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Author SHA1 Message Date
Garry TanandClaude Fable 5 d1f03cb346 test(dream): conform dream-dir-source-stamp to canonical PGLite isolation pattern
check:test-isolation R3/R4 flagged the new test file: engine was created
in beforeEach (outside beforeAll) and never disconnected in afterAll.
Switch to the canonical shared-engine pattern (beforeAll create,
beforeEach resetPgliteState, afterAll disconnect) per
test/helpers/reset-pglite.ts.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-07-22 10:47:02 -07:00
Garry TanandClaude Fable 5 e41e3948cd fix(autopilot): close the engine on SIGTERM/SIGINT instead of hard-exiting (#1872)
systemctl stop (SIGTERM) previously hard-exited autopilot without ever
closing the engine. On PGLite the cycle steps run INLINE in the autopilot
process, so a mid-write exit kills WASM Postgres with the WAL dirty and
can corrupt the brain.

Now both exit paths close the engine first:
- autopilot's own shutdown() (SIGINT + internal stops like max_crashes /
  cycle-failure-cap) aborts the in-flight inline cycle via an
  AbortController threaded into runCycle, drains it briefly, and awaits
  engine.disconnect() before process.exit(0).
- process-cleanup's SIGTERM handler (installed at cli.ts module load,
  exits within its 3s cleanup deadline) reaches the same closeEngine via
  a registered 'autopilot-engine-close' cleanup callback.

PGLite's disconnect() drains the pending query and checkpoints before
closing; a second call is a no-op, so both paths firing is safe.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-07-21 15:12:48 -07:00
edad6b1d5f fix(dream): stamp path-derived sources so --dir runs land cycle freshness (#1869)
gbrain dream --dir <path> (and the configured sync.repo_path fallback)
never wrote last_source_cycle_at / last_full_cycle_at because runCycle's
stamp gate reads opts.sourceId and dream only set it from --source.
Doctor's cycle_freshness stayed perpetually stale on path-scoped brains.

Fix at the command level: dream derives the source id from the resolved
brain dir via resolveSourceForDir (now exported from cycle.ts) and passes
it as opts.sourceId. runCycle's stamp/lock semantics are untouched, so
legacy global callers (autopilot-global-maintenance runs GLOBAL_PHASES
with a brainDir and no sourceId) cannot falsely stamp per-source
freshness — the flaw that sank the runCycle-wide variant in PR #2549.
A derived match on an archived source is skipped (mirrors the explicit
--source archived guard).

Takeover of #2549.

Co-authored-by: javieraldape <javieraldape@users.noreply.github.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-07-21 15:12:48 -07:00
18 changed files with 255 additions and 515 deletions
+1 -3
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@@ -1411,8 +1411,7 @@ This is the dispatcher. Skills are the implementation. **Read the skill file bef
| "get more out of gbrain", "is my brain set up right", "weekly brain checkup", "advise me on my brain", "gbrain advisor" | `skills/gbrain-advisor/SKILL.md` |
| Save or load reports | `skills/reports/SKILL.md` |
| "Create a skill", "improve this skill" | `skills/skill-creator/SKILL.md` |
| "save this learning to the vault", "capture this skill in Obsidian", "record this workflow in my notes", "put this setup change in the vault" | `skills/skill-vault-capture-policy/SKILL.md` |
| "Skillify this", "is this a skill?", "make this proper", "add tests and evals for this" | `skills/skillify/SKILL.md` |
| "Skillify this", "is this a skill?", "make this proper" | `skills/skillify/SKILL.md` |
| "Compress my resolver", "AGENTS.md too large", "RESOLVER.md too big", "functional area dispatcher", "shrink routing table" | `skills/functional-area-resolver/SKILL.md` |
| "Is gbrain healthy?", morning health check, skillpack-check | `skills/skillpack-check/SKILL.md` |
| "harvest this skill into gbrain", "publish this skill to gbrain", "lift this skill upstream", "share this skill with other gbrain clients", "promote my skill to gbrain" | `skills/skillpack-harvest/SKILL.md` |
@@ -1430,7 +1429,6 @@ This is the dispatcher. Skills are the implementation. **Read the skill file bef
| "Set up GBrain", first boot | `skills/setup/SKILL.md` |
| "Now what?", "fill my brain", "cold start", "bootstrap", "import my data", "what should I import first" | `skills/cold-start/SKILL.md` |
| "Migrate from Obsidian/Notion/Logseq" | `skills/migrate/SKILL.md` |
| "Connect Obsidian to gbrain", "import my vault to gbrain", "sync vault and gbrain", "embed gbrain after vault update", "is gbrain synced with my vault" | `skills/obsidian-gbrain-safe-index/SKILL.md` |
| Brain health check, maintenance run | `skills/maintain/SKILL.md` |
| "Extract links", "build link graph", "populate timeline" | `skills/maintain/SKILL.md` (extraction sections) |
| "Run dream", "process today's session", "synthesize my conversations", "consolidate yesterday's conversations", "what patterns did you see", "did the dream cycle run" | `skills/maintain/SKILL.md` (dream cycle section) |
+2 -3
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@@ -39,8 +39,8 @@
"skills/briefing",
"skills/citation-fixer",
"skills/concept-synthesis",
"skills/cron-scheduler",
"skills/cross-modal-review",
"skills/cron-scheduler",
"skills/daily-task-manager",
"skills/daily-task-prep",
"skills/data-research",
@@ -54,11 +54,10 @@
"skills/media-ingest",
"skills/meeting-ingestion",
"skills/minion-orchestrator",
"skills/obsidian-gbrain-safe-index",
"skills/perplexity-research",
"skills/query",
"skills/repo-architecture",
"skills/reports",
"skills/repo-architecture",
"skills/signal-detector",
"skills/skill-creator",
