Release v0.48.5.0 · javaDer/gbrain

The community fix wave: 57 contributor pull requests adopted or reworked
with credit, 42 verified open issues fixed directly, and a hostile review
pass over the whole set. Your nightly extraction stops re-spending money on
transcripts that never yield anything, code repositories registered as code
sources are indexed the way you registered them instead of silently skipped,
Chinese, Japanese and Korean pages get real overlap between search chunks,
tool calls from the Claude CLI lane stop being dropped, and the doctor stops
crying wolf about transcript-minted atoms. Every adopted fix carries a
regression test proven red before the fix.

Behavior changes (read before you upgrade)

Code sources sync as code everywhere. A source registered with
--strategy code is now indexed as code from autopilot, the dream cycle,
the MCP sync tool and a plain gbrain sync, not only from sync --all.
Markdown pages that were imported into such a source under the old
fallback will be soft-deleted (72 hours recoverable) on the next sync when
they are modified; switch the source to auto if you want both kinds.
Code pages imported before this release pick up their file path on the
next change, sync --force, or gbrain reindex-code --force. (garrytan#4903,
contributed by @Jey2311; fixes garrytan#4899, garrytan#4900)
Migration v146 adds a small table that remembers which transcripts
returned nothing from atom extraction. The first run after upgrading
tombstones every transcript that yields zero atoms (editing the file makes
it eligible again), so the nightly work pool shrinks and stays shrunk.
(garrytan#4916, contributed by @mariokarras)
gbrain serve refuses an unknown GBRAIN_SOURCE. A stdio serve whose
environment names a source that is missing or archived now exits with the
value and the fix instead of silently serving an empty scope. Unset,
__all__, and malformed values behave as before. (garrytan#4851, contributed by
@NothoiMatt; fixes garrytan#4850)
gbrain think and gbrain graph-query resolve their source like
search does. A bare think gathers from your resolved default source
plus federated sources, honoring GBRAIN_SOURCE, .gbrain-source and
sources.default; a bare graph-query walks only the resolved source and
--include-foreign genuinely widens it. --source __all__ spans the brain
on both. Single-source brains see identical output. (garrytan#4652, garrytan#4765)
recall honors since together with an entity. gbrain recall <entity> --since (and --watch / --since-last-run) now returns only
facts from that window, ordered by event time, instead of the full entity
card every tick; an unparseable since is rejected instead of silently
widening the window. (garrytan#4882, contributed by @bhattman-dev)
delta cursors carry microseconds. since and next_cursor.since
now keep the stored timestamp's six fractional digits, so pages saved in
the same millisecond are never re-delivered. Callers that pattern-match a
three-digit fraction see the longer form. (garrytan#4681, contributed by
@jeanpierre121)
gbrain sync --json keeps stdout pure. Human progress lines go to
stderr, so sync --json | jq works as documented. Runs without --json
are unchanged. (garrytan#4888)
Autopilot skips checkouts that are not on this machine. Sources
registered elsewhere or with an unmounted path are reported as
skipped_unavailable_path once per tick instead of enqueuing jobs that
fail every tick; managed remote clones still dispatch. (garrytan#4865,
contributed by @javieraldape; fixes garrytan#4729)
CJK chunk overlap applies to pages chunked from now on. Existing
Chinese, Japanese and Korean pages keep their current chunks until the
chunker version is bumped (a whole-brain re-embed, tracked in TODOS.md);
English and Latin pages are byte-identical. (garrytan#4871, contributed by
@G0-0000)
Entity slugs for names with Latin stroke letters changed grammar.
Names containing d-stroke, l-stroke, o-slash, eth, thorn, sharp s, ae or
oe now fold to their ASCII form when an entity slug is minted (duc-example
where the old code produced uc-example). Entity pages minted under the old
spelling keep their slug; new facts about the same person resolve to the
folded slug, so a brain with such names can grow a second page until the
old one is renamed (tracked in TODOS.md). (garrytan#4855, contributed by @LongPV)
gbrain import --source <id> now requires a registered source. A typo
fails with the same one-line error sync --source gives instead of one
foreign-key failure per file; a bare --source with no value is refused.
gbrain bootstrap harness --source <id> is validated, and an implicit
source resolves through the same ladder gbrain serve uses (environment,
dotfile, working directory, brain default), so hooks stop binding to a
source the serve never resolved. Under a live PGLite serve the harness
cannot read that ladder: without a token it refuses with the two escape
hatches (pre-mint a token, or stop the serve), and the --token lane, when
no --source is given, wires the hooks unpinned with a warning, since an
unpinned hook resolves through the live serve's own binding (the receipt
records source_pinned: false).
Smaller contract changes. gbrain import --json gains additive
failures, unchanged and malformed_skipped keys (garrytan#4803, contributed by
@afshaker); code_blast and code_flow gain additive status and
ready fields (garrytan#4773, contributed by @armandovargash);
extract-conversation-facts exits 1 when a page changed mid-extraction
(garrytan#4869); subagent tool calls are validated like MCP calls, so a
wrong-typed argument is rejected with a named error (garrytan#4925, contributed by
@Walliiee); a persistently rate-limited Gmail request now waits out the
limit for up to two minutes instead of six seconds (garrytan#4894, contributed by
@johnerik); concept synthesis on a thinking-by-default model requests
8,000 output tokens instead of 500 (garrytan#4889, contributed by @awilhite); the
cwd .env guard now also ignores a project DATABASE_URL in
.env.development.local, .env.production.local and .env.test.local
(garrytan#4895); atom extraction may now legitimately return zero atoms for a
thin page (garrytan#4948, contributed by @gagecane).

