repo's call graph isn't built. Build it now?
>
> ELI10: `gbrain code-callers`/`code-callees` (who calls this function / what it
> calls) return nothing until the `resolve_symbol_edges` phase runs for this
> source. `gbrain dream --source <this source>` runs it (scoped to this
> worktree's code, takes a few minutes). It only produces a graph if this
> source's schema pack extracts code symbols; if it doesn't, the run completes
> but the graph stays empty and the dream row will say so.
>
> Recommendation: A — call-graph queries return 0 until this runs, and the code
> index is already populated. If A comes back as a WARN ("pack does not extract
> code symbols"), the fix is a code-aware schema pack, not re-running dream.
>
> Note: options differ in kind, not coverage — no completeness score.
>
> A) Run /sync-gbrain --dream now (recommended)
> B) Skip — I'll run it later

If A: re-invoke the orchestrator with `--dream --code-only` (skips memory +
brain-sync; the dream stage still runs because it's gated on `--dream`). Then
report the dream stage's ACTUAL row — `OK call graph built (N edges)` vs a
`WARN` that names why the graph is still empty (non-code-aware pack, missing
embedding key, or 0 edges matched). Do not claim success on a WARN.
If B: continue to Step 4 with the call-graph-not-built state recorded for the
verdict.

If `CYCLE == completed` or `unknown`, do not prompt — but note `completed` means
only that a cycle has run, not that edges exist (a non-code-aware pack reports
`completed` with an empty graph). Step 5's verdict row surfaces the real state.

---

## Step 4: Refresh `## GBrain Search Guidance` block in CLAUDE.md

Capability check (per /plan-eng-review §6):

```bash
bun run ~/.claude/skills/gstack/bin/gstack-gbrain-read-capability.ts <user-args>
```

The helper reports JSON `status: ready` only after the successful code sync's
source and real worktree match `.gbrain-source`, the source registration points
to that worktree, and a bounded, source-scoped list/get returns the same page.
It never creates or deletes a page. A `get` may update gbrain's internal
retrieval metadata; the guarantee is no page or source mutation, not zero
internal writes. `status: unknown` (including transient CLI errors, stale state,
or an unverified response) is NOT evidence that the brain is unusable. A
`status: skipped` result for `--no-code`, `--dry-run`, `--refresh-cache`, or
`--audit` means no code-read probe was attempted. Do not run a write probe,
switch to another source, or claim a successful read.

Then update CLAUDE.md based on the helper's status:

**If `status=ready`** — write or update the block. Idempotent: find the
HTML-comment-delimited block; replace its body if it exists; append at the
end of CLAUDE.md if it doesn't. NEVER duplicate. Block is machine-AGNOSTIC
(no engine, no page counts, no last-sync time — those are in the existing
`## GBrain Configuration` block).

Verbatim block content (copy exactly):

```markdown
## GBrain Search Guidance (configured by /sync-gbrain)
<!-- gstack-gbrain-search-guidance:start -->

This worktree's pinned code source answered a source-scoped page read. This
does not verify semantic search or write availability. Prefer gbrain over Grep
when the question is semantic or when you don't know the exact identifier yet;
if a query fails, report that failure rather than assuming the index is healthy.

**This worktree is pinned to a worktree-scoped code source** via the
`.gbrain-source` file in the repo root (kubectl-style context).
`gbrain code-def`, `code-refs`, `code-callers`, `code-callees`, `search`, and
`query` from anywhere under this worktree route to that source by default —
no `--source` flag needed (gbrain >= 0.41.38.0; on older gbrain the call-graph
commands need `--source "$(cat .gbrain-source)"`). Conductor sibling worktrees
of the same repo each have their own pin and their own indexed pages, so
semantic results match the code on disk here.

Call-graph queries (`code-callers`/`code-callees`) also need the graph to be
built first — run `/sync-gbrain --dream` (or `--full`) if they return
`count: 0`. This only works if this source's gbrain schema pack extracts code
symbols; on a non-code-aware pack `--dream` completes but the graph stays empty
and reports a WARN. `code-def`/`code-refs` need the same extraction.

Two indexed corpora available via the `gbrain` CLI:
- This worktree's code (auto-pinned via `.gbrain-source`).
- `~/.gstack/` curated memory (registered as `gstack-brain-<user>` source via
  the existing federation pipeline).

Prefer gbrain when:
- "Where is X handled?" / semantic intent, no exact string yet:
    `gbrain search "<terms>"` or `gbrain query "<question>"`
- "Where is symbol Y defined?" / symbol-based code questions:
    `gbrain code-def <symbol>` or `gbrain code-refs <symbol>`
- "What calls Y?" / "What does Y depend on?":
    `gbrain code-callers <symbol>` / `gbrain code-callees <symbol>`
- "What did we decide last time?" / past plans, retros, learnings:
    `gbrain search "<terms>" --source gstack-brain-<user>`

Grep is still right for known exact strings, regex, multiline patterns, and
file globs. Run `/sync-gbrain` after meaningful code changes; for ongoing
auto-sync across all worktrees, run `gbrain autopilot --install` once per
machine — gbrain's daemon handles incremental refresh on a schedule.

Safety: don't run `/sync-gbrain` while `gbrain autopilot` is active — the
orchestrator refuses destructive source ops when it detects a running autopilot
to avoid racing it (#1734). Prefer registering user repos with `gbrain sources
add --path <dir>` (no `--url`): URL-managed sources can auto-reclone, and the
sync code walk for them requires an explicit `--allow-reclone` opt-in.

<!-- gstack-gbrain-search-guidance:end -->
```

Use the Read + Edit tools. The find-and-replace target is the entire region
from `<!-- gstack-gbrain-search-guidance:start -->` through
`<!-- gstack-gbrain-search-guidance:end -->`. If those markers are missing,
search for `## GBrain Search Guidance (configured by /sync-gbrain)` heading
and replace from there to the next `## ` or EOF. If no heading exists, append
the entire block at the end of CLAUDE.md.

