* fix(write-through): guard mkdir against EEXIST on Bun+Windows
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
* fix(budget): resolve non-Anthropic model pricing via canonical table under --max-cost
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
* fix(enrich): exclude dream-generated pages from thin candidates
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
When link_resolution.global_basename is enabled, extend basename-index
resolution to frontmatter link fields (FRONTMATTER_LINK_MAP), mirroring the
body bare-wikilink path added in #972.
Problem: a bare-title wikilink in a frontmatter list -- e.g.
sources:
- "[[2025-12-25_mentor-extraction]]"
never resolves. SlugResolver.resolve() has no '/' to hit the slug-direct
getPage, and the field's dirHint (sources -> ['source','media']) may name
folders absent from the brain, so the dir-scoped exact + fuzzy steps also
miss. The frontmatter path never consulted resolveBasenameMatches -- that was
wired only for body bare-wikilinks. On a PARA/Obsidian vault this silently
drops the bulk of sources:/related: provenance edges.
Fix: extractFrontmatterLinks takes a globalBasename flag (threaded from
extractPageLinks). On a resolve() miss, unwrap [[ ]] and fall back to
resolver.resolveBasenameMatches -- UNIQUE-MATCH-ONLY, so ambiguous basenames
(archive dupes, generic hubs like _index) stay unresolved rather than create
a wrong edge. Purely additive; resolved frontmatter edges are unchanged.
Scope: covers the db-source extract and live put_page paths (real
makeResolver). The --source fs extract uses an inline resolver without a
basename index, so it gracefully no-ops there (typeof guard).
Tested: 3 new cases (resolves-when-on, ambiguous-stays-unresolved,
gated-off-by-flag); full link-extraction suite green (130 pass).
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The hybrid recency stage in runPostFusionStages imported
DEFAULT_RECENCY_DECAY directly, so operator overrides via the
GBRAIN_RECENCY_DECAY env var and the gbrain.yml `recency:` section were
honored only on the get_recent_salience SQL path and silently ignored on
the hot hybridSearch path. Non-default vault layouts therefore stayed on
the baked-in defaults / DEFAULT_FALLBACK (90d / 0.5) regardless of
tuning.
Call resolveRecencyDecayMap() (already used by the SQL path) so the
configured decay map reaches the boost stage. Behavior is unchanged when
no override is set — resolveRecencyDecayMap() returns DEFAULT_RECENCY_DECAY.
Adds test/hybrid-recency-config.test.ts asserting the env override
reaches the applied recency factor (fails against the prior wiring).
Single-file `frontmatter validate` derived the expected slug from the
absolute path: relative(resolve(target), file) is empty when target IS the
file, so it fell back to `|| file` (the full path), yielding "root/<abs>"
slugs and a false SLUG_MISMATCH. The pre-commit hook from install-hook
validates staged files one-by-one, so this rejected every commit in a
markdown brain (only bypassable with --no-verify).
Walk up to the brain root (nearest .git) and use relative(brainRoot, file)
|| basename(file), matching runAudit/runGenerate and sync/extract. Files
above the root fall back to basename instead of a ../-prefixed slug.
Reopens#565. Present since v0.32.0; reproduced on v0.42.51.
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
OpenRouter (and potentially other proxy providers) expose OpenAI's
text-embedding-3 models with a provider prefix in the model ID, e.g.
`openai/text-embedding-3-large` rather than bare `text-embedding-3-large`.
`dimsProviderOptions()` checks `modelId.startsWith('text-embedding-3')`
which fails for the prefixed form, so the `dimensions` parameter is never
sent. The upstream provider returns its native dimensionality (3072 for
-large) instead of the configured value (e.g. 1536), causing an immediate
"dim mismatch" error on first embed.
The default OpenRouter embedding (`text-embedding-3-small` at 1536d)
masked this because its native size happens to match the default config.
The bug surfaces when using `-large`, or `-small` with a non-1536 dim
(512, 768, 1024 — all listed in the recipe's `dims_options`).
Fix: strip the provider prefix before the `startsWith` check. The full
prefixed ID is preserved in the error message for user clarity.
* feat(subagent): claude-cli MessagesClient adapter (baseline, no tool use)
Closes#334 (partially — text-only baseline; tool use lands in the next
commit on this branch).
Adds a MessagesClient adapter that shells out to `claude --print
--output-format json --model <model>` instead of the Anthropic SDK. When
`GBRAIN_USE_CLAUDE_CLI=1` is set, the subagent worker registers the adapter
in place of the SDK client; the default path (Anthropic SDK with
ANTHROPIC_API_KEY) is unchanged when the env var is unset or set to
anything else.
The benefit is that Claude Max subscribers can run Minions subagents
against their existing OAuth subscription, no ANTHROPIC_API_KEY needed.
New: src/core/minions/handlers/claude-cli-adapter.ts
- Implements the MessagesClient interface exported from subagent.ts.
- Strips provider prefixes (`anthropic:`, `litellm:`) from the model id
because `claude --print` only accepts CLI-native aliases (`sonnet`,
`opus`, `haiku`, or the bare `claude-*-N-M` form).
- Flattens the Anthropic messages array into a single text prompt for
claude-cli stdin. Tool blocks (tool_use / tool_result) are stringified
as placeholders so multi-turn conversations stay coherent in this
baseline; native tool_use round-tripping is the follow-up commit.
- Spawns claude with stdio piped, captures stdout, parses the
`{type:"result", subtype:"success", result, usage, ...}` JSON envelope,
and returns it as a properly shaped Anthropic.Message with
`stop_reason: 'end_turn'`.
- Token totals propagate from the claude usage block so the subagent
handler's `ctx.updateTokens()` reports usable numbers.
- AbortSignal is wired through to SIGTERM the child so the subagent loop's
cancellation path stays correct.
Modified: src/commands/jobs.ts (worker registration)
- Conditionally constructs a MessagesClient via the new adapter when
GBRAIN_USE_CLAUDE_CLI=1.
