The dependabot bump to actions/setup-node@8207627860 (v7.0.0)
left the review-agent-workflow.test.ts pin allowlist pointing at the old v6.4.0 SHA, failing CI.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
* fix(lbug): scale the buffer-pool budget by the OS-page discard-granule ratio (#2631)
LadybugDB bills buffer-pool budget per discard granule, not per 4 KiB frame:
the engine's vm_region.cpp sets discardGranuleSize = max(frameSize, osPageSize),
claimFrame charges the whole granule when its first frame becomes resident, and
releaseFrame refunds only when the granule's last frame leaves — while
BufferManager::reserve measures eviction progress in refunded bytes and throws
'The buffer pool is full and no memory could be freed!' after three zero-refund
passes. On a 64 KiB-page kernel (Ascend/aarch64 openEuler — the #2631
reporter's host) that is 16 frames per granule: the same COPY bills up to 16×
the budget it needs on x86, and whole eviction passes can evict frames yet
refund nothing. Apple Silicon macOS (16 KiB pages) is the same mechanism at 4×.
Measured with the reporter's exact command and version: vllm-ascend needs a
(128, 256] MiB pool on 4 KiB pages — 64/128 MiB reproduce the reporter's
byte-identical error, 256 MiB and the 576 MiB adaptive pool succeed — so their
64 KiB host cannot survive on a page-size-blind budget.
Scale every derived pool size by granuleRatio = max(1, osPageSize/4096):
the per-element estimate, the COPY-safety floor, and the default cap (still
bounded by 80% of RAM). 4 KiB hosts are byte-identical to before — proven by
pinning the existing sizing tests to an explicit 4096 page size, which also
stops them drifting on 16 KiB Apple Silicon runners. GITNEXUS_LBUG_BUFFER_POOL_SIZE
keeps absolute precedence and 0 still restores the native default.
Also: bufferPoolExhaustionRemedy() gives the exhaustion error an actionable
cause→consequence→remedy message; the isLbugPageSizeFrameError comment that
called pool exhaustion 'a sizing problem, not a page-size one' is corrected —
that framing inverted when #2582 made pool size a function of a page-size-blind
estimate. Cannot execute on a 64 KiB kernel here: the scaled path is proven by
unit stubs plus the engine-source math above; the env override remains the
field escape hatch.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* feat(cli): actionable pool-exhaustion remedies at the COPY sites and a doctor pool line (#2631)
The node-COPY throw and the relationship-COPY warning now append
bufferPoolExhaustionRemedy() when the failure is the engine's pool-exhaustion
class: the raw binder text gave the operator nothing to act on, and on
non-4K-page hosts the pool bills up to pageSize/4KiB × faster than the sizing
was calibrated for. The relationship path appends the remedy once per bulk
load, not once per failed pair. doctor prints the effective pool size next to
the page-size line ('pool size 2048 MiB', with an '(×N page-size scaling)'
suffix on non-4K hosts) so support triage sees the sizing inputs at a glance.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* refactor(lbug): re-anchor getEffectiveBufferPoolSize's placement and reuse granuleRatio in doctor
Self-review fixes: the getter's insertion had orphaned resolveBufferManagerSize's
doc comment (it read as documenting the wrong function), and doctor's scale note
duplicated the granule math with a hardcoded 4096. granuleRatio is now exported
(it already carried the test-seam default param) and doctor consumes it.
No behavioral change — the sizing suite pins byte-identical outputs.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* fix(lbug): keep the hintless pool default unscaled and make both remedies visible (#2631)
Review fixes:
- Scale only the analyze-path cap (scaledAnalyzePoolCap), not
defaultBufferPoolSize: the pool is an eager native allocation at DB open
(measured, see POOL_BYTES_PER_ELEMENT), so a page-size-scaled hintless
default would hand a long-lived MCP process up to 80% of RAM — the #2557
OOM exposure the 2 GiB cap removed. Fix the MAP_NORESERVE claim that
contradicted that measurement.
- Log the rel-pair pool remedy (loadGraphToLbug returns warnings that no
call site reads) and dedup it with a local boolean instead of matching
the remedy's own wording.
- Label the GITNEXUS_LBUG_BUFFER_POOL_SIZE=0 sentinel as the native
80%-of-RAM default in both the remedy and doctor instead of '0 MiB'.
- Extract poolSizeDoctorLine (pageSizeDoctorLines convention): mark env
overrides, drop the scaling suffix that misdescribed absolute values.
- Fold _resetOsPageSizeCacheForTest into _setOsPageSizeForTests(undefined).
- Document the analyze-path scaling in both README env tables.