**Atomic write:** write the new CLAUDE.md content to a tmp file alongside it
(e.g., `CLAUDE.md.sync-gbrain.tmp`) then `mv` to atomic-rename, so a crash
mid-write never leaves the file half-modified.

**If `status=unknown`** — preserve the existing guidance block, if any, and
report the helper's reason as WARN with advice to retry `/sync-gbrain` or the
read check when the transient failure clears. Do not install new guidance on
an unknown result or remove the existing guidance merely because this read
could not verify it. The `## GBrain Configuration` block stays in place.

**If `status=skipped`** — leave guidance unchanged. Report that code readiness
was not probed in this mode, not that it passed or failed.

Do NOT crash if CLAUDE.md is missing or unwritable — log a warning and
continue.

---

## Step 5: Verdict block (idempotent doctor output)

Print a status block matching `/setup-gbrain` Step 10 conventions. Each row
is `[OK]/[FIX]/[WARN]/[ERR]`. Reuse `gbrain doctor --json --fast` for
informational rows but DO NOT gate the guidance block on doctor (per
/plan-eng-review §6 — doctor is too strict for unrelated reasons).

```
gbrain status: GREEN

  CLI ............. OK   <gbrain version>
  Engine .......... OK   <pglite|supabase>
  Capability ...... OK   source-scoped page read verified (no page/source mutation)
  CWD source ...... OK   <gstack-code-{repo_slug}> (page_count=<N>)
  Call graph ...... OK   <N> edges resolved (code-callers/callees live)
  ~/.gstack source. OK   <gstack-brain-{user}> (page_count=<N>) — managed by /setup-gbrain
  Memory sync ..... OK   <artifacts_sync_mode>
  CLAUDE.md ....... OK   ## GBrain Search Guidance present
  Last sync ....... OK   <last_sync from state file>

Run `/sync-gbrain` again any time gbrain feels off; safe and idempotent.
```

The **Call graph** row reports the most authoritative signal available:

1. **If a dream stage ran this invocation** (`--dream`, or `--full` auto-build),
   mirror its row verbatim — it's the ground truth for this run:
   - `OK   <N> edges resolved (code-callers/callees live)`
   - `WARN dream ran but this source's schema pack does not extract code symbols
     — switch to a code-aware pack (\`gbrain schema use <pack>\`)`
   - `WARN dream ran but the embed phase failed (missing embedding key)`
   - `WARN dream ran but resolved 0 edges (no code symbols matched yet)`
2. **Otherwise** fall back to the `CYCLE` value from Step 3.5, with honest wording
   (a completed cycle proves a cycle ran, NOT that edges exist):
   - `completed` → `OK   cycle complete — code-callers/callees live IF this source's pack extracts code symbols`
   - `never` → `WARN call graph not built — run /sync-gbrain --dream`
   - `unknown` → `WARN could not probe call graph (doctor unavailable) — run /sync-gbrain --dream if code-callers returns 0`

Any `WARN` Call graph row flips the verdict to YELLOW.

If any row is YELLOW or RED, the verdict line says so and the failing rows
surface a one-line next action. An unknown read gives `Capability ...... WARN
source-scoped read unverified; guidance preserved — retry /sync-gbrain` and
flips the verdict to YELLOW, not RED.
For a skipped probe, show `Capability ...... WARN  code read not probed in
this mode; guidance unchanged` and do not print a GREEN capability verdict.
A `never`/`unknown` Call graph row flips the verdict to YELLOW.

---

## Concurrency note

This skill is safe to run concurrently from multiple terminals on the same
Mac. The orchestrator acquires a lock at `~/.gstack/.sync-gbrain.lock` before
any state-file or CLAUDE.md mutation and exits with code 2 if another sync is
in flight. Stale locks (process died) auto-clear after 5 minutes.

## Cross-machine note

The `## GBrain Search Guidance` block is committed to the repo's CLAUDE.md
and travels with `git push`/`git pull` — NOT through `~/.gstack/.brain-allowlist`
(which is for `~/.gstack/` brain-sync only). On a different Mac with a synced
CLAUDE.md but no local gbrain, /sync-gbrain reports an unknown read and
preserves the block rather than deleting committed instructions based on a
transient or machine-local failure. Agents must not treat unknown as ready.

## Status reporting

End with a Completion Status (per the preamble protocol):
- **DONE** — all stages green, CLAUDE.md guidance block present, verdict GREEN.
- **DONE_WITH_CONCERNS** — sync ran but at least one stage failed or capability
  read was unverified. List which and preserve retry guidance.
- **BLOCKED** — could not acquire lock, gbrain not on PATH, or per-repo policy
  is deny. State the blocker.
- **NEEDS_CONTEXT** — /setup-gbrain has not been run, or `gbrain doctor` shows
  a state that requires user decision (e.g., engine migration).