- Passes it into makeSubagentHandler({ engine, client: subagentClient }).
- Logs `[minion worker] subagent routing via claude-cli (GBRAIN_USE_CLAUDE_CLI=1)`
on startup so the env var status is operator-visible.
Limitations of this commit (addressed in the follow-up):
- Tool use is not yet supported. Tools in params.tools are ignored; the
adapter returns a single text block with stop_reason='end_turn'.
- Token counts come from claude-cli's reporting and may not match the
Anthropic API's accounting precisely (especially for cache tiers).
Original design from #334; this commit preserves that author's attribution.
The follow-up commits on this branch carry the tool-use implementation.
* feat(subagent): tool use + context isolation + convention rename on top of jarvisdoes baseline
Builds on the previous commit (jarvisdoes's #334 baseline) by adding three
things the upstream issue called out as gaps or that surfaced during review:
1. Tool use support via system-prompt-instructed JSON emission.
2. Context isolation flags so claude-cli does not load operator-level
CLAUDE.md, skills, and local project context into every subagent call.
3. Env var rename from GBRAIN_USE_CLAUDE_CLI=1 to
GBRAIN_SUBAGENT_PROVIDER=claude-cli to match the existing
GBRAIN_<noun>_<role>=<value> convention used by GBRAIN_CHAT_MODEL,
GBRAIN_EMBEDDING_MODEL, GBRAIN_EXPANSION_MODEL.
## Tool use
The MessagesClient interface returns Anthropic.Message objects whose
content array may include tool_use blocks. The subagent handler filters
those blocks and dispatches each tool, so any backend that produces
correctly shaped tool_use blocks gets the same loop behavior as the
Anthropic SDK.
The adapter injects a system-prompt addendum describing the tool registry
plus an emission protocol:
<use_tools>
[{"id": "...", "name": "...", "input": {...}}, ...]
</use_tools>
After the response comes back, extractToolCalls() scans for the block,
parses the JSON (tolerant of optional ```json fencing), and converts each
entry into a tool_use content block. Multiple parallel tool calls in one
turn are supported via the array shape; this is the exact case that
breaks today on the codex-proxy / litellm GPT-5.x bridge where parallel
tool-call response IDs get dropped.
Defensive fallbacks:
- Malformed JSON inside the block: drop to text-only, stop_reason='end_turn'.
- Unterminated <use_tools> (no close tag): drop to text-only.
- Model omits id field: adapter synthesizes a toolu_claude_cli_<rand> id.
- Empty response: still hand the subagent loop a well-formed content
array so the .filter chain does not crash.
## Context isolation
claude-cli auto-discovers CLAUDE.md from cwd upward and injects the
operator's skills + plugins + auto-memory into the default system prompt.
On a real install that is ~42-65k tokens of contamination per subagent
call, with both cost and behavioral consequences (the subagent picks up
the operator's coding conventions, opinions, and preferences).
The maximum suppression that still preserves OAuth / Claude Max
subscription auth is:
- Spawn from a dedicated clean cwd (tmpdir-based) so LOCAL CLAUDE.md
auto-discovery has nothing to find. -13k tokens on a real gbrain
install where CLAUDE.md is substantial.
- --disable-slash-commands so skill resolution does not pull in
/skill-name handlers.
- --system-prompt <gbrain prompt> so the default system prompt is
replaced rather than appended to.
The --bare flag would also strip user-level ~/.claude/CLAUDE.md but it
forces ANTHROPIC_API_KEY auth, defeating the whole point of this adapter.
The remaining ~42k cached tokens from user-level instructions are
accepted as a cost-trivial trade-off because the Max subscription absorbs
the per-call cost. Behavioral contamination is mitigated by gbrain's
strong per-call system prompt overriding any operator-level drift.
## Env var rename
Surveyed all ~140 GBRAIN_* env vars in src/. The codebase uses three
patterns: GBRAIN_NO_<feature> (negative toggles), GBRAIN_<noun>_<role>
=<value> (routing keys), GBRAIN_ALLOW_<feature> (permissive toggles).
GBRAIN_USE_* does not appear anywhere except jarvisdoes's original
commit; it would introduce a fourth pattern.
GBRAIN_SUBAGENT_PROVIDER=claude-cli aligns with the routing-keys family
and is value-extensible — adding codex-cli / meridian-proxy / etc. later
means a new value, not a new env var. The scope ('SUBAGENT_*') is also
unambiguous about which calls the toggle covers; GBRAIN_USE_CLAUDE_CLI
was silent on whether it applied to all gbrain LLM calls or only the
subagent path.
Unknown values are rejected with a fail-fast error message naming the
two valid values rather than silently falling through to the default.
## Tests
New file: test/claude-cli-adapter.test.ts — 12 tests, 33 assertions:
- Text-only round trip (single text block, usage propagation, end_turn).
- Provider prefix stripping ('anthropic:claude-sonnet-4-6' -> 'claude-sonnet-4-6').
- Single tool_use parsing.
- Multiple parallel tool calls in one block (the case that triggered
the codex-proxy regression).
- Fenced JSON inside <use_tools> block.
- Model-omitted id gets synthesized to toolu_claude_cli_<rand>.
- Malformed JSON falls back to text.
- Unterminated block falls back to text.
- AbortSignal SIGTERMs the child.
- Error envelope rejected with informative message.
- Non-JSON output rejected with raw-output excerpt in the error.
- argv + cwd assertion: --disable-slash-commands + --system-prompt are
present and cwd is the dedicated tmpdir.
Tests use a POSIX shell stub at GBRAIN_CLAUDE_CLI_BIN that emits a
scripted --output-format json envelope, so the suite runs without
claude-cli installed and without API credits.
* feat(ai): claude-cli recipe with native gateway integration (supersedes #334 baseline)
Replaces the MessagesClient adapter + GBRAIN_USE_CLAUDE_CLI=1 env-var
gate from the previous commit on this branch with a proper gateway recipe.