"skills/skillify",
+1 -3
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@@ -60,8 +60,7 @@ This is the dispatcher. Skills are the implementation. **Read the skill file bef
| "get more out of gbrain", "is my brain set up right", "weekly brain checkup", "advise me on my brain", "gbrain advisor" | `skills/gbrain-advisor/SKILL.md` |
| Save or load reports | `skills/reports/SKILL.md` |
| "Create a skill", "improve this skill" | `skills/skill-creator/SKILL.md` |
| "save this learning to the vault", "capture this skill in Obsidian", "record this workflow in my notes", "put this setup change in the vault" | `skills/skill-vault-capture-policy/SKILL.md` |
| "Skillify this", "is this a skill?", "make this proper", "add tests and evals for this" | `skills/skillify/SKILL.md` |
| "Skillify this", "is this a skill?", "make this proper" | `skills/skillify/SKILL.md` |
| "Compress my resolver", "AGENTS.md too large", "RESOLVER.md too big", "functional area dispatcher", "shrink routing table" | `skills/functional-area-resolver/SKILL.md` |
| "Is gbrain healthy?", morning health check, skillpack-check | `skills/skillpack-check/SKILL.md` |
| "harvest this skill into gbrain", "publish this skill to gbrain", "lift this skill upstream", "share this skill with other gbrain clients", "promote my skill to gbrain" | `skills/skillpack-harvest/SKILL.md` |
@@ -79,7 +78,6 @@ This is the dispatcher. Skills are the implementation. **Read the skill file bef
| "Set up GBrain", first boot | `skills/setup/SKILL.md` |
| "Now what?", "fill my brain", "cold start", "bootstrap", "import my data", "what should I import first" | `skills/cold-start/SKILL.md` |
| "Migrate from Obsidian/Notion/Logseq" | `skills/migrate/SKILL.md` |
| "Connect Obsidian to gbrain", "import my vault to gbrain", "sync vault and gbrain", "embed gbrain after vault update", "is gbrain synced with my vault" | `skills/obsidian-gbrain-safe-index/SKILL.md` |
| Brain health check, maintenance run | `skills/maintain/SKILL.md` |
| "Extract links", "build link graph", "populate timeline" | `skills/maintain/SKILL.md` (extraction sections) |
| "Run dream", "process today's session", "synthesize my conversations", "consolidate yesterday's conversations", "what patterns did you see", "did the dream cycle run" | `skills/maintain/SKILL.md` (dream cycle section) |
+1 -11
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@@ -2,7 +2,7 @@
"name": "gbrain",
"version": "0.32.3.0",
"conformance_version": "1.0.0",
"description": "Personal knowledge brain with hybrid RAG search GStack mod for agent platforms",
"description": "Personal knowledge brain with hybrid RAG search \u2014 GStack mod for agent platforms",
"skills": [
{
"name": "ingest",
@@ -34,11 +34,6 @@
"path": "migrate/SKILL.md",
"description": "Universal migration from Obsidian, Notion, Logseq, markdown, CSV, JSON, Roam"
},
{
"name": "obsidian-gbrain-safe-index",
"path": "obsidian-gbrain-safe-index/SKILL.md",
"description": "Connect and sync an Obsidian-style Markdown vault with gbrain using a cost-controlled import-first workflow, explicit embedding gates, and durable skill/workflow capture."
},
{
"name": "setup",
"path": "setup/SKILL.md",
@@ -268,11 +263,6 @@
"name": "skill-optimizer",
"path": "skill-optimizer/SKILL.md",
"description": "Self-evolving skill optimization via gbrain skillopt — SkillOpt-paper-grounded text-space optimizer with validation gating (median-of-3 + epsilon=0.05), bundled-skill safety, bootstrap review sentinel, per-skill DB lock, and atomic versioned writes."
},
{
"name": "skill-vault-capture-policy",
"path": "skill-vault-capture-policy/SKILL.md",
"description": "Capture durable operational learnings, new agent skills, and environment/setup changes into the Obsidian vault instead of transient chat memory."
}
],
"dependencies": {
-137
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@@ -1,137 +0,0 @@
---
name: obsidian-gbrain-safe-index
version: 1.0.0
description: |
Connect, maintain, and sync an Obsidian-style Markdown vault with gbrain while preserving a cost-controlled workflow: the vault remains the source of truth, gbrain is the searchable/embedded index, durable skills/workflows are captured into the vault, and paid embedding runs only after explicit approval.
triggers:
- "connect Obsidian to gbrain"
- "import my vault to gbrain"
- "sync vault and gbrain"
- "capture this skill in my vault"
- "embed gbrain after vault update"
- "is gbrain synced with my vault"
tools:
- terminal
- read_file
- search_files
- write_file
- patch
mutating: true
---
# Obsidian → gbrain Safe Index and Capture
## Contract
This skill guarantees:
- Treats the user's Obsidian-style Markdown vault as the source of truth before gbrain indexing.
- Keeps gbrain in conservative mode unless the user explicitly approves a more expensive mode.
- Imports vault changes with `--no-embed` first, then embeds only after explicit approval for the specific paid action.
- Captures durable new skills, workflows, and environment learnings into the vault instead of leaving them only in chat memory.
- Verifies every sync with concrete `gbrain stats`, search mode, and, when embeddings run, exact embedded chunk counts.
## Phases
1. **Resolve the vault path.**
- Prefer an existing environment variable such as `OBSIDIAN_VAULT_PATH` or `WIKI_PATH`.
- If no path is configured, search likely note directories and ask the user before writing.
- Verify the directory exists and contains markdown files or an `.obsidian` directory.
2. **Read vault operating rules before writing.**
- If the vault has `SCHEMA.md`, `index.md`, `log.md`, `AGENTS.md`, or similar operating files, read them before ingest/query/major edit.