---------
Co-authored-by: Gergo Magyar <abhigyan1.patwari@gmail.com>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
LadybugDB ≤0.18.2 mis-evaluated `r.type IN [...]` on relationship table
groups: the boolean-filter fallback skipped writing selection buffers for
single-row unflat chunks, dropping/duplicating callers in context() and
impact() (upstream LadybugDB#692, fixed by LadybugDB#699, shipped in
0.18.3). Floor the dependency at ^0.18.3 and lock core + all five platform
packages.
Resurrect the caller-identity regression test from PR #2553 (closed as
superseded by the upstream fix): it pins context()/impact() to exact
caller IDs across CodeRelation sub-table pairs so any future predicate
regression fails loudly. Note: with CREATE-seeded data the test also
passes on 0.18.2 (the upstream repro needs COPY-written chunk layouts) —
it is a behavioural pin, not a bug reproduction.
Fixes#2508
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
* feat(lbug): add ensureEmbeddingRowDmlSafe VECTOR gate for embedding-row DML
LadybugDB refuses every mutation of a table carrying an HNSW index while the
VECTOR extension is not loaded on that connection: DELETE and CREATE raise a
Binder exception, DROP TABLE is refused while the index references it, and SET
segfaults the process. Dropping the index is not an available recovery either —
CALL DROP_VECTOR_INDEX is itself a VECTOR-extension function and is undefined in
exactly that state.
Add a single primitive that loads VECTOR under the analyze install policy and,
only when that fails, reads CALL SHOW_INDEXES (which works without the
extension) to decide whether an index actually exists to trip over. No call
sites yet.
Refs #2623
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* test(lbug): pin the #2623 VECTOR gate for embedding-row DML
Three cases: no index + VECTOR unavailable stays safe (no needless
escalation); index present + VECTOR unavailable is reported blocked AND the
raw deleteNodesForFiles genuinely throws 'extension is not loaded' (proving the
hazard is real, not theoretical); index present + VECTOR loadable is safe, the
delete works, and the HNSW index survives — the invariant run-analyze relies on
when it keeps the index across a surgical incremental run.
Refs #2623
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* fix(analyze): load VECTOR before the incremental writeback touches embedding rows
Incremental analyze died on every content change once a repo had built
code_embedding_idx:
Analysis failed: Binder exception: Trying to delete from an index on table
CodeEmbedding but its extension is not loaded.
The surgical writeback's first statement is deleteNodesForFiles' CodeEmbedding
join-delete, but nothing on that path loaded VECTOR until Phase 4 — so the
engine refused the delete. This is an ordering defect, not an environment one:
it reproduces on machines where VECTOR loads fine. The dirty-flag recovery then
forced a full rebuild on the next run, which is why it read as 'just slow'.
Call ensureEmbeddingRowDmlSafe() once, before the escalation gate and before any
row is touched — the same 'index lifecycle before row DML' seam dropSearchFTSIndexes
occupies for FTS (#2589). Unconditional, because a DB carrying the index from an
earlier --embeddings run hits the same wall on a plain incremental run. When
VECTOR truly cannot load the table is immutable (the index cannot be dropped
without the extension either), so the run falls through to the existing
wipe-and-COPY escalation with a message naming cause, consequence and remedy.
Fixes#2623
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* test(analyze): pin the #2623 VECTOR-before-embedding-DML ordering end-to-end
Sibling of the #2589 FTS drop-before-delete suite, same shape: drive the real
runFullAnalysis incremental path over a real git repo and a real LadybugDB,
seed real embedding rows, build the HNSW index, then assert the index state at
the exact moment deleteNodesForFiles is invoked.
Both cases were confirmed to discriminate — with the run-analyze change
reverted they fail with the reported 'Trying to delete from an index on table
CodeEmbedding but its extension is not loaded', and pass with it:
- surgical path: the run completes, the index is still present AND
extension_loaded at delete time, exactly one row per nodeId survives, and
the untouched file's rows are preserved
- blocked path: with GITNEXUS_LBUG_EXTENSION_INSTALL=never the run escalates
to a full DB write and says so, instead of crashing
Also applies prettier's reindent to the run-analyze log ternary.
Refs #2623
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* docs(lbug): cite the pinned LadybugDB version in the #2623 probe note
The probe matrix behind ensureEmbeddingRowDmlSafe was first recorded on
0.18.0, but gitnexus/package-lock.json pins 0.18.2 (#2587). Re-ran every case
on 0.18.2: refused DELETE, refused CREATE, SIGSEGV on SET, DROP_VECTOR_INDEX
undefined, DROP TABLE refused, SHOW_INDEXES readable with extension_loaded
intact. Identical on both, so the design is unchanged — only the citation was
wrong.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* fix(analyze): preserve embeddings across the VECTOR-blocked rebuild, and check the catalog before loading
Three follow-ups from reviewing the fix itself.