AI providers

Claude Fable 5.1 is accepted by the Anthropic and claude-cli recipes and
priced with its published 0.025x cache-read rate, so pinning a tier to it
no longer silently degrades. (garrytan#4794, contributed by @morven-ai)
The DeepSeek API key can be stored in gbrain config and is picked up in
launchd, cron and MCP contexts with no shell environment. (garrytan#4843,
contributed by @javieraldape; fixes garrytan#4808)
Thinking-by-default models such as DeepSeek v4 get the same output
headroom as Claude 5 in subagent jobs, skillopt rollouts and any chat call
without its own cap, so they stop returning empty answers after spending
the budget on reasoning. (garrytan#4847, contributed by @awilhite)
Query expansion works when your utility or expansion model runs through
the Claude CLI subscription lane. (garrytan#4861, contributed by @LongPV)
Gemini embedding models reached through OpenRouter or another
OpenAI-compatible router honor your configured embedding dimensions.
(garrytan#4868, contributed by @morven-ai)
Claude CLI tool calls are no longer dropped when the model mentions the
tool tag in prose before the real block (garrytan#4898, contributed by
@mariokarras), and calls that put their arguments beside the name instead
of inside a wrapper now reach the tool with those arguments (garrytan#4924,
contributed by @Walliiee; fixes garrytan#4922).
Voyage's preview rerank-3 and rerank-3-lite rerankers can be selected;
the default stays rerank-2.5. (garrytan#4940, contributed by @malachany; fixes
garrytan#4938)
Short model aliases such as claude-cli:haiku price like the model they
resolve to under a cost cap, so gbrain enrich no longer stops at the
first call. (garrytan#4942, contributed by @johnerik)
Documents sent to the reranker are capped by size and token count, so a
self-hosted reranker with a small batch no longer fails and silently
serves unranked order. (garrytan#4947, contributed by @gagecane)
MiniMax M2 and M3 are recognized as tool-capable, so capability checks
and the doctor give the accurate reason when the subagent loop is refused.
(garrytan#4782)

Dream / cycle

Nightly dream stops rebuilding link manifests and re-repairing,
re-stamping and re-embedding pages for transcripts whose synthesis
already completed. (garrytan#4805, contributed by @jeanpierre121)
On durability-hardened brains, cycle lint and gbrain lint --fix commit
each repaired page so the post-commit hook pushes it. (garrytan#4815, contributed
by @mike-tech-ship-it)
Oneshot synthesis children get a prompt that matches their tool-less
JSON-only contract, and a reply that hit the output cap is reported as a
length fallback instead of unparseable, so fewer transcripts double-bill
through the agentic fallback. (garrytan#4886, contributed by @mvanhorn; fixes
garrytan#4785)
Concept synthesis gives reasoning-by-default models enough output headroom
to actually answer, so concept pages stop coming back as stubs. (garrytan#4889,
contributed by @awilhite)
gbrain dream --json stdout stays parseable through the extract phase,
and totals.pages_extracted counts pages, not links. (garrytan#4890, contributed
by @tomatkins)
Dream reports exclude_patterns hits in one stderr line instead of
silently saying there was nothing to process. (garrytan#4926, contributed by
@Walliiee; fixes garrytan#4923)
Installs whose only chat provider is not Anthropic or OpenAI now run
extract_atoms and the other default-model phases on the provider they
configured instead of stopping with a provider failure. (garrytan#3813)
Concept pages written by synthesize_concepts carry graph edges to and
from every atom they were synthesized from, so they appear in backlinks,
relational recall and graph coverage instead of landing as orphans;
re-running the phase backfills existing brains. (garrytan#4589)
gbrain dream with GBRAIN_SOURCE set scopes the cycle to that source
exactly like --source. (garrytan#4778)