- Respect immutable source folders such as `raw/` when the vault declares them.
- Use the vault's native link convention, usually Obsidian `[[wikilinks]]`, for durable relationships.
3. **MECE/capture decision.**
- If new knowledge belongs on an existing page, update that page.
- If it is a distinct recurring workflow or operational policy, create a small meta or concept page following the vault schema.
- Update the vault index/catalog for every new page when the vault maintains one.
- Append a log entry for meaningful vault updates when the vault maintains a log.
4. **Safe gbrain import path.**
- Pre-check source directory; do not import a nonexistent path.
- Run `gbrain config set search.mode conservative` before/after risky reinit steps.
- Run `gbrain import "$OBSIDIAN_VAULT_PATH" --no-embed`.
- Run `gbrain extract links --source fs --dir "$OBSIDIAN_VAULT_PATH"` when wikilinks changed materially.
5. **Paid embedding gate.**
- Do not run `gbrain embed --stale` unless the user explicitly asks or a prior instruction clearly approved this exact paid action.
- Before embedding, verify provider readiness with `gbrain providers test --model <provider:model>`.
- Confirm the configured embedding dimensions match the local schema.
- After embedding, verify `gbrain stats` and record exact `Pages`, `Chunks`, `Embedded`, and `Links` counts.
6. **Final verification and vault echo.**
- Run `gbrain stats` and `gbrain search modes`.
- If vault files changed, re-import with `--no-embed`; if embedding was approved, embed stale chunks afterward.
- Report what changed, what was free/local, what used API billing, and what remains pending.
## Output Format
Use a compact status table:
| Item | Status |
|---|---|
| Vault path | `/path` |
| Vault updated | yes/no + files |
| gbrain mode | conservative/balanced/tokenmax |
| Import | `--no-embed` completed / skipped / failed |
| Pages/chunks | exact counts from `gbrain stats` |
| Embeddings | exact count; note whether this run used API billing |
| Links | exact count |
| Background jobs | none / list exact jobs |
Then include:
- **Safe next step:** free/local action.
- **Paid next step:** embedding/LLM action, if any, with explicit approval requirement.
## Anti-Patterns
- Creating a duplicate skill/page when an existing Obsidian, gbrain, or vault-ingest skill already covers the workflow.
- Running `gbrain embed --stale`, `gbrain dream`, `gbrain autopilot --install`, `gbrain onboard --auto`, or `tokenmax` without explicit cost approval.
- Importing a nonexistent or wrong directory and treating a zero-page import as success.
- Forgetting to update the vault index/catalog and log after creating or materially updating vault pages.
- Recording API keys, tokens, or raw secrets in the vault or final response.
## Tools Used
- `read_file` — read vault schema/index/log and target notes.
- `search_files` — find existing vault pages and avoid duplicates.
- `write_file` / `patch` — create or update vault pages.
- `terminal` — run `gbrain`, `git`, and environment checks with secret values redacted.
## Safe Commands
```bash
export PATH="$HOME/.bun/bin:$PATH"
gbrain config set search.mode conservative
gbrain import "$OBSIDIAN_VAULT_PATH" --no-embed
gbrain extract links --source fs --dir "$OBSIDIAN_VAULT_PATH"
gbrain stats
gbrain search modes
```
## Paid / Approval-Gated Commands
```bash
gbrain providers test --model <provider:model>
gbrain embed --stale
gbrain dream
gbrain autopilot --install
gbrain onboard --auto --max-usd 5
gbrain config set search.mode tokenmax
```
## Verification Checklist
- [ ] Vault path exists and is the intended source.
- [ ] Vault operating files were read before edits when present.
- [ ] Existing pages/skills were searched to avoid duplicates.
- [ ] New/updated vault pages follow the vault schema and link convention.
- [ ] Vault index/catalog updated for new pages when present.
- [ ] Vault log appended for meaningful actions when present.
- [ ] `gbrain import ... --no-embed` completed.
- [ ] `gbrain stats` recorded pages/chunks/embeddings/links.
- [ ] `gbrain search modes` confirms conservative mode unless a different mode was explicitly approved.
- [ ] No paid/background commands ran without approval.
@@ -1,11 +0,0 @@
// Routing eval fixtures for skills/obsidian-gbrain-safe-index.
// Positive cases: intents embed a trigger phrase in natural surrounding context
// (never verbatim-identical to a trigger — the fixture linter rejects tautologies).
{"intent": "help me connect Obsidian to gbrain for my notes", "expected_skill": "obsidian-gbrain-safe-index"}
{"intent": "import my vault to gbrain but skip embeddings for now", "expected_skill": "obsidian-gbrain-safe-index"}
{"intent": "please sync vault and gbrain after I edit notes", "expected_skill": "obsidian-gbrain-safe-index"}
{"intent": "run embed gbrain after vault update tonight", "expected_skill": "obsidian-gbrain-safe-index"}
{"intent": "hey is gbrain synced with my vault right now", "expected_skill": "obsidian-gbrain-safe-index"}
// Negative cases: related but owned by other skills. Assert NO route to this skill.
{"intent": "migrate my notes from Notion to gbrain", "expected_skill": null}
{"intent": "what is on my calendar tomorrow", "expected_skill": null}
-100
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@@ -1,100 +0,0 @@
---
name: skill-vault-capture-policy
version: 1.0.0
description: |
Use when the user wants a durable operational learning, new agent skill, or
important environment/setup change to be captured into the Obsidian vault
instead of left only in transient chat memory. Covers the capture rule,
preferred page patterns, and index/log update obligations.
triggers:
- "save this learning to the vault"
- "capture this skill in Obsidian"
- "record this workflow in my notes"
- "put this setup change in the vault"
- "should we add this to the knowledge base"
tools:
- read_file
- search_files
- write_file
- patch
mutating: true
---
# Skill Vault Capture Policy
## Contract
This skill guarantees:
- Durable operational learnings, newly adopted skills, and important environment/setup changes are captured into the Obsidian vault rather than left only in chat memory.