1. Data loss on the blocked path. Escalating wipes the DB files, and Phase 3.5
restores embedding rows from cachedEmbeddings — which deriveEmbeddingMode
only populates when meta.stats.embeddings > 0. A DB holding embedding rows
that its meta does not account for therefore had every vector destroyed
silently by a rebuild it never asked for. Probe on a 3-file repo: 3 rows
before, 0 after, no warning. Read the rows before escalating (a plain MATCH,
no extension needed) so the existing restore has something to restore, and
say so in the log. The blocked-path test now asserts the seeded rows survive
exactly once, and that assertion fails without this rescue.
2. Catalog before extension. ensureEmbeddingRowDmlSafe loaded VECTOR first and
only read SHOW_INDEXES on failure, so every incremental analyze on a machine
without VECTOR paid a bounded out-of-process INSTALL attempt plus an
'extension unavailable' warning — including repos that never built an
embedding index and can never hit this bug. One local catalog read settles
that case first; the load is attempted only when an index actually gates DML,
or when the catalog cannot be read.
3. Dead branch. targetConn is always the module singleton there, so the
isSharedSingletonConn ternary could never take its second arm. Collapsed to
withConnLock.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* feat(doctor): live-probe the VECTOR extension instead of printing the static platform capability
Review finding on #2624 (MEDIUM), and exactly what #2623's reporter hit:
doctor printed 'VECTOR index: available' — derived from a static platform
check — while every incremental analyze on the same machine was dying on an
unloaded VECTOR extension. The FTS line was switched to a live LOAD probe for
the identical contradiction under #2374; VECTOR now gets the same treatment.
probeVectorExtensionLoad shares the FTS probe's implementation (bounded,
offline-safe, never runs the installer) and doctor's semantic-mode line now
follows the probe, not the platform: without a loadable extension the vector
index can be neither built nor queried, so search really is on exact scan.
The load-error classifier's remedies are label-parameterized so the VECTOR row
stops dispensing FTS-specific advice — 'run analyze --repair-fts' repairs FTS
indexes only and was actively wrong for a missing vector extension. Default
label stays 'FTS'; every existing caller and pinned remedy string is unchanged.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* fix(lbug): remove the stale Windows VECTOR gate — the extension ships for win_amd64
The codebase categorically refused VECTOR on Windows (platform !== 'win32' in
isVectorExtensionSupportedByPlatform, plus a hard early-return in
loadVectorExtension) on the strength of an early-era report that in-process
INSTALL VECTOR could SIGSEGV (#1365). That belief is stale, verified directly:
- the extension server hosts win_amd64 VECTOR artifacts for every 0.18.x
extension version — v0.18.0 and v0.18.1 both serve a real 14 MB PE32+ DLL
(curl-probed; 'file' confirms PE32+ x86-64)
- the pinned 0.18.2 core resolves its extension directory to 0.18.1
(strace-verified LOAD open()), so the pinned version's Windows artifact
exists too
- INSTALL now runs in a spawned child (installDuckDbExtensionOutOfProcess), so
even a crashing installer kills only the child and degrades to unavailable —
the original hazard cannot reach the parent process any more
Windows now takes the same runtime path as every other OS: try LOAD, install
out-of-process when policy allows, degrade to exact scan when it truly fails.
The MCP semantic-search lane loses its static platform gate too — it always
attempts the vector index and falls back to the exact scan on runtime failure,
with a once-per-backend diagnostic naming the real error instead of a
platform-policy message. isVectorExtensionSupportedByPlatform is deleted;
getRuntimeCapabilities reports the platform capability as available everywhere
and defers machine truth to the live probe.
Windows CI is the enforcement: the vector suites skip visibly only when the
extension genuinely cannot load, so green Windows lanes now actually exercise
VECTOR instead of silently skipping by policy.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* test(lbug): pin the catalog-read-failure fallback in ensureEmbeddingRowDmlSafe
Review finding on #2624 (LOW): the one branch where the gate cannot cheaply
prove safety — SHOW_INDEXES itself erroring — was exercised only by inference.