Atoms / extraction / facts

The mention scan honours the link_resolution.cross_source opt-in the
same way wikilink resolution does, and a same-name entity in the page's
own source always wins over a cross-source twin. (garrytan#4793, contributed by
@paul-0320)
Fact reconciliation runs under the same per-page lock the fence writers
use and refuses to delete rows when the Markdown on disk is newer than the
page cache, so a fact you just remembered is no longer wiped by a sweep
that runs before sync. (garrytan#4835, contributed by @bhattman-dev)
Atoms distilled from an imported transcript link back to the conversation
page the session was rendered into. (garrytan#4853, contributed by @Natetgmaxwell)
Names containing Latin stroke letters (d-stroke, eth, o-slash, l-stroke,
dotless i, sharp s, ae, oe, thorn) get the ASCII entity slug and wikilink
key you would expect. (garrytan#4855, contributed by @LongPV)
Atom extraction no longer produces zero atoms when a free local chat model
is paired with an unpriced embedding route; the cost cap checks both models
and honors pricing.overrides. (garrytan#4878, contributed by @NothoiMatt; fixes
garrytan#4877)
Durable facts-absorb jobs honor the 10-minute handler default instead of a
hard-coded 3-minute timeout. (garrytan#4887, contributed by @javieraldape; fixes
garrytan#4864)
Models that emit a <thinking> block before their JSON answer are
recovered the same way as <think> (garrytan#4912), and the atoms array is found
even when the reply opens with bracketed prose (garrytan#4913; both contributed by
@mariokarras).
extract_atoms stops re-spending budget on transcripts that keep returning
malformed or empty output; they get the same bounded retry and tombstone
as pages. (garrytan#4916, contributed by @mariokarras)
Meeting pages your agent wrote directly are found by gbrain extract timeline --from-meetings and dated from their frontmatter. (garrytan#4943,
contributed by @johnerik)
Atom extraction no longer burns retries on metadata-only pages; the model
is told to return an empty list when there is nothing to extract. (garrytan#4948,
contributed by @gagecane)
Failed facts extraction jobs record a bounded error-type label (auth,
rate limit, and so on) in the job error text. (garrytan#4950, contributed by
@Masashi-Ono0611)
The maintenance sweep honors the cross-source link opt-in and your
configured default source, so cross-source links extract created are kept
instead of dropped (garrytan#3757, garrytan#4611), and relative ./page.md links count as
live references so their edges are no longer pruned (garrytan#4873).
Forgetting a fact sticks: the next reconcile no longer brings it back
(garrytan#4696). Facts whose entity came back as the literal text null are
filed as unparented (garrytan#4755). A page's first Facts fence lands above a bare
--- + ## Timeline separator, so template-shaped pages stop freezing
with FACTS_FENCE_BELOW_SENTINEL (garrytan#4756). Facts extracted on a thin-client
brain record the page they came from (garrytan#4819). Queued fact extraction
honors a medium-and-up notability filter (garrytan#4870). gbrain remember keeps
the database page body in sync with the fence it wrote to disk, so a
get-and-put round trip no longer drops the fact (garrytan#4872).
migrate-embeddings --status stops counting checkpoint rows as pending
fact embeddings (garrytan#4875).

Doctor / brain health

atom_provenance_drift no longer reports transcript-minted atoms as
drifted or as missing their source page; they are counted in their own
slug-unbound bucket outside the warning ratio, and the check finishes in
seconds on large brains instead of stalling health monitors. (garrytan#4799,
contributed by @Masashi-Ono0611; garrytan#4806, garrytan#4937)
A failed binary self-update no longer leaves a permanent doctor warning.
(garrytan#4814, contributed by @mike-tech-ship-it)
Skill triggers written in non-Latin scripts match intents in
check-resolvable and the doctor skill checks instead of being stripped
to nothing. (garrytan#4820, contributed by @hyunje-ethan-jang)
The resolver health check reports a skills folder that belongs to another
tool as a warning instead of a failure (garrytan#4822, contributed by
@Masashi-Ono0611), and raises one orphan warning per unregistered skill
pointing at manifest.json instead of one per trigger blaming
RESOLVER.md (garrytan#4831).
Pages whose recorded source path is only a basename while the slug lives
in a directory are no longer flagged as DB-only, and write-through
resolves them to the real file. (garrytan#4933, contributed by @javieraldape;
fixes garrytan#4744)
eval_drift inspects gbrain's own source checkout instead of whatever
repository you ran the doctor from, and says so on an installed CLI.
(garrytan#4606)