The recipe path gives per-call routing as a native capability: a model
string like `claude-cli:claude-sonnet-4-6` lands here while a sibling
`litellm:gpt-5.4` continues through the litellm-proxy / codex-proxy path
in the same worker. No global env-var switch, no agent.use_gateway_loop
bypass, no MessagesClient injection at jobs.ts worker startup.
The previous commit on this branch (jarvisdoes baseline) is preserved
in the history for #334 authorship attribution. Its functional changes
are backed out here because the recipe pattern is gbrain's established
integration seam; introducing a parallel MessagesClient + env-var path
would have created two routing mechanisms competing for the same job.
New: src/core/ai/recipes/claude-cli.ts
- Recipe declaration: id 'claude-cli', tier 'native', implementation
'claude-cli', chat-only (no embedding or expansion touchpoints).
- Models: claude-opus-4-7, claude-sonnet-4-6, claude-haiku-4-5-20251001.
- supports_tools and supports_subagent_loop both true.
- supports_prompt_cache false because the CLI handles caching internally
and does not surface cache_control via the standard control plane.
- auth_env.required is the empty array because the CLI owns auth (OAuth
session managed by `claude login`).
- Friendly aliases mirror the `anthropic` recipe: `sonnet`, `haiku`,
`opus` and the same legacy-id rewrites for back-compat with stale
config strings.
New: src/core/ai/providers/claude-cli-language-model.ts
- ClaudeCliLanguageModel class implementing the ai-sdk LanguageModelV2
interface.
- doGenerate: renders the ai-sdk prompt array into a system text + user
text, injects the use_tools protocol instructions when tools are
present, spawns `claude --print --output-format json --model <X>
--disable-slash-commands --system-prompt <gbrain prompt>` from a
dedicated tmpdir (contamination suppression: no local CLAUDE.md
auto-discovery), parses the JSON envelope, extracts <use_tools>
blocks, and returns ai-sdk-shaped LanguageModelV2Content (text +
tool-call parts with stringified-JSON input matching the V2 contract).
- Tolerates fenced JSON inside use_tools blocks, malformed JSON
(falls back to text), missing close tag (falls back to text),
model-omitted ids (synthesizes toolu_claude_cli_<rand>).
- Parallel tool calls in one block round-trip cleanly: this is the
case that drops IDs on the litellm + codex-proxy bridge today.
- AbortSignal SIGTERMs the child for proper cancellation.
- doStream throws not-supported (gateway.toolLoop is non-streaming).
Modified: src/core/ai/gateway.ts
- Adds case 'claude-cli' to instantiateChat (returns ClaudeCliLanguageModel).
- Adds case 'claude-cli' to instantiateExpansion (same wrapper, reserved
for a future expansion touchpoint declaration).
- Adds case 'claude-cli' to instantiateEmbedding (throws, no embedding
model, mirrors the native-anthropic path).
- Lazy require() at the call site keeps the gateway module load cheap
for users who never use the claude-cli path.
Modified: src/core/ai/recipes/index.ts
- Registers `claudeCli` in the ALL[] array next to `anthropic`.
Modified: src/core/ai/types.ts
- Adds 'claude-cli' to the Implementation union so the gateway switch
is exhaustive at compile time.
Reverted: src/commands/jobs.ts
- Drops the GBRAIN_USE_CLAUDE_CLI=1 env-var gate the prior commit
added. Routing now happens at the gateway based on the model string.
Deleted: src/core/minions/handlers/claude-cli-adapter.ts
- The MessagesClient adapter is superseded by the recipe + LanguageModelV2
path. Two routing mechanisms competing for the same job would have
forced users to reason about which one wins; the recipe is the single
source of truth.
New file: test/claude-cli-recipe.test.ts (16 tests, 46 assertions):
- Recipe registration: getRecipe returns chat-only Recipe; aliases map
short names (sonnet/haiku/opus) to canonical model ids.
- Text round trip: single text content block, usage propagation, stop
finish reason.
- Provider prefix stripping.
- Single tool-call parsing.
- Multiple parallel tool calls in one block.
- Fenced JSON inside the block.
- Model-omitted id synthesizes toolu_claude_cli_<rand>.
- Malformed JSON falls back to text + stop reason.
- Unterminated block falls back to text + stop reason.
- Tools offered but model declines: returns text-only with stop reason
so the gateway-loop treats it as a final answer rather than wedging
for tool calls that never come.
- AbortSignal SIGTERMs the child.
- is_error envelope rejected.
- Non-JSON output rejected.
- doStream throws.
- argv + cwd assertion: --print, --disable-slash-commands,
--system-prompt are present and cwd is the dedicated tmpdir.
Tests use a POSIX shell stub at GBRAIN_CLAUDE_CLI_BIN so the suite runs
without claude-cli installed and without API credits.
End-to-end smoke verified against a real `claude --print --model haiku`
invocation: model emitted `<use_tools>` block with toolu_add_001 +
{"a":12,"b":30}, adapter parsed back into a `tool-call` content block,
finishReason 'tool-calls'.
* feat(ai/claude-cli): harden subagent isolation, env scrub, verbose + stdin robustness
Four defensive fixes to the claude-cli provider so a subagent call behaves
identically regardless of the host's ambient Claude Code config:
- Agent isolation: pass `--tools ''` and `--strict-mcp-config` so the subprocess
runs as a raw LLM with no built-in tools and no inherited user MCP servers.
Without `--strict-mcp-config`, each call boots the user's MCP servers (including
gbrain's own), causing recursion plus PGLite single-writer lock contention.
- Env scrub: drop ANTHROPIC_API_KEY / ANTHROPIC_AUTH_TOKEN / ANTHROPIC_BASE_URL
from the child env so the CLI authenticates via its own OAuth subscription
session. An inherited API key silently flips billing to per-token API usage,
the exact setup this recipe exists to replace.
- Verbose-mode compat: with `"verbose": true` in ~/.claude/settings.json,
`--print --output-format json` emits an event array instead of a bare result
object. Tolerate both shapes and select the result event.