Force it with a Connection.prototype.query spy over the real DB: the catalog
read fails, and the gate must fall through to actually attempting the
extension load (asserted via the recorded statement stream) rather than
guessing, returning true here because the extension is loadable.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* fix(mcp): load VECTOR on the pool's shared Database so the semantic vector lane actually works
Review finding on #2624 (MEDIUM): extension load scope is per-Database
(probe-verified — LOAD on one connection enables QUERY_VECTOR_INDEX on every
connection of the same Database), and the pool pre-warm loaded only FTS. So
LocalBackend's vector lane has ALWAYS raised 'Catalog exception: function
QUERY_VECTOR_INDEX is not defined' through the pool and silently fallen back
to the exact scan — repos above the 10k exact-scan cap got empty semantic
results. The serve path was unaffected (the embedding pipeline loads the
extension itself).
Mirror the FTS line at BOTH load sites — doInitLbug's pre-warm and
initLbugWithDb's external-Database adoption — under the same load-only
contract (the read pool never triggers a network install), tracked by a new
SharedDB.vectorLoaded flag reset where ftsLoaded resets.
The new pool test is discriminating and deliberately closes the writable core
adapter before the pool opens: a shared/injected Database would inherit the
VECTOR load from test seeding and pass either way, so the case forces the pool
onto its OWN fresh read-only Database where only the pre-warm can make the
lane legal. Verified: fails at the pre-fix tree with the exact Catalog
exception, passes with the fix.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* ci: run the #2623 ordering suite on Windows/macOS and pre-install VECTOR alongside FTS
Two review findings on #2624, both landing in existing seams:
- scripts/cross-platform-tests.ts gains incremental-vector-extension-ordering
.test.ts: the win32 VECTOR gate is gone in this PR, so the #2623
drop-ordering + blocked-path escalation must be proven on the
windows-latest native addon, not just Ubuntu. (The review's claim that
lbug-delete-nodes-for-files.test.ts was also missing was wrong — it has
been on the roster since #2409.)
- scripts/ensure-fts.ts now pre-installs VECTOR under the same best-effort
auto-policy contract, so every sharded CI process LOADs from ~/.lbdb
instead of racing its own bounded out-of-process INSTALL; the workflow's
extension cache already covers it (path is the whole extension dir — key
kept for cache continuity). The cross-platform job sets
GITNEXUS_REQUIRE_VECTOR=1 beside GITNEXUS_REQUIRE_FTS so a genuinely
unavailable VECTOR is a loud failure, never a silent skip.
Windows/macOS cannot be executed locally; the PR's CI lanes are the proof for
this commit. Linux smoke: ensure-fts.ts reports both extensions ready; all 79
roster entries resolve.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* test(pool): register loadVectorExtension in the pool unit-suite mocks
The pool adapter's new loadVectorExtension import surfaced in four suites that
mock lbug-adapter.js with explicit factories (vitest fails loudly on a missing
mocked export). Register the export in each — resolving false where the
suite's world assumes no vector, true where it mirrors FTS — and extend
lbug-pool-fts-load.test.ts, the suite that owns pre-warm extension loading,
with the vector pair: successful load cached per shared Database, failed load
retried on the next open, both pinned to policy load-only.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* test(analyze): use POSIX literals for graph paths in the #2623 ordering suite
First Windows CI run of this suite (it joined the cross-platform roster this
PR) failed with 'Parser exception: Invalid input <MATCH (n:Function) WHERE
n.filePath = '>' — path.join produces backslashes on Windows, and a backslash
inside the seed helper's single-quoted Cypher literal breaks the parser. The
graph stores repo-relative filePaths with forward slashes on every OS, so
graph-side paths are POSIX literals now (the incremental-orchestration
convention); path.join stays only for real filesystem access.
The same Windows lane also proved the substance this suite exists for:
lbug-vector-extension passed 7/7 on windows-latest — the extension installed,
loaded, and built a real HNSW index there — and the pool vector-lane and DML
gate suites passed too. This commit fixes the harness, not the fix.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---------
Co-authored-by: Gergo Magyar <abhigyan1.patwari@gmail.com>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* fix(eval): give vitest a writable .vite-temp inside read-only dependency mounts
Every task verify command and every hidden oracle ends in `npx vitest run
<test>`, and both run through run_verify with read_only_workspace=True. Vite
transpiles a TypeScript config by writing
<node_modules>/.vite-temp/<config>.timestamp-*.mjs before it loads anything, so
against a read-only dependency mount vitest dies with EROFS before a single
test executes:
EROFS ... /workspace/gitnexus/node_modules/.vite-temp/vitest.config.ts.timestamp-*.mjs
This is pre-existing and was masked: until #2627 the verify command died at
`npx: not found`, short-circuiting the `&&` chain before vitest ran. Confirmed
by reproducing it at that merge base with npx bypassed entirely
(`./node_modules/.bin/vitest`), so it is independent of the node-prefix mount.