- An existing page is updated when the knowledge clearly belongs there; a new page is created only when the topic is distinct and likely to recur.
- Every new vault page is added to `index.md`.
- Every meaningful create/update appends a dated entry to `log.md`.
- Small linked pages are preferred over one giant running note.
## Phases
1. **Classify the learning.**
- New gbrain operating rule, cost control, or embedding/provider change.
- New agent-fork / harness / coding-tool integration fact.
- New Obsidian vault workflow or structure decision.
- New recurring agent skill that changes how the agent should operate here.
2. **Avoid duplicates.**
- Search the vault for an existing page that already owns the topic.
- If found, update it with a new section or dated note rather than creating a near-duplicate.
3. **Create when distinct.**
- Place new pages under the vault schema: `_meta/` for operating notes, `concepts/` for workflows, `entities/` for tools/people.
- Use YAML frontmatter and at least two `[[wikilinks]]` unless it is a short seed page.
4. **Update navigation.**
- Add the page to `index.md` under the correct type heading.
- Append a `## [YYYY-MM-DD] create|update | subject` entry to `log.md`.
5. **Report the capture.**
- State which files changed and whether `index.md` / `log.md` were updated.
## Output Format
Use a short status block:
| Item | Status |
|---|---|
| Learning classified | type |
| Page created/updated | path |
| index.md updated | yes/no |
| log.md updated | yes/no |
## Anti-Patterns
- Leaving durable learnings only in chat memory.
- Creating a near-duplicate page instead of updating the existing one.
- Forgetting to update `index.md` and `log.md`.
- Writing one giant running note instead of small linked pages.
- Recording secrets, API keys, or raw credentials in the vault.
## Tools Used
- `read_file` — read `SCHEMA.md`, `index.md`, `log.md`, and target pages.
- `search_files` — find existing pages to avoid duplicates.
- `write_file` / `patch` — create or update vault pages and navigation.
## Safe Commands
```bash
# inspect vault navigation before writing
read SCHEMA.md index.md log.md
# create or update a page, then refresh catalog/log
# index.md: add [[page-slug]] under the matching type heading
# log.md: append ## [YYYY-MM-DD] create|update | subject
```
## Verification Checklist
- [ ] Vault schema/read files were checked before writing.
- [ ] Existing pages were searched to avoid duplicates.
- [ ] New/updated page has frontmatter and wikilinks.
- [ ] `index.md` updated for new pages.
- [ ] `log.md` appended for meaningful actions.
- [ ] No secrets or raw credentials were written.
@@ -1,10 +0,0 @@
// Routing eval fixtures for skills/skill-vault-capture-policy.
// Positive cases: intents embed a trigger phrase in natural surrounding context
// (never verbatim-identical to a trigger — the fixture linter rejects tautologies).
{"intent": "please save this learning to the vault so we keep it", "expected_skill": "skill-vault-capture-policy", "ambiguous_with": ["idea-ingest"]}
{"intent": "we should capture this skill in Obsidian for reuse", "expected_skill": "skill-vault-capture-policy", "ambiguous_with": ["capture"]}
{"intent": "can you record this workflow in my notes for next time", "expected_skill": "skill-vault-capture-policy"}
{"intent": "put this setup change in the vault before we forget", "expected_skill": "skill-vault-capture-policy"}
// Negative cases: related but owned by other skills or out of scope.
{"intent": "connect my Obsidian vault to gbrain", "expected_skill": null}
{"intent": "what is on my calendar tomorrow", "expected_skill": null}
+42 -1
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@@ -38,6 +38,7 @@ import { logSelfUpgrade } from '../core/audit/self-upgrade-audit.ts';
import { detectInstallMethod } from './upgrade.ts';
import { evaluateQuietHours } from '../core/minions/quiet-hours.ts';
import { inspectLock } from '../core/db-lock.ts';
import { registerCleanup } from '../core/process-cleanup.ts';
/**
* v0.37.7.0 #1162 — classify autopilot reconnect-loop errors.
@@ -433,6 +434,37 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
let stopping = false;
let childSupervisor: ChildWorkerSupervisor | null = null;
// #1872: graceful engine shutdown. On PGLite the cycle steps run INLINE in
// this process, so a hard `process.exit` mid-write (systemctl stop →
// SIGTERM) kills WASM Postgres with the WAL dirty and can corrupt the
// brain. Two exit paths must both close the engine:
// - autopilot's own shutdown() below (owns SIGINT + internal stops like
// max_crashes / cycle-failure-cap), and
// - process-cleanup's SIGTERM handler (installed at cli.ts module load;
// it runs the cleanup registry with a 3s deadline and then exits) —
// which is why closeEngine is ALSO registered there.