- stdin robustness: handle the child stdin 'error' event and wrap write/end so a
missing binary (ENOENT) or early child death (EPIPE) rejects cleanly instead of
crashing the worker with an unhandled error.
Adds unit coverage for the env scrub, the isolation argv, and the verbose event
array. Verified against claude CLI 2.1.x.
* test(ai/claude-cli): cover verbose-array no-result + missing-binary reject paths
Two error branches in the hardened claude-cli provider had no coverage: the
verbose event-array path when no result event is present, and a missing binary
surfacing as a clean spawn-failed rejection. The missing-binary case is the
deterministic form of the stdin/EPIPE robustness; a synchronous stdin-write
throw is not reliably triggerable in a unit test, so the real ENOENT path the
handlers defend is exercised instead. Both reuse the existing shell-stub harness.
---------
Co-authored-by: jarvisdoes <258486803+jarvisdoes@users.noreply.github.com>
Co-authored-by: Marco Maldonado <34176133+loweaxerium@users.noreply.github.com>
queue.add() with an idempotency_key returns any existing row regardless
of status. This means dead jobs (exhausted retries from a transient
provider outage) permanently block re-submission of the same work —
even after the underlying issue is fixed.
Fix: when the existing row is dead or cancelled, NULL its
idempotency_key (preserving the row for audit) and fall through to the
INSERT path so a fresh job can be created.
Affects dream synthesize children that died during provider migrations
(429 rate-limit on old Anthropic proxy, tool-results-missing on old
OpenRouter). 45 dead children were blocking re-synthesis of transcripts
in production.
Includes 4 new tests covering dead, cancelled, completed, and active
status interactions with idempotency dedup.
Co-authored-by: Rafael Reis <rafael.reis@contabilizei.com.br>
OpenRouter's POST /api/v1/rerank is wire-compatible with gateway.rerank()
({query, documents, model} → {results: [{index, relevance_score}]}). This
adds a recipe-only reranker touchpoint declaring four models:
- cohere/rerank-v3.5 (default; $0.001/search)
- cohere/rerank-4-fast ($0.002/search, 32K context)
- cohere/rerank-4-pro ($0.0025/search, SOTA quality)
- nvidia/llama-nemotron-rerank-vl-1b-v2:free (multimodal)
Unlike embedding/chat, the reranker path strictly enforces the models
allowlist — the openai-compat extended-model bypass does not apply. New
rerank models must be added to this recipe before they can be called.
The cost_per_1m_tokens_usd value is a pseudo-rate for the budget tracker's
chars/4 heuristic — Cohere bills per-search, not per-token. At ~4K chars
the estimated cost is in the right ballpark.
Recipe-only change; no gateway or search-layer modifications. gateway
auto-concatenates path → .../api/v1/rerank.
Adds hermetic unit test (test/openrouter-reranker-recipe.test.ts) covering
shape, models, default_model, path, max_payload_bytes, default_timeout_ms,
and cost field. No DB, no env mutation — survives the parallel 8-shard
fan-out.
Verified: bun run verify (30/30 green); 285 targeted recipe+rerank+budget
tests pass.
Co-authored-by: Hippityy <Hippityy@users.noreply.github.com>
`gbrain doctor --remediation-plan` printed two consecutive lines that
contradicted each other when the brain was below target AND the target
was unreachable with autonomous remediation:
Brain score: 45/100 → target 90
Target unreachable: max with autonomous remediation is 70/100.
No remediations needed. Brain is at target.
The second sentence hid the real next step (configure the prereqs that
would lift `max_reachable_score`) and made the brain look healthy when it
was not.
Fix: gate the "Brain is at target" line on `brain_score_current >=
targetScore`. When the plan is empty AND the brain is below target, the
"Target unreachable" line above is already the user-facing explanation;
the `Blocked checks` block below surfaces the manual gap.
Extracted `renderRemediationPlanLines(plan, targetScore): string[]` as a
pure helper alongside `runRemediationPlan` so the regression coverage
asserts on the rendered output directly rather than mocking
`console.log`. `runRemediationPlan` now joins the lines verbatim through
console.log; behavior is byte-identical for every case other than the
fixed contradiction.
Five regression tests cover: unreachable-and-below-target (the bug
case), reachable-and-at-target, exact-target, below-target-with-plan,
unreachable-with-partial-plan. 38 tests across the adjacent doctor test
files stay green; `bun run typecheck` clean.
Idempotency was keyed on atom rows alone — a page the LLM judges
un-atomizable leaves no row, so it re-entered the discovery window every
run. Two production consequences: --drain false-stopped with
no_progress once the window head was mostly zero-yield pages (remaining
frozen while batches report +0), and every nightly re-spent extraction
budget on the same pages.
Fix:
- After a SUCCESSFUL chat call that parses to zero atoms, stamp the
source page with frontmatter.atoms_scan_hash = contentHash16. LLM
failures take the catch path and stay retryable.
- discoverExtractablePages + countExtractAtomsBacklog (both variants)
exclude pages whose stamp matches the CURRENT content hash prefix —
content edits re-eligibilize, mirroring atom-row staleness semantics.
- Drain no_progress now recounts the backlog on a zero-atom batch and
only stops when it genuinely didn't shrink — tombstoning IS progress.
Tests: +2 pure-loop drain cases (shrinking backlog continues / flat
backlog stops) and +3 PGLite integration cases (stamp + exclusion /
content-change re-eligibility / failed chat does not stamp).
29 pass / 0 fail across the two files; tsc clean.
Co-authored-by: 陈源泉 <chenyuanquan@chenyuanquandeMac-mini.local>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
synthesize-concepts.ts's design comment says extract_atoms stamps a
`concepts:` frontmatter field on each atom and :92 consumes ONLY that
field — but the extractor never wrote it, so the atoms → concepts
pipeline was dead end-to-end: every cycle reported "synthesize_concepts:
skipped — no atoms with concept refs" no matter how many atoms
accumulated (696 page-derived atoms / 0 with concepts on our production
brain before an external backfill).