Because it blocks the oracle as well as the authored-test verify, `resolved`
stays 0/N without this.
bwrap cannot create a mount point inside an already-read-only bind -- the same
constraint that put SANDBOX_NODE under /opt/claude -- so overlaying a tmpfs only
works if the directory already exists in the mounted bytes. It cannot be
mkdir'd into the dependency snapshot after capture either: the snapshot is
digest-bound and validate_dependency_binding fails closed on drift. So the empty
directory is captured during dependency capture, before the manifest and both
dependency digests are computed, making it part of the snapshot rather than an
untracked mutation of it. The sandbox then overlays a tmpfs on exactly that
path; everything else in the mount, and the whole workspace, stays read-only,
and the overlay never reaches the host clone the credited patch comes from.
Scoped to dependency mounts whose target basename is node_modules, so hidden
oracle and skill mounts stay wholly read-only with no writable island.
Note: this shifts sandbox_dependency_content_digest and
sandbox_dependency_manifest_digest, so promotion evidence recorded before this
change is no longer comparable. That is already true of any harness fix that
changes what the sandbox exposes.
Verified on the self-hosted runner through the real path -- TaskAssetCache
.prepare -> stage_task_assets -> prepare_sandbox -> run_verify with the actual
trivial-version-alias verify string: passed, 15/15 tests, no EROFS. Full eval
suite there with GITNEXUS_REQUIRE_BWRAP_CANARY=1: 337 passed, 4 skipped.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* fix(eval): only overlay .vite-temp where the mount source actually carries it
The tmpfs overlay keyed purely on the mount target basename being
node_modules, which also matched the trusted GitNexus runtime mount at
/opt/gitnexus/node_modules. That mount's source is the built runtime and does
not carry a .vite-temp, and bwrap cannot create a mount point inside an
already-read-only bind, so the containment CI job failed:
bwrap: Can't mkdir /opt/gitnexus/node_modules/.vite-temp: Read-only file system
FAILED test_real_bubblewrap_runtime_mount_imports_cli_without_exposing_checkout
My runner probe only exercised the dependency-mount path, so it missed this.
Gate the overlay on the mount SOURCE actually containing the directory rather
than on the target name. task_assets.py captures .vite-temp only into
dependency-snapshot node_modules, so the overlay now fires exactly there and
never on the runtime mount -- and the gate is correct by construction, since a
tmpfs can only overlay a mount point that already exists in the bound bytes.
Adds a regression test for a node_modules mount whose source has no captured
.vite-temp (the runtime-mount shape) getting no overlay, and updates the
positive test to create the directory in its mount source.
Verified on the self-hosted runner: the exact failing test now passes, and the
full containment selection is 124 passed, 4 skipped.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---------
Co-authored-by: Gergo Magyar <gergomagyar@icloud.com>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* fix(eval): ignore Claude Code bootstrap noise nested below the workspace root
The planning-phase boundary check excluded Claude Code's own sandbox-bootstrap
paths only at the workspace root: workspace_snapshot tested relative.parts[0]
against WORKSPACE_SNAPSHOT_BOOTSTRAP_NOISE. But Claude Code bootstraps into
whatever directory it is running in, and the benchmark's task prompts cd into
gitnexus/, so the same noise landed one level down as
gitnexus/.claude/.cc-writes -- whose parts[0] is "gitnexus", so it was never
excluded.
In skill-evolution run 29861768554 that accounted for 13 of 18 sessions, each
failing with error_kind plan-evidence-invalid and the identical error_detail
"phase changed unauthorized workspace path(s): gitnexus/.claude/.cc-writes".
The same code path also guards the review phase (runner.py:499), so review arms
hit it as review-evidence-invalid.
Widening the whole set to match at any depth would be wrong: it also contains
package.json, package-lock.json, node_modules and the .env family, and both
gitnexus/package.json and gitnexus/.claude/settings.local.json are real tracked
files whose edits must still be caught. So the root-anchored rule is unchanged,
and a second narrow rule matches only the entries Claude Code itself creates
inside a .claude directory (.cc-writes, agents, commands) at any depth -- never
.claude itself.
The predicate moves into _is_bootstrap_noise so it is directly testable. It is
still evaluated before pending.append, so an excluded directory is never
descended into.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* fix(eval): mount the node install prefix so npx and npm resolve in the sandbox
_runtime_mount_args bound only the `node` binary itself to SANDBOX_NODE. npm
and npx are not standalone binaries -- they are symlinks into
../lib/node_modules/npm/bin/*-cli.js -- so the install prefix carrying both
bin/ and lib/node_modules has to be mounted for them to resolve at all.