Google / open loops

Google connect via paste or --code accepts a real loopback redirect URL
again, which Google now stamps with iss=accounts.google.com. (garrytan#4891,
contributed by @johnerik; fixes garrytan#4917)
Gmail backfill waits out rate limits with a patient retry budget, never
marks a rate-limited thread as poisoned, and defers the rest of a
throttled batch to the next run. (garrytan#4894, contributed by @johnerik)

Search / eval

Search-mode settings load from your brain in one query instead of one per
setting, so every search on a hosted Postgres brain starts sooner. (garrytan#4781,
contributed by @hpamike)
Chinese, Japanese and Korean pages get a real, bounded overlap between
search chunks, and emoji are no longer split in half at chunk boundaries.
(garrytan#4871, contributed by @G0-0000)

MCP / schema / auth

Listing pages sorted by slug pages deterministically across federated
sources that share a slug, and list_pages rejects a malformed
source_id loudly instead of silently widening to every source. (garrytan#4857,
contributed by @proxynico)
Remote MCP OAuth discovery advertises /mcp as the protected resource and
serves RFC 9728 path-based metadata, with the root path kept as an alias.
(garrytan#4866, contributed by @amirelion)
Ontology reads hide values whose provenance page is private from untrusted
callers and resolve the newest value they are allowed to see. (garrytan#4881,
contributed by @bhattman-dev)
A stdio serve started with --stdio-idle-timeout no longer risks a hung
handshake when the client's first frame arrives before boot finishes.
(garrytan#4935, contributed by @Masashi-Ono0611)
The thin-client doctor report confines its page count and brain score to
the caller's granted sources (garrytan#4592); reading with an explicit source_id
that names a removed source fails with a clear unknown_source error
(garrytan#4620); the sources_list and sources_status tool descriptions state
that results are scope-filtered (garrytan#4811); and the OpenClaw bundle plugin
starts its MCP server through the shipped launcher, so a global install
works without building a binary (garrytan#4841).

Sync / import

gbrain import --json lists each rejected file with its error, so a
scripted import can tell a failed file from an unchanged one. (garrytan#4803,
contributed by @afshaker)
Empty code files such as a package __init__.py are reindexed by
gbrain reindex-code instead of being reported as failures. (garrytan#4904,
contributed by @Jey2311; fixes garrytan#4902)
Incremental sync removes the stale duplicate a renamed frontmatter-slug
file leaves behind (garrytan#4597); gbrain features stops telling a multi-source
brain to configure sync (garrytan#4767); Markdown files saved with a UTF-8 byte
order mark get their title from the first heading (garrytan#4798); and
gbrain import accepts --source <id> like every other command (garrytan#4862).

Transcripts / code intel

code_blast and code_flow report whether the code graph is ready, so an
empty blast radius on an unbuilt graph is no longer mistaken for zero
callers. (garrytan#4773, contributed by @armandovargash)
The Codex session-end hook recovers rollouts Codex has moved into its
archived store. (garrytan#4929, contributed by @mariokarras)
Repos with YAML files stop logging a false "semantic parsing unavailable"
warning on every sync (garrytan#4669); transcripts ingest honors --limit under
--dry-run (garrytan#4762); Claude Code subagent logs are no longer treated as
sessions, ending a permanent not-yet-imported backlog and a false drift
warning (garrytan#4796); and transcript pages no longer inherit a facts fence from
a page the session quoted (garrytan#4821).

CLI

gbrain get <slug> --json returns the page as JSON, and an ambiguous slug
returns a machine-readable error envelope. (garrytan#4813, contributed by
@mike-tech-ship-it)

Minions / autopilot

Live minion workers no longer vanish from gbrain jobs and the doctor on
hosts whose timezone differs from the runtime's. (garrytan#4856, contributed by
@proxynico; fixes garrytan#4885)
Contextual re-embed jobs on Postgres release their rate lease as soon as
each call finishes, so backfills run at the configured concurrency.
(garrytan#4880, contributed by @spiky02plateau)
Subagent tool calls that omit a required parameter get back a message
naming it, so the model can retry instead of hitting an opaque crash.
(garrytan#4925, contributed by @Walliiee)
The autopilot lock check recognizes a live process on Windows (garrytan#4563), and
the autopilot wrapper falls back to the gbrain on PATH when the binary it
was installed against has moved, instead of failing silently on every boot
(garrytan#4728).

Bootstrap / hooks

On Windows, gbrain serve binds its resolve-IPC socket again after an
unclean exit or reboot (garrytan#4333); a short-lived serve for the same brain no
longer takes down the long-lived serve's socket (garrytan#4896); and gbrain bootstrap harness without --source binds its hooks to the source the
serve actually resolves (garrytan#4897).