Fix, all on the extractor side (no synthesize change needed):
- EXTRACT_PROMPT asks for `concepts` (1-3 kebab-case TOPIC labels) with
an explicit reuse-over-coinage instruction — labels must cluster,
since synthesize_concepts only materializes groups of >=2.
- parseAtomsResponse validates labels (kebab regex, max 3, drop
invalid; empty -> undefined).
- The putPage frontmatter write stamps `concepts` alongside lesson /
source_quote.
Tests: 4 parse cases + an end-to-end regression that goes extractor ->
real frontmatter -> synthesize_concepts' OWN DB query path -> concept
page. The existing tests fed synthesize via the `_atoms` seam, which is
exactly how this gap survived.
Validated in production ahead of this PR by stamping the same shape
externally: the next synthesize_concepts run wrote 33 concept pages
(T2=7/T3=26) from 60 stamped atoms, zero failures.
Co-authored-by: 陈源泉 <chenyuanquan@chenyuanquandeMac-mini.local>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
The wrapper script that 'gbrain autopilot --install' writes to
~/.gbrain/autopilot-run.sh sources ~/.bashrc to inherit PATH for the
exec'd gbrain binary (which has a '#!/usr/bin/env bun' shebang). The
standard Debian/Ubuntu ~/.bashrc ships a non-interactive guard that
returns early when bash is launched non-interactively (cron, launchd,
systemd) — so PATH exports operators add to ~/.bashrc never reach the
wrapper subprocess.
The result: the wrapper dies silently with 'env: bun: No such file or
directory', leaves a stale lockfile, and every subsequent cron tick
hits the lockfile and bails. The nightly dream cycle hangs waiting on
a worker that never comes back, and the wrapper's own 10-min
stale-lock window is the only thing that can recover it.
This bites every operator whose bashrc is the standard distro default
(which is the default), and there is no warning at install time.
Fix: prepend ~/.bun/bin to PATH directly in the wrapper, so it is
self-contained regardless of which init file the OS loaded. Add a
regression test alongside the existing zshenv/zshrc source-order test
(v0.36.1.x #966) so this class of bug stays caught.
The conversation_format_coverage check recommended `gbrain config set
conversation_parser.llm_fallback_enabled true`, but that config key is dead
(never read) — see #1890. The recommendation is a no-op and misleads users into
thinking a fallback will kick in. Drop it; keep the actionable `scan` hint.
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
Backlinks Minion jobs submitted with an empty payload (the
sync→embed→backlinks chains enqueued after every ingestion) defaulted to
action='fix', rewriting tracked brain pages with generated "Referenced in"
timeline bullets on every routine run — 129 vault files polluted in one
day on our production brain before we traced it.
This contradicts the documented intent in src/core/cycle.ts
(runPhaseBacklinks): "Maintenance cycles must not rewrite tracked brain
pages with generated 'Referenced in' timeline bullets. [...] the legacy
filesystem fixer remains available explicitly via `gbrain check-backlinks
fix`." — the jobs-worker handler simply inverted that default.
Fix: default to 'check'; 'fix' requires explicit opt-in via
'{"action":"fix"}' (the documented submit shape) or
`gbrain check-backlinks fix`. Both explicit paths are unchanged.
Adds a structural regression test (fix-wave-structural.test.ts precedent)
pinning the default, since the handler dynamically imports
runBacklinksCore and walks a real repo dir — a behavioral test would
require mocking that hides the regression behind a test seam.
Co-authored-by: Valentin Ferriere <valentin@v-labs.fr>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
`extractStaleFromDB` stamped `links_extracted_at` with each page's read
`updated_at` (the D4 race-fix). But the stale predicate also flags
`links_extracted_at < LINK_EXTRACTOR_VERSION_TS`. Any page last edited
BEFORE the version timestamp got stamped below the threshold, so the
version arm re-flagged it stale on every run — an infinite re-extract
loop that never cleared the lag.
Since the v112 watermark column ships with no backfill, every
pre-existing page starts stale, and most pre-date the version bump. In
practice this left ~97% of pages permanently stale: `extract --stale`
reported "done" each run but `links_extraction_lag` never dropped.
Fix: stamp `GREATEST(read updated_at, versionTs)`. Old pages lift to the
threshold so the version arm clears; a real future edit still advances
`updated_at` past the stamp, so the CDX-1 edited-after-stamp race
protection is preserved.
Adds a regression test: a page with `updated_at` before
LINK_EXTRACTOR_VERSION_TS must clear after extract AND stay clear on a
second run (the existing tests only used now()-dated pages, so the
old-page case was uncovered).
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
* fix(drift): skip node_modules/dist/build in multi-source drift walk
The drift walker recursed into node_modules (50k+ files in RN/Astro repos),
exhausting the time budget before completing, so multi_source_drift always
reported 'walk hit limit/timeout' on real projects. Skip heavy non-content
dirs + add a deadline check on directory descent.
* fix(integrity): skip inline-code spans + [Source:] citations in bare-tweet detection
Recipe/doc pages that show the CORRECT citation format inline (e.g.
`Tweeted about {topic} [Source: X, @handle, date]`) were false-flagged.
The fenced-code skip didn't cover inline backticks; add inline-code
stripping + an explicit-citation exemption.
---------
Co-authored-by: Son Le <tuanson1200@gmail.com>
* test(e2e): drop flaky wall-clock bounds in minions-resilience
The runaway-dead-letter and cascade-kill tests asserted tight real-clock
upper bounds (<2000ms, <3000ms) on top of already-complete terminal-state
checks. Those bounds carry no correctness signal — the dead/cancelled status
and abortedChildren==10 assertions fully prove behavior — and flake on loaded
CI runners where the stall/timeout sweep cadence varies. Removed both bounds,
kept the diagnostic values, de-promised the test titles.