// closeEngine aborts the in-flight inline cycle (runCycle checks the
// signal between phases and threads it into phase sub-work), gives it a
// short bounded window to wind down, then disconnects. PGLite's
// disconnect() drains the pending query and checkpoints before closing;
// a second call is a no-op (disconnect snapshots + nulls the handle), so
// both paths firing is safe.
const shutdownAbort = new AbortController();
let inflightInlineCycle: Promise<unknown> | null = null;
const closeEngine = async () => {
shutdownAbort.abort(new Error('autopilot shutdown'));
if (inflightInlineCycle) {
// ponytail: 2s cap keeps us inside process-cleanup's 3s deadline; a
// between-phase abort resolves instantly, a mid-phase one may not.
await Promise.race([
inflightInlineCycle.catch(() => { /* cycle errors already logged by the loop */ }),
new Promise((r) => setTimeout(r, 2_000)),
]);
}
try { await engine.disconnect(); } catch { /* best-effort */ }
};
const deregisterEngineClose = registerCleanup('autopilot-engine-close', closeEngine);
if (spawnManagedWorker) {
const cliPath = resolveGbrainCliPath();
// Cgroup-aware auto-sized RSS watchdog cap (issue #1678). The old flat
@@ -520,6 +552,10 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
childSupervisor.killChild('SIGKILL');
}
}
// #1872: abort the in-flight inline cycle and close the engine BEFORE
// process.exit — a hard exit mid-write corrupts PGLite's WASM Postgres.
await closeEngine();
deregisterEngineClose();
try { unlinkSync(lockPath); } catch { /* already gone */ }
process.exit(0);
};
@@ -1008,16 +1044,21 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
// path's phase set). Now both converge on the same primitive.
try {
const { runCycle } = await import('../core/cycle.ts');
const report = await runCycle(engine, {
// #1872: track the promise so closeEngine can drain it on shutdown,
// and pass the abort signal so the cycle winds down between phases.
const cyclePromise = runCycle(engine, {
brainDir: repoPath,
// Autopilot daemon path: pulls by default (matches
// pre-v0.17 autopilot behavior). CLI dream defaults false
// for cron safety; that choice is scoped to dream only.
pull: true,
signal: shutdownAbort.signal,
yieldBetweenPhases: async () => {
await new Promise(r => setImmediate(r));
},
});
inflightInlineCycle = cyclePromise;
const report = await cyclePromise.finally(() => { inflightInlineCycle = null; });
// Only 'failed' (every attempted phase failed) trips the autopilot
// circuit breaker. 'partial' means at least one phase warned or
// failed while others ran — that's a soft signal, not a fatal
+23 -3
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@@ -26,6 +26,7 @@
import type { BrainEngine } from '../core/engine.ts';
import {
runCycle,
resolveSourceForDir,
ALL_PHASES,
type CyclePhase,
type CycleReport,
@@ -380,9 +381,9 @@ Options:
--source <id> Scope the cycle to one source so doctor's
cycle_freshness check sees a fresh stamp on
completion. Without this, gbrain dream's
timestamp never lands and federated brains
see "stale cycle" forever.
completion. When omitted, gbrain derives the
source from --dir / the configured checkout
when it matches a source's local_path (#1869).
--source-id <id> Alias for --source. Matches the v0.37.7.0+
naming used by import/extract/graph-query.
@@ -634,6 +635,25 @@ export async function runDream(engine: BrainEngine | null, args: string[]): Prom
);
process.exit(1);
}
// #1869: a path-scoped run (--dir, or the configured sync.repo_path) whose
// directory matches a registered source's local_path IS that source's cycle
// — derive the source id so runCycle writes last_source_cycle_at /
// last_full_cycle_at on success and doctor's cycle_freshness check stops
// reading perpetually stale. Explicit --source still wins (resolved above).
// Fixed here at the command level, NOT in runCycle's stamp gate, so legacy
// global callers (autopilot-global-maintenance runs GLOBAL_PHASES with a
// brainDir and no sourceId) can't falsely stamp per-source freshness.
// A derived match on an archived source is skipped silently (falls back to
// legacy unscoped behavior) — stamping it would mask staleness on restore,
// mirroring the explicit --source archived guard above.
if (resolvedSourceId === undefined && engine !== null && brainDir !== null) {
const derived = await resolveSourceForDir(engine, brainDir);
if (derived !== undefined) {
const src = await fetchSource(engine, derived);
if (src?.archived !== true) resolvedSourceId = derived;
}
}
// ─── issue #1678: bounded single-hold extract_atoms drain ──────────
if (opts.drain) {
if (engine === null) {
+9 -1
View File
@@ -855,8 +855,16 @@ interface SyncPhaseResult extends PhaseResult {
* Resolve the source id for a brain directory by looking up the sources
* table. Returns undefined when no registered source matches (falls back
* to pre-v0.18 global config.sync.* keys).
*
* Exported for dream.ts (#1869): a `gbrain dream --dir <path>` run whose
* path matches a registered source's local_path is a per-source cycle in
* everything but name, so dream derives the source id up front and passes
* it as opts.sourceId — landing the freshness stamp without changing
* runCycle's stamp/lock semantics for legacy global callers (the
* autopilot-global-maintenance handler runs GLOBAL_PHASES with a brainDir
* and MUST NOT stamp per-source freshness; see rejected PR #2549).
*/
async function resolveSourceForDir(
export async function resolveSourceForDir(
engine: BrainEngine,
brainDir: string | null,
): Promise<string | undefined> {
@@ -0,0 +1,63 @@
/**
* #1872 — autopilot SIGTERM/SIGINT must close the engine before exit.
*
* On PGLite the cycle steps run INLINE in the autopilot process, so a hard
* `process.exit` mid-write (systemctl stop → SIGTERM) kills WASM Postgres
* with the WAL dirty and can corrupt the brain. Two exit paths must both
* close the engine:
*
* - autopilot's own shutdown() (owns SIGINT + internal stops like
* max_crashes / cycle-failure-cap), and
* - process-cleanup's SIGTERM handler (installed at cli.ts module load,
* which exits within its 3s cleanup deadline) — reached via the
* registered 'autopilot-engine-close' cleanup callback.
*
* Because the shutdown path is deep inside `runAutopilot()` (a long-running
* daemon loop that ends in process.exit), a behavioral test would have to
* spawn + signal a real daemon. Following the established precedent
* (test/autopilot-supervisor-wiring.test.ts, test/autopilot-fanout-wiring.test.ts),
* these static-shape regressions pin the load-bearing wiring instead.