On GitHub-hosted images node lives in /usr/local/bin, whose prefix (/usr/local)
is already inside the wholesale /usr read-only bind, so npm and npx came along
for free and the gap stayed invisible. A self-hosted runner's actions/setup-node
installs into its own tool cache, outside /usr, so only the single node file was
bound. Every task's verify command is "cd gitnexus && npx tsc --noEmit && npx
vitest run <test>", so in skill-evolution run 29861768554 all 18 of 18 result
records carried the identical verify_output "/bin/sh: 1: npx: not found" -- no
run could resolve regardless of model output. It reached the model too: the
session transcripts show 12 "npm: not found" failures, with
gitnexus/scripts/build.js dying on `npm ci` with status 127.
Binds Path(node_bin).resolve().parent.parent read-only at /opt/claude/nodejs,
a fresh target outside the already-read-only trees (same constraint that put
SANDBOX_NODE under /opt/claude), and adds its bin/ to SANDBOX_PATH. The bind is
skipped when the prefix already sits inside /usr, /bin, /lib or /lib64, so the
already-covered case does not widen the mount surface redundantly.
SANDBOX_NODE is deliberately unchanged -- sanitized_graph.py and
runner_sessions.py invoke it directly. SANDBOX_PATH is now derived from
SANDBOX_NODE_PREFIX so the two cannot drift, and the minimal-mounts probe
asserts against the constant instead of a duplicated literal.
The real-Bubblewrap npx canary lives in test_proposer_sandbox.py deliberately:
test_workflow_bench.py pins the set of files carrying the canary marker, and it
runs in the eval-containment-linux job, where actions/setup-node also installs
into the tool cache -- so the canary exercises the real failure shape.
Combines plan steps 3-5 into one commit: the mount, SANDBOX_PATH and the pinned
probe assertion are one behavioural change, and splitting them would leave a
commit whose asserted PATH disagrees with the mounted reality.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* fix(eval): only bind a verified node prefix, and stop excluding .claude/agents
Addresses two findings from the branch review of the two preceding commits.
1. The prefix was derived as Path(node_bin).resolve().parent.parent with no
check that the layout is really <prefix>/bin/node. Probed: /opt/bin/node
bound ALL of /opt (every tool cache on a hosted runner), /mnt/tools/node
bound /mnt, and a bare <dir>/node bound <dir>'s parent. That last shape is
not hypothetical -- the pre-existing real-Bubblewrap node canary builds
exactly it (tmp_path/toolcache/node), so eval-containment-linux would have
silently read-only mounted the whole pytest tmp_path inside a containment
test, passing while doing it. This function exists to keep the sandbox
surface minimal, so an unrecognized layout now binds nothing extra and
simply leaves npx unavailable, exactly as before the mount was added.
2. CLAUDE_BOOTSTRAP_ENTRIES also excluded "agents" and "commands" on the theory
that they might appear nested too; only .cc-writes ever was observed. Every
excluded name is a blind spot: once a .claude directory exists
(gitnexus/.claude/settings.local.json is tracked) anything written under an
excluded entry is invisible to the phase-boundary check, and Claude Code
loads .claude/agents relative to its cwd -- which these tasks point at
gitnexus/. Probed: a planning phase could plant
gitnexus/.claude/agents/planted.md with the check reporting nothing, then
the work phase reads it. Narrowed to .cc-writes alone; extend the set from
an observed failure, never pre-emptively.
Re-probed after both fixes: the over-broad mounts are gone while a genuine
tool-cache prefix carrying npm still binds; planted agents/commands content is
caught again; gitnexus/.claude/.cc-writes (the real run-29861768554 failure)
stays ignored; and edits to gitnexus/.claude/settings.local.json are still
caught.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* fix(eval): gate the node-prefix bind on a working npx, not on an npm directory
The guard tested (prefix)/lib/node_modules/npm as a proxy for "this prefix
supplies npx". Test the property actually required instead: a working npx
sitting beside node in a real bin/ directory. .exists() follows the symlink, so
a dangling npx correctly fails the check -- it would not survive the mount
either. The "bin" name requirement stays, because it is what keeps the
parent.parent derivation honest; an npx sitting directly beside node in a flat
directory would make that derivation name the wrong prefix.
This matters because the guard can silently disable the fix it guards: if a
runner's layout failed the proxy check, the prefix would not be bound and npx
would still be missing, reproducing the original failure with no signal.
Testing npx directly means the guard can only pass when the bind will actually
achieve its purpose.