* test(e2e): kill order-dependence + no-op assertions in mechanical
- traverse_graph: self-contained (re-adds its own idempotent link) and asserts
the linked company is reachable, instead of depending on a prior it() and
only checking array shape.
- file_list-without-slug: seeds its own >100 rows instead of relying on the
previous test's 150 surviving in the DB; asserts the cap is exercised.
- precision@5: add a loose floor (every known-item query surfaces >=1 truth doc
in top-5) so a 0% retrieval regression no longer passes silently.
- get_health: assert value bounds (page_count==16, embed_coverage 0..1) not just
typeof; get_chunks: assert non-empty text, numeric non-decreasing chunk_index,
and that the page name appears, instead of toBeTruthy on chunks[0].
* test(e2e): strengthen graph/search quality assertions + close coverage gaps
graph-quality: truncate+reseed 'config' in truncateAll (kills config leak where a
setConfig test throwing before its finally bleeds into later tests); replace
toBeGreaterThan(0) link/timeline floors with fixture-derived minimums; assert exact
attendee slugs are 'attended' instead of a vacuous .every; pin autoLinks.created to
the provable 2 (Alice+Acme); add direction out/both + depth:2 multi-hop and a
cycle-safety (A->B->A terminates) test.
search-quality: fix the vacuous detail=low vector test; assert pedro returns >=2
chunks; assert detail=high includes the timeline chunk; add empty-query and
zero-vector no-throw edge tests.
* test(e2e): self-contain multi-source sync test + assert ledger cascade
Break the sequential dependency where 'performSync no sourceId' relied on a prior
test writing sync.repo_path — it now sets its own config. Add the missing
file_migration_ledger COUNT(*)==0 cascade assertion. Tighten the source_id default
check from toContain('default') to exact "'default'::text".
* test(e2e): make migration-flow HOME/PATH swap throw-safe
The suite repoints process.env.HOME/PATH to a temp dir and only restored them in
afterAll, so a mid-test throw left HOME dead for the rest of the bun process and
silently broke sibling suites. Wrap each test body in try/finally restore + a
defensive restore at the top of beforeEach.
* test(e2e): loud-skip jsonb-roundtrip + doctor-progress
Both skipped silently with no DATABASE_URL, giving zero signal the regression guard
never ran. Add the console.log skip line matching the sibling e2e files.
* test(e2e): robust check-update contract + find_orphans tool coverage
upgrade: the 'no-releases' test hard-asserted update_available===false, which flips
to failing the moment the repo has a real release. Assert the JSON contract shape
(boolean update_available, current_version===VERSION, typed optional fields) instead.
mcp: add find_orphans to the asserted generated tool names.
splitLargeNode can only break up a node that exposes a `body` with >= 2
named children. A node without one -- a giant object/array literal, a single
huge assignment, a massive template literal -- is emitted whole. On real
source that yields a chunk far larger than the embedder's context window; the
embedder then rejects it ("input exceeds context length") and it is never
embedded. Example: a 372 KB service file produced 113 chunks, one a single
281 KB (~70k-token) node -> permanently unembedded.
Add a final safety-net pass (capOversizedChunks) that recursively re-splits
any chunk over a token budget (default 2000, configurable via maxChunkTokens),
with a hard character split as a last resort for no-whitespace content
(minified one-liners). Normal files are untouched.
Verified: that 372 KB file now yields 188 chunks, max ~1.5k tokens, zero
oversized; a small file is unchanged.
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
gbrain think printed "## Gaps" twice: the synthesis prompt asked the model for a Gaps section inside the answer body AND a separate structured gaps array, then both render paths printed both — the CLI human output (src/commands/think.ts) and the --save page (persistSynthesis in src/core/think/index.ts).
Make the structured gaps array the single source. The prompt now routes gaps into the array, not an answer-body section. New exported stripGapsSection(answer) defensively removes any "## Gaps" section a model still emits (any heading level, case-insensitive, bounded by the next same/higher heading); both render sites call it, so the dedup is structural rather than dependent on the model obeying the prompt.
Adds test/think-gaps.test.ts (hermetic): strip helper across heading levels / case / no-section / mid-document / false-match, the one-render-only repro, and the prompt contract.
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-authored-by: Time Attakc <89218912+time-attack@users.noreply.github.com>
PGLite can return zero rows from INSERT ... ON CONFLICT DO UPDATE ...
RETURNING in no-op/trigger edge cases. The previous code called
rowToPage(rows[0]) unconditionally, so rows[0] was undefined and
rowToPage threw "undefined is not an object (evaluating 'row.deleted_at')",
which aborted the import and silently skipped the file during sync.
getPage() already has the empty-rows guard; putPage() was missing the
parallel one. The row was in fact written by the upsert, so re-read it
via getPage() instead of crashing. On a real monorepo index this
recovered ~19% of files (985/5148) that were failing to embed.
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-authored-by: Time Attakc <89218912+time-attack@users.noreply.github.com>
DEF_TYPES listed only canonical symbol-type names (function, class, interface, ...). But normalizeSymbolType in the code chunker canonicalizes only some tree-sitter node types and lets the rest fall through type.replace(/_/g, ' '). So method_declaration is stored as 'method declaration', struct_specifier as 'struct specifier', protocol_declaration as 'protocol declaration'. None were in DEF_TYPES, so code-def returned 0 hits for every method, constructor, field, C struct, and Swift protocol. The plain 'struct' entry never matched either. Add the fallthrough definition forms. Read-path only; no reindex needed (0 -> N on existing indexes).
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-authored-by: Time Attakc <89218912+time-attack@users.noreply.github.com>
The code-fence-wrap detector in lintContent used the /m multiline flag, so
^/$ matched start/end of any line. The rule fired on any page that simply
contained a ```markdown code block, not only pages wrapped end-to-end.
The matching fixer in fixContent has no /m flag, so it can only strip
whole-file wrappers. Result: detected issues were marked fixable: true,
yet fixContent could never strip them. `gbrain dream` reported
"0 fix(es) applied, N remaining" perpetually for the rule.