*/
import { describe, expect, it } from 'bun:test';
import { readFileSync } from 'fs';
import { join } from 'path';
const AUTOPILOT_SRC = readFileSync(
join(import.meta.dir, '..', 'src', 'commands', 'autopilot.ts'),
'utf8',
);
describe('autopilot.ts graceful engine shutdown (#1872)', () => {
it('registers an engine-close callback in the process-cleanup registry (SIGTERM path)', () => {
// process-cleanup owns SIGTERM (installed at cli.ts:10) and hard-exits
// after its cleanup pass; without this registration the engine is never
// closed on `systemctl stop`.
expect(AUTOPILOT_SRC).toContain(
"import { registerCleanup } from '../core/process-cleanup.ts';",
);
expect(AUTOPILOT_SRC).toContain(
"registerCleanup('autopilot-engine-close', closeEngine)",
);
});
it('closeEngine aborts the in-flight inline cycle then disconnects the engine', () => {
// Abort first (runCycle checks the signal between phases and threads it
// into phase sub-work), bounded drain, then disconnect.
expect(AUTOPILOT_SRC).toMatch(
/const closeEngine = async \(\) => \{[\s\S]{0,900}shutdownAbort\.abort\([\s\S]{0,900}engine\.disconnect\(\)/,
);
});
it('the inline runCycle call carries the shutdown abort signal and is tracked as in-flight', () => {
// PGLite / --inline path: the cycle runs in-process, so shutdown must be
// able to (a) signal it to wind down and (b) await it before closing.
expect(AUTOPILOT_SRC).toMatch(/signal:\s*shutdownAbort\.signal/);
expect(AUTOPILOT_SRC).toMatch(/inflightInlineCycle\s*=\s*cyclePromise/);
});
it('shutdown() awaits closeEngine() before process.exit(0) (SIGINT + internal-stop path)', () => {
expect(AUTOPILOT_SRC).toMatch(
/await closeEngine\(\);[\s\S]{0,400}process\.exit\(0\)/,
);
});
});
+99
View File
@@ -0,0 +1,99 @@
/**
* #1869 — `gbrain dream --dir <path>` stamps cycle freshness when the path
* matches a registered source's local_path.
*
* Pre-fix, only `--source <id>` runs wrote last_source_cycle_at /
* last_full_cycle_at (runCycle's stamp gate reads opts.sourceId, and dream
* never derived one from --dir), so a path-scoped brain showed doctor's
* cycle_freshness as perpetually stale.
*
* The fix lives in dream.ts (derive the source id from the resolved brain
* dir via resolveSourceForDir), NOT in runCycle's stamp gate — a runCycle-
* wide change would make the autopilot-global-maintenance handler (global
* phases, brainDir set, no sourceId) falsely stamp per-source freshness
* (the #2194 poisoning class; see rejected PR #2549).
*
* Same real-PGLite/no-mocks discipline as test/dream.test.ts; same
* GBRAIN_HOME isolation as test/cycle-last-full-cycle-at.test.ts (the
* cycle's PGLite file lock lives under ~/.gbrain).
*/
import { describe, test, expect, beforeAll, afterAll, beforeEach, afterEach } from 'bun:test';
import { mkdtempSync, rmSync } from 'fs';
import { join } from 'path';
import { tmpdir } from 'os';
import { PGLiteEngine } from '../src/core/pglite-engine.ts';
import { resetPgliteState } from './helpers/reset-pglite.ts';
import { runDream } from '../src/commands/dream.ts';
import { withEnv } from './helpers/with-env.ts';
let engine: PGLiteEngine;
let brainDir: string;
let gbrainHome: string;
beforeAll(async () => {
engine = new PGLiteEngine();
await engine.connect({});
await engine.initSchema();
}, 60_000);
afterAll(async () => {
await engine.disconnect();
});
beforeEach(async () => {
await resetPgliteState(engine);
brainDir = mkdtempSync(join(tmpdir(), 'gbrain-dream-stamp-'));
gbrainHome = mkdtempSync(join(tmpdir(), 'gbrain-dream-stamp-home-'));
}, 60_000);
afterEach(() => {
rmSync(brainDir, { recursive: true, force: true });
rmSync(gbrainHome, { recursive: true, force: true });
});
async function seedSource(id: string, archived = false): Promise<void> {
await engine.executeRaw(
`INSERT INTO sources (id, name, local_path, config, archived, created_at)
VALUES ($1, $2, $3, '{}'::jsonb, $4, NOW())`,
[id, id, brainDir, archived],
);
}
async function readLastFullCycleAt(sourceId: string): Promise<string | null> {
const rows = await engine.executeRaw<{ config: Record<string, unknown> | null }>(
`SELECT config FROM sources WHERE id = $1`,
[sourceId],
);
const raw = rows[0]?.config?.last_full_cycle_at;
return typeof raw === 'string' ? raw : null;
}
describe('gbrain dream --dir <path> freshness stamp (#1869)', () => {
test('--dir matching a source local_path stamps last_full_cycle_at', async () => {
await withEnv({ GBRAIN_HOME: gbrainHome }, async () => {
await seedSource('path-scoped');
expect(await readLastFullCycleAt('path-scoped')).toBeNull();
const report = await runDream(engine, ['--dir', brainDir, '--phase', 'lint', '--json']);
expect(report).toBeTruthy();
if (report) expect(['ok', 'clean']).toContain(report.status);
// Pre-fix this stays null forever: dream never passed a sourceId, so
// runCycle's stamp gate skipped the write.
expect(await readLastFullCycleAt('path-scoped')).not.toBeNull();
});
}, 60_000);
test('--dir matching an ARCHIVED source does not stamp it', async () => {
await withEnv({ GBRAIN_HOME: gbrainHome }, async () => {
await seedSource('mothballed', true);
const report = await runDream(engine, ['--dir', brainDir, '--phase', 'lint', '--json']);
expect(report).toBeTruthy();
// Stamping an archived source would mask data staleness when it is
// later restored (mirrors the explicit --source archived guard).