Validated against a real extracted Node distribution (the official nodejs.org
tarball layout that actions/setup-node unpacks into the tool cache) staged at a
tool-cache-shaped path: bin/node is a real file, bin/npx resolves to
../lib/node_modules/npm/bin/npx-cli.js, and the prefix binds while SANDBOX_NODE
is preserved.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---------
Co-authored-by: Gergo Magyar <gergomagyar@icloud.com>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* chore(deps)(deps): bump js-yaml from 4.3.0 to 5.0.0 in /gitnexus
Bumps [js-yaml](https://github.com/nodeca/js-yaml) from 4.3.0 to 5.0.0.
- [Changelog](https://github.com/nodeca/js-yaml/blob/master/CHANGELOG.md)
- [Commits](https://github.com/nodeca/js-yaml/compare/4.3.0...5.0.0)
---
updated-dependencies:
- dependency-name: js-yaml
dependency-version: 5.0.0
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
* fix(spring-config): migrate YAML parsing to js-yaml 5 event API
js-yaml 5 removed the loadAll `listener` callback, the EventType/State
types, and DEFAULT_SCHEMA that spring-config relied on, breaking the build.
Rebuild the per-key line tree from parseEvents()/constructFromEvents()
(positions are source offsets → mapped to lines), apply the `<<` merge tag
via CORE_SCHEMA.withTags(mergeTag) (CORE alone leaves merge keys unexpanded),
and resolve aliases by anchor name, which lets the object-identity WeakMap go.
Behavior preserved: 9 unit + 8 integration spring-config tests pass, including
merged-key declaration-line, cyclic-alias termination, and the depth budget.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* fix(spring-config): restore v4 tag coverage, cover the v5 rewrite with tests
Review follow-up for #2618.
CORE_SCHEMA.withTags(mergeTag) was a narrowing, not a port: js-yaml 5
throws "unknown tag" on !!timestamp/!!binary/!!set/!!omap/!!pairs, and an
unknown tag aborts the whole parse, which readConfigKeys swallows — so an
application.yml using any of them would have gone from its full key set to
zero keys, silently. Carry the rest of what DEFAULT_SCHEMA was; none of
these tags can execute code.
Add tests for every path the review flagged as uncovered: multi-document
files, empty/comment-only/bare-`---`/bare-scalar documents, sequence-form
merge keys, and explicitly tagged values (which fail against the one-tag
schema, so they target the changed line).
Clear the anchor map per document. It cannot change output today —
constructFromEvents rejects a cross-document alias before the event tree is
built, now asserted — but it keeps both layers on YAML's scoping rule.
Drop the stale @types/js-yaml devDependency; js-yaml 5 ships its own types
and tsc --noEmit is clean without it. Lockfile hand-edited because npm
uninstall also strips every libc field.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* chore(autofix): apply prettier + eslint fixes via /autofix command
* fix(spring-config): flatten !!set members, walk YAML iteratively
Review follow-up for #2618.
js-yaml 5 constructs `!!set` as a native Set; v4 built a plain
`{member: null}` object. Object.entries of a Set is empty, so a tagged set
collapsed to a bare leaf key and lost every member. Enumerate the Set
instead. Sets arrive as mapping events with key/value scalar pairs, so
member lines resolve through the usual lookup. !!binary and !!timestamp are
unaffected — both are scalar events and take the leaf path, which is why a
Uint8Array never explodes into one key per byte.
Convert findYamlMappingLocation and flattenYamlValue from recursion to an
explicit stack. Children are pushed in reverse so pops happen in
declaration order, preserving "first match" and `out` insertion order;
`leave` frames release the cycle guard where the old `finally` did. The
depth budget still throws at the same boundary with the same message.
Cover the gaps the review named: !!pairs (both duplicate entries survive),
anchor-name reuse resolving to the nearest preceding declaration, and
marker-only leading documents staying index-aligned across the two streams.
buildYamlEventTree keeps no node budget by design — one node per event over
an already-materialized array, bounded by MAX_CONFIG_FILE_BYTES. The
docstring now says so rather than implying MAX_YAML_TRAVERSAL_NODES covers
it.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Address review finding (LOW — docs/help staleness): the --skip-skills help
text and README omitted that skills also mirror to .agents/skills/ when
.agents/ exists.
- index.ts + i18n (en/zh): --skip-skills now reads "directly under
.claude/skills/ and .agents/skills/".
- skip-git-cli.test.ts: assert the help text covers .agents/skills/.