Drops the /m flag from the detector so detector and fixer stay in sync.
Whole-file wrapper detection is preserved; inner code blocks no longer
trigger the rule.
Real-world impact: a brain with 5 docs pages containing markdown examples
(skill READMEs, decision registry, journal templates) reports 5 phantom
"fixable: true" issues every dream cycle, never converging. After this
fix, the dream-cycle lint phase reports only real-and-unfixable issues
(missing frontmatter, missing title/type) which is the intended behavior.
Two regression tests added in test/lint.test.ts:
- Page contains a single inner ```markdown block
- Page contains multiple inner ```markdown blocks
Both assert no code-fence-wrap issue is reported. The existing
"detects wrapping code fences" test (true-positive case) continues to
pass; total tests in the file are 18 -> 20.
Co-authored-by: Thomas Chung <thomaschung@macbookair.lan>
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-authored-by: Time Attakc <89218912+time-attack@users.noreply.github.com>
`findByTitleFuzzy` on both `postgres-engine.ts` and `pglite-engine.ts`
has no `source_id` filter and no `deleted_at IS NULL` filter. `tryFuzzyMatch`
in `src/core/entities/resolve.ts` got both of those filters via #1436
(v0.41.13.0) for exactly the reasons that apply to its sibling here:
fuzzy resolution can suggest cross-source slug candidates that the
caller then silently drops at the FK filter (or worse, picks a
soft-deleted page).
This is the missing twin of #1436. In multi-source brains, the live-mode
auto-link resolver invoked from `put_page` (`operations.ts:937`) calls
`engine.findByTitleFuzzy` with no scope. When two sources contain pages
with similar titles (`people/alice-example` on `source-a`,
`people/alice-other` on `source-b`), the fuzzy lookup can return the
wrong-source slug, which then fails the downstream `allSlugs` /
`addLink` FK filter — the link silently doesn't get created, and from
the caller's view the resolver "failed" even though the page existed
under the right source.
Reproducible with a 2-source PGLite setup + identical-title pages on
both sides; the fuzzy call returns a slug whose `source_id` doesn't
match the put_page caller's source.
- 2-source brains: auto-links between same-title-different-source pages
now resolve under the caller's source instead of the wrong neighbor.
- Soft-deleted pages can no longer be returned as fuzzy candidates
(mirroring the resolve.ts fix from #1436).
- 1-source brains: no behavior change. `sourceId` is optional; when
omitted the SQL takes the pre-existing unscoped path.
- `engine.ts`: add optional 4th `sourceId` param to the
`findByTitleFuzzy` interface + JSDoc explaining the scope semantics.
- `postgres-engine.ts` / `pglite-engine.ts`: implement the param via a
conditional SQL branch that adds `AND source_id = $N AND
deleted_at IS NULL` when `sourceId` is set; existing query path
unchanged when omitted.
- `link-extraction.ts`: add optional `sourceId` to `makeResolver` opts,
forward to `findByTitleFuzzy` in step 3 of the resolve chain.
- `operations.ts`: pass `opts?.sourceId` to `makeResolver` from the
live-mode put_page resolver (the place that already knows the
caller's source).
- New unit tests in `test/link-extraction.test.ts` (2 cases):
- `opts.sourceId` is forwarded to `findByTitleFuzzy` when set.
- `opts.sourceId` omitted → `findByTitleFuzzy` receives `undefined`
(back-compat).
- `bun run typecheck` clean.
- `bun test test/link-extraction.test.ts test/entity-resolve.test.ts
test/operations.test.ts test/extract.test.ts` — 145/145 pass.
Co-authored-by: Time Attakc <89218912+time-attack@users.noreply.github.com>
* fix(models): dispatch subcommand reads args[0] not args[1]
`gbrain models doctor` silently fell through to the read view
instead of running the reachability probe.
`runModels` checks `args[1] === 'doctor'`, but the caller —
`handleCliOnly(command, subArgs)` in `src/cli.ts:113` — passes
`subArgs` (the leading command token already stripped). So inside
`runModels`, args[0] is the subcommand. args[1] is undefined.
The doctor probe path has been unreachable from the CLI since the
handleCliOnly refactor. `gbrain models help` happened to work by
falling through to the `--help` flag detection.
Two-char fix: `args[1]` → `args[0]` on both branches of the
ternary.
Verified by manual probe — `gbrain models doctor` now prints
"Model reachability probe:" with per-model results (real production
brain, 4 touchpoints probed):
```
Model reachability probe:
embedding_config ollama:bge-m3 ok (0ms)
reranker_config (none) ok (0ms)
chat lmstudio:mistralai/magistral-small-2509 unknown (5012ms)
[chat(lmstudio:mistralai/magistral-small-2509)] probe timed out after 5s
expansion lmstudio:google/gemma-4-e2b ok (535ms)
Summary: 3/4 reachable.
```
RECOVERY REBUILD 2026-05-26 of original 20ed0eee.
* fix: honor --help before doctor dispatch to avoid running probes on `models doctor --help`
Codex review of #1428 flagged that the args[1]→args[0] rewrite
regressed `gbrain models doctor --help` into running network
probes instead of printing usage. The original args[1]-shaped
ternary happened to dodge this by always falling through to the
args.includes('--help') branch when args[1] === 'doctor' was
false; the new args[0] code checks doctor first, so --help no
longer wins.
Reorder ternary: `hasHelp` is computed FIRST from
(--help / -h / args[0] === 'help'), then the sub is hasHelp ?
'help' : args[0] === 'doctor' ? 'doctor' : 'read'.
Addresses codex review P2 on PR #1428.