expect(await readLastFullCycleAt('mothballed')).toBeNull();
});
}, 60_000);
});
+14 -4
View File
@@ -562,12 +562,22 @@ describe('runDream — --source / --source-id (v0.41.13)', () => {
// ─── Back-compat: bare `gbrain dream` does NOT write per-source stamp ─
test('gbrain dream (no --source) leaves all sources untouched (back-compat regression)', async () => {
await seedSource('alpha');
await seedSource('beta');
test('gbrain dream (no --source) stamps only the source whose local_path matches --dir (#1869)', async () => {
// Pre-#1869 this asserted NO source was ever stamped without an explicit
// --source — which is exactly the bug: a path-scoped `gbrain dream --dir`
// run never landed a freshness stamp and doctor's cycle_freshness stayed
// stale forever. New truth: the source whose local_path matches the
// resolved brain dir is derived and stamped; unrelated sources stay
// untouched (cross-source isolation).
await seedSource('alpha'); // local_path = repo → derived + stamped
await engine.executeRaw(
`INSERT INTO sources (id, name, local_path, config, archived, created_at)
VALUES ($1, $2, $3, '{}'::jsonb, false, NOW())`,
['beta', 'beta', '/somewhere/else'],
);
const report = await runDream(engine, ['--dir', repo, '--phase', 'lint', '--json']);
expect(report).toBeTruthy();
expect(await readLastFullCycleAt('alpha')).toBeNull();
expect(await readLastFullCycleAt('alpha')).not.toBeNull();
expect(await readLastFullCycleAt('beta')).toBeNull();
}, 60_000);
@@ -1,61 +0,0 @@
/**
* E2E smoke for skills/obsidian-gbrain-safe-index.
*
* Verifies the from-trigger-to-side-effect path that skillify requires:
* a real user trigger phrase routes to the skill, the resolver/check
* pipeline treats it as reachable, and the skill file exposes the
* gbrain commands the workflow actually runs.
*
* This stays local-only (no paid embedding, no external API): it asserts
* the documented safe/import path is present and parseable, not that it
* mutates a live brain.
*/
import { describe, expect, it } from 'bun:test';
import { existsSync, readFileSync } from 'fs';
import { join } from 'path';
const SKILLS = join(import.meta.dir, '..', '..', 'skills');
const SKILL_MD = join(SKILLS, 'obsidian-gbrain-safe-index', 'SKILL.md');
const RESOLVER = join(SKILLS, 'RESOLVER.md');
const TRIGGER_PHRASES = [
'connect my Obsidian vault to gbrain',
'import my vault to gbrain',
'sync vault and gbrain',
'capture this skill in my vault',
'embed gbrain after vault update',
'is gbrain synced with my vault',
];
describe('obsidian-gbrain-safe-index E2E', () => {
it('resolver maps real trigger phrasings to the skill', () => {
const resolver = readFileSync(RESOLVER, 'utf-8');
expect(resolver).toContain('obsidian-gbrain-safe-index/SKILL.md');
// Each representative phrase shares a token substring with a resolver row.
const rows = resolver
.split('\n')
.filter((l) => l.includes('obsidian-gbrain-safe-index/SKILL.md'))
.join('\n');
for (const phrase of TRIGGER_PHRASES) {
const hit = phrase
.toLowerCase()
.split(/\s+/)
.some((tok) => tok.length > 3 && rows.toLowerCase().includes(tok));
expect(hit, `no resolver token for: ${phrase}`).toBe(true);
}
});
it('skill documents the gbrain import-first safe path', () => {
const body = readFileSync(SKILL_MD, 'utf-8');
expect(body).toContain('gbrain import');
expect(body).toContain('--no-embed');
expect(body).toContain('gbrain config set search.mode conservative');
// Paid gate must be explicit, not a silent default.
expect(body).toContain('gbrain embed --stale');
});
it('skill is reachable from the skill tree', () => {
expect(existsSync(SKILL_MD)).toBe(true);
});
});
@@ -1,52 +0,0 @@
/**
* E2E smoke for skills/skill-vault-capture-policy.
*
* Verifies the from-trigger-to-side-effect path: a real capture request
* routes to the skill, and the skill documents the vault navigation
* obligations (index.md / log.md) that make a capture durable.
*
* Local-only: it asserts documented behavior, not live vault writes.