Other

Pages whose chunks straddle a stale-embedding batch boundary get their
embedding signature stamped by whichever batch finishes them, so they are
no longer skipped by later model-swap checks. (garrytan#4825, contributed by
@morven-ai)

For contributors

Cancelling a running test suite stops every shard instead of leaving them
holding memory until the shard timeout. (garrytan#4774, contributed by
@armandovargash)
bun run ci:local on a stock macOS shell no longer aborts with an
unbound-variable error in a plain clone. (garrytan#4930, contributed by
@arisgysel-design; fixes garrytan#4911)
The local CI lane's timeout multiplier reaches the CLI-spawning unit tests
(garrytan#4659), and the open-loops reopen test no longer depends on the database
clock advancing between statements (garrytan#4928).

Review hardening

A hostile review over the composed set (eight lenses, two independent
refuters per finding) confirmed thirteen defects that were only visible in
composition, all fixed before ship: gbrain sync --source <id> --json kept
stdout pure on the full-sync path too, not only for incremental runs;
gbrain graph-query --source <id> on a thin-client install now errors
instead of silently walking the wrong scope; a pasted Google consent-page
URL with no scheme is rejected by host again instead of being taken as an
authorization code; gbrain remember and forget keep the page's content
hash so the next sync re-chunks the new or struck fact text instead of
skipping the page; an implicit default source in gbrain bootstrap harness is treated as the federated floor, matching dream and doctor; and
three reference doc entries brought back to current state. The slug-extension
change proposed in garrytan#4807 was tried, found to need a data migration with
collision rules the maintainer should decide, and returned to the queue.

A second pass with independent reviewers (including an outside model) then
closed the interactions between fixes: an honest empty atoms array is accepted
at any offset of the model's reply while a non-atom-shaped array is a failure
rather than a permanent tombstone; an explicitly configured extraction budget
stays enforced even when the embedding route is unpriced; extract timeline --from-meetings never dates a meeting from its import timestamp, skips
private meetings, and honors the cross-source gate on attendee edges as well as
mentions; a remote run_doctor on a source-scoped token no longer reveals
other sources' ids or backlog; concept synthesis on a thinking model uses the
same output headroom as every other call; forget strikes the page body under
the page lock and stamps a hash that makes the next sync re-chunk; every
Facts-fence writer places the first fence above the timeline sentinel;
gbrain import --source validates the source like sync does and refuses a
missing value; sync trigger --json prints JSON; GBRAIN_SOURCE=__all__ makes
dream span the brain; graph-query refuses --source with
--include-foreign instead of silently dropping the scope; and the bootstrap
harness binds hooks to the source the serve actually resolves.

With thanks to every contributor whose pull request this wave adopts:
@afshaker, @amirelion, @arisgysel-design, @armandovargash, @awilhite,
@bhattman-dev, @G0-0000, @gagecane, @hpamike, @hyunje-ethan-jang,
@javieraldape, @jeanpierre121, @Jey2311, @johnerik, @LongPV, @malachany,
@mariokarras, @Masashi-Ono0611, @mike-tech-ship-it, @morven-ai, @mvanhorn,
@Natetgmaxwell, @noelboss, @NothoiMatt, @paul-0320, @proxynico,
@spiky02plateau, @tomatkins, @Walliiee, and to the reporters whose verified
issues drove the direct fixes.

To take advantage of 0.48.5.0

gbrain upgrade runs migration v146 for you. If it did not, or if
gbrain doctor warns about a partial migration:

Run the orchestrator manually:
```
gbrain apply-migrations --yes
```
Verify the upgrade:
```
gbrain --version
gbrain doctor
```
Code sources: the stored strategy now applies to every sync entry
point. If a source registered as code also holds Markdown you want kept,
an explicit flag always wins for that run:
```
gbrain sync --source <id> --strategy auto
```
Autopilot and cycle syncs use the stored strategy, so modified Markdown
pages under a code source are soft-deleted on their next sync and stay
recoverable for 72 hours (gbrain sources archived, gbrain sources restore).
CJK brains: new pages chunk with overlap automatically. To re-chunk
existing Chinese, Japanese or Korean pages, wait for the chunker version
bump in a later release or re-import the pages you care about.

Say to your agent: "check my brain's health" (your agent runs
gbrain doctor) — "sync my code repo into the brain" (your agent runs
gbrain sync --source <id>; code sources now index as code from every
entry point) — "show me only what changed for this person since Monday"
(your agent runs gbrain recall <entity> --since <date>).

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