---------
Co-authored-by: Time Attakc <89218912+time-attack@users.noreply.github.com>
The HTTP MCP server's 401 responses missed the `resource_metadata`
parameter in the WWW-Authenticate header. MCP authorization spec
(2025-06-18 draft §5.1) and RFC 9728 require:
WWW-Authenticate: Bearer resource_metadata="<url>"
MCP-aware OAuth clients (claude.ai, Cursor, etc.) use that URL to find
the authorization-server discovery doc without the user manually
configuring the issuer. Pre-fix the header shipped only `Bearer
error="invalid_token", error_description="..."` and MCP clients silently
failed to begin the OAuth flow — symptom on claude.ai's UI was "Couldn't
reach the MCP server" even when discovery + /token + /register all
responded 200 individually.
The `requireBearerAuth` middleware in @modelcontextprotocol/sdk's
BearerAuthMiddlewareOptions already supports a `resourceMetadataUrl`
parameter. Two call sites (`/mcp` and `/ingest`) now pass it.
Verified against a real claude.ai connector attempt: pre-fix the
connector showed "Couldn't reach the MCP server" with no OAuth redirect.
Post-fix the connector successfully begins the authorization flow.
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-authored-by: Time Attakc <89218912+time-attack@users.noreply.github.com>
llama.cpp's llama-server rejects /v1/embeddings requests with more inputs
than its launch --batch-size (default 32): "batch size 100 > maximum allowed
batch size 32". gbrain sends batches of 100, so any page with >32 chunks fails
to embed, and embed --stale then trips the Postgres statement_timeout retrying
the doomed batches. The existing token-based protection (max_batch_tokens)
can't bound item count — N tiny chunks fit under any token budget.
Add an optional max_batch_items count cap to EmbeddingTouchpoint, enforced as a
hard re-split after the token split in embed(), and set it to 32 on the
llama-server recipe (replacing no_batch_cap: true, which wrongly assumed
llama.cpp has no per-request item cap). A declared item cap also suppresses the
missing-max_batch_tokens startup warning.
Co-authored-by: Time Attakc <89218912+time-attack@users.noreply.github.com>
The cron daily briefing writes 90_Briefings/<date>.md, which gets
re-ingested on the next sync and then dominates tomorrow's
getRecentSalience output as pure self-reference (observed: top
result score 0.9956, everyone else clustered at 0.587).
Filter `p.slug LIKE 'briefings/%'` out of getRecentSalience in both
the PG and PGLite engines. Suppressed by default; callers can still
opt in by passing `slugPrefix: 'briefings/'` (or `--kind briefings/`
from the CLI). search and list_pages are unaffected.
Co-authored-by: CTO <cto@timelycare.local>
Co-authored-by: Paperclip <noreply@paperclip.ing>
Co-authored-by: Time Attakc <89218912+time-attack@users.noreply.github.com>
On Windows, `core.autocrlf=true` is the default and SKILL.md files are
checked out with CRLF line endings. `extractTriggers` used regexes
anchored to `\n` (`/^---\n.../` and `/^triggers:\s*\n.../`), which
never matched `\r\n`, so the parser returned `[]` for every skill.
Result: `gbrain doctor --fast --json` on Windows reported every skill
not in `OVERLAP_WHITELIST` (39 of 42) as a false `mece_gap` warning —
even though `skill_conformance` in the same run reported "42/42 skills
pass". CI runs Ubuntu-only so the divergence never surfaced.
Fix: normalize CRLF → LF at the top of `extractTriggers`. Single-line
change preserves existing LF behavior. Function is now exported so the
test can target it directly.
Tests: added `describe("extractTriggers")` block covering LF input,
CRLF input (regression case), missing frontmatter, missing triggers
field, and quote-stripping. All 30 tests in `check-resolvable.test.ts`
pass.
Verified locally on Windows: `gbrain doctor --fast --json` now reports
`resolver_health: ok, 42 skills, all reachable` (health_score 90 → 95).
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-authored-by: Time Attakc <89218912+time-attack@users.noreply.github.com>
The signal-handler test asserted an absolute liveReporters===0 on a
module-global set, so any other test file in the shard holding a live
reporter flaked it — it red-flagged ~12 unrelated PR runs and one master
push in two days, purely as a function of shard composition. The delta
form pins the same claim (50 reporter lifecycles leak nothing).
The 15-minute shard timeout cancelled 13 fully-passing runs under
parallel PR load (PGLite WASM cold-starts stretch shards); the
test-status gate then reported the cancellations as failures.
Co-authored-by: Garry Tan <garrytan@gmail.com>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Qwen3-Embedding family on Ollama supports Matryoshka truncation via the
'dimensions' field on /v1/embeddings. Without this passthrough, gbrain
ignores user-selected reduced dims and the provider returns its native
size, causing dim-mismatch errors against brains configured for narrower
widths (e.g. existing 1536-dim brains).
Matches by bare name 'qwen3-embedding' or any tag variant
'qwen3-embedding:0.6b' / ':4b' / ':8b'.
Native dims: 0.6B=1024, 4B=2560, 8B=4096. All MRL-truncatable.
5 new tests; full AI suite 137/137 green.
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-authored-by: Time Attakc <89218912+time-attack@users.noreply.github.com>
Add the OpenClaw-required top-level id to openclaw.plugin.json, export a
direct register(api) entrypoint from src/openclaw-context-engine.ts, add a
manifest regression test, and document that skillpack harvest must preserve
OpenClaw-native manifest fields (id, configSchema, contracts).
llms bundles regenerated (bun run build:llms) — no content drift.
Co-authored-by: Garry Tan <garrytan@gmail.com>
Co-authored-by: Filip <FilipHarald@users.noreply.github.com>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Takeover of #2719 (fork head; rebased onto origin/master).
- writeProposed now writes both best.md (current-best pointer) and
proposed.md (stable human-review artifact); returns the proposal path.
- Orchestrator reports the real proposed.md path for accepted --no-mutate runs.
- Tutorial updated; llms bundles regenerated (no content drift — tutorial
is not inlined in the bundle).
Co-authored-by: Garry Tan <garrytan@gmail.com>
Co-authored-by: Ziyang Guo <121015044+RerankerGuo@users.noreply.github.com>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