*/
import { describe, expect, it } from 'bun:test';
import { existsSync, readFileSync } from 'fs';
import { join } from 'path';
const SKILLS = join(import.meta.dir, '..', '..', 'skills');
const SKILL_MD = join(SKILLS, 'skill-vault-capture-policy', 'SKILL.md');
const RESOLVER = join(SKILLS, 'RESOLVER.md');
const TRIGGER_PHRASES = [
'save this learning to the vault',
'capture this skill in Obsidian',
'record this workflow in my notes',
'put this setup change in the knowledge base',
];
describe('skill-vault-capture-policy E2E', () => {
it('resolver maps real capture phrasings to the skill', () => {
const resolver = readFileSync(RESOLVER, 'utf-8');
expect(resolver).toContain('skill-vault-capture-policy/SKILL.md');
const rows = resolver
.split('\n')
.filter((l) => l.includes('skill-vault-capture-policy/SKILL.md'))
.join('\n');
for (const phrase of TRIGGER_PHRASES) {
const hit = phrase
.toLowerCase()
.split(/\s+/)
.some((tok) => tok.length > 3 && rows.toLowerCase().includes(tok));
expect(hit, `no resolver token for: ${phrase}`).toBe(true);
}
});
it('skill documents index.md and log.md update obligations', () => {
const body = readFileSync(SKILL_MD, 'utf-8');
expect(body).toContain('index.md');
expect(body).toContain('log.md');
});
it('skill is reachable from the skill tree', () => {
expect(existsSync(SKILL_MD)).toBe(true);
});
});
-51
View File
@@ -1,51 +0,0 @@
import { describe, expect, it } from 'bun:test';
import { readFileSync, existsSync } from 'fs';
import { join } from 'path';
const SKILL_DIR = join(import.meta.dir, '..', 'skills', 'obsidian-gbrain-safe-index');
const SKILL_MD = join(SKILL_DIR, 'SKILL.md');
const RESOLVER = join(import.meta.dir, '..', 'skills', 'RESOLVER.md');
function parseFrontmatter(raw: string): Record<string, unknown> {
const m = raw.match(/^---\n([\s\S]*?)\n---/);
if (!m) throw new Error('no frontmatter');
const out: Record<string, unknown> = {};
for (const line of m[1].split('\n')) {
const mm = line.match(/^([a-zA-Z_]+):\s*(.*)$/);
if (mm) out[mm[1]] = mm[2].trim();
}
return out;
}
describe('obsidian-gbrain-safe-index skill', () => {
it('has a SKILL.md with required frontmatter', () => {
expect(existsSync(SKILL_MD)).toBe(true);
const fm = parseFrontmatter(readFileSync(SKILL_MD, 'utf-8'));
expect(fm['name']).toBe('obsidian-gbrain-safe-index');
expect(fm['description']).toBeTruthy();
});
it('has the required conformance sections', () => {
const body = readFileSync(SKILL_MD, 'utf-8');
for (const section of ['## Contract', '## Phases', '## Output Format', '## Anti-Patterns']) {
expect(body.includes(section), `missing ${section}`).toBe(true);
}
});
it('is registered in RESOLVER.md', () => {
expect(existsSync(RESOLVER)).toBe(true);
const resolver = readFileSync(RESOLVER, 'utf-8');
expect(resolver.includes('obsidian-gbrain-safe-index/SKILL.md')).toBe(true);
});
it('has routing-eval fixtures that exercise real trigger phrasings', () => {
const evalPath = join(SKILL_DIR, 'routing-eval.jsonl');
expect(existsSync(evalPath)).toBe(true);
const lines = readFileSync(evalPath, 'utf-8')
.split('\n')
.filter((l) => l.trim() && !l.trim().startsWith('//'))
.map((l) => JSON.parse(l));
const positives = lines.filter((l) => l.expected_skill === 'obsidian-gbrain-safe-index');
expect(positives.length).toBeGreaterThanOrEqual(5);
});
});
-64
View File
@@ -1,64 +0,0 @@
import { describe, expect, it } from 'bun:test';
import { readFileSync, existsSync } from 'fs';
import { join } from 'path';
import { DEFAULT_PRIVATE_PATTERNS } from '../src/core/skillpack/harvest-lint.ts';
const SKILL_DIR = join(import.meta.dir, '..', 'skills', 'skill-vault-capture-policy');
const SKILL_MD = join(SKILL_DIR, 'SKILL.md');
const RESOLVER = join(import.meta.dir, '..', 'skills', 'RESOLVER.md');
function parseFrontmatter(raw: string): Record<string, unknown> {
const m = raw.match(/^---\n([\s\S]*?)\n---/);
if (!m) throw new Error('no frontmatter');
const out: Record<string, unknown> = {};
for (const line of m[1].split('\n')) {
const mm = line.match(/^([a-zA-Z_]+):\s*(.*)$/);
if (mm) out[mm[1]] = mm[2].trim();
}
return out;
}
describe('skill-vault-capture-policy skill', () => {
it('has a SKILL.md with required frontmatter', () => {
expect(existsSync(SKILL_MD)).toBe(true);
const fm = parseFrontmatter(readFileSync(SKILL_MD, 'utf-8'));
expect(fm['name']).toBe('skill-vault-capture-policy');
expect(fm['description']).toBeTruthy();
});
it('has the required conformance sections', () => {
const body = readFileSync(SKILL_MD, 'utf-8');
for (const section of ['## Contract', '## Phases', '## Output Format', '## Anti-Patterns']) {
expect(body.includes(section), `missing ${section}`).toBe(true);
}
});
it('is registered in RESOLVER.md', () => {
expect(existsSync(RESOLVER)).toBe(true);
expect(readFileSync(RESOLVER, 'utf-8').includes('skill-vault-capture-policy/SKILL.md')).toBe(true);
});
it('contains no private user or agent-fork names (privacy rule)', () => {
for (const file of [SKILL_MD, join(SKILL_DIR, 'routing-eval.jsonl')]) {
const body = readFileSync(file, 'utf-8');
// DEFAULT_PRIVATE_PATTERNS[0] is the banned fork-name pattern; sourced
// from harvest-lint so this file never contains the literal itself
// (scripts/check-privacy.sh would reject it).
const forkName = new RegExp(DEFAULT_PRIVATE_PATTERNS[0], 'i');
for (const name of [/\bAdam\b/, /\bHermes\b/, /\bHerdr\b/, /\bArk\b/, forkName]) {
expect(name.test(body), `private name ${name} in ${file}`).toBe(false);
}
}
});
it('has routing-eval fixtures', () => {
const evalPath = join(SKILL_DIR, 'routing-eval.jsonl');
expect(existsSync(evalPath)).toBe(true);
const positives = readFileSync(evalPath, 'utf-8')
.split('\n')
.filter((l) => l.trim() && !l.trim().startsWith('//'))
.map((l) => JSON.parse(l))
.filter((l) => l.expected_skill === 'skill-vault-capture-policy');
expect(positives.length).toBeGreaterThanOrEqual(4);
});
});