Co-Authored-By: Claude <noreply@anthropic.com>
* fix(lbug): re-open the read pool when analyze rebuilds the index under it
The MCP read pool's initLbug early-returned on an existing pool entry with no
freshness check, so after analyze rebuilt or mutated the on-disk index the
pool kept serving the old (POSIX: unlinked-but-open) inode until LRU/idle
eviction — a silent stale-read window of up to IDLE_TIMEOUT_MS (5 min).
Record the file identity {ino, mtimeMs, size} on each PoolEntry at open, and
re-stat in initLbug: unchanged → reuse; changed & idle → closeOne + reopen the
new file; changed while a query is in flight → serve the current handle (a
later idle initLbug reopens, since closing an in-use connection is a native
use-after-free). A stat failure (ENOENT during a full rebuild's unlink window)
is treated as unchanged so the reader keeps its valid open inode until the new
file appears. Mirrors the bridge cache's mtime-invalidation pattern.
Step 1 of docs/plans/2026-07-21-...-analyze-atomic-swap-invalidation. The
end-to-end reopen-on-swap path is exercised by the reader-during-rebuild
integration test in a later step.
* fix(analyze): publish a full rebuild via an atomic swap (POSIX)
The full-rebuild path wiped the live index (wipeLbugDbFiles(lbugPath)) and
rebuilt it in place, so a concurrent MCP reader that opened mid-build could
see an empty/half-loaded DB, and a crash between the wipe and the end-of-run
left the index destroyed (recoverable only by --force).
Build the fresh index at <lbugPath>.new and swap it over the live index in one
atomic rename at the end. All DB work flows through the singleton connection,
so only initLbug/wipeLbugDbFiles take the temp target; the close already
checkpoint-consolidates the build to a single file (verified: no residual
.wal/.shadow), so the rename publishes a complete index in one step. A reader
opening mid-build only ever sees the previous complete index; a reader holding
the old inode keeps a consistent stale snapshot until the pool re-opens onto
the new one (the pool staleness invalidation from the prior commit). On
failure the swap is skipped, leaving the previous index byte-for-byte intact.
POSIX only: the common CLI/serve-worker analyze paths skip the native close
(closeLbugBeforeExit, #2264) and leave the build handle open at swap time.
POSIX renames an open file cleanly; a same-process open handle blocks the
rename on Windows, so Windows keeps the current in-place behavior
(buildPath === lbugPath) until that is resolved. The Windows atomic swap and a
deterministic concurrent reader-during-rebuild test are deferred follow-ups.
Steps 2b + partial 3 of docs/plans/2026-07-21-...-analyze-atomic-swap-invalidation.
Integration test asserts the no-temp-leak + inode-swap invariants and the
crash-safety guarantee (a load failure leaves the live index untouched).
* test(analyze): end-to-end read-pool reopen after an atomic swap
Adds the deferred reader-during-rebuild / pool-reopen integration test:
analyze v1 -> read pool serves it -> rebuild with a renamed function (atomic
swap) -> the same repoId's initLbug detects the swapped inode and re-opens the
pool onto the new index. Asserts the pool sees the renamed function and NOT the
stale v1 name, exercising #1 (invalidation) and #2 (swap) together end to end.
* fix(lbug): bound pooled read queries with setQueryTimeout
The read pool relied only on a JS-side Promise.race (QUERY_TIMEOUT_MS) that
frees the waiter but leaves the native call running. Set the engine-level
setQueryTimeout on every pooled connection so a pathological query is bounded
at the source too.
* fix(lbug): name the held-open cause for WAL checkpoint failures (#2599)
A WAL-checkpoint IO error that also carries a busy/lock signal means another
handle (a gitnexus mcp server, or this process's own reader) holds the store
open, not a disk fault. Add isLbugCheckpointBusyError (reusing the tested
isDbBusyError keyword set) and, when the checkpoint driver exhausts its retry
budget on such an error, annotate the surfaced error with the actionable
held-open cause instead of a raw IO string.
Note: overlaps in-flight work on repro/issue-2599-windows-wal-checkpoint;
bundled here at the maintainer's request.
* feat(analyze): opt-in atomic incremental + best-effort Windows swap
Extends the atomic-swap publish (POSIX full rebuild) to two more cases:
- Windows: the swap now applies when a real close is safe to release the build
handle before the rename — i.e. non-pdg runs (windowsSwapOk excludes --pdg,
the #2264 destructor-crash case), forcing a real close on the swap path.
UNVERIFIED on Windows (no Windows runner here); --pdg and any failure fall
back to today's in-place behavior, so it can never corrupt.
- Incremental (opt-in, GITNEXUS_ATOMIC_INCREMENTAL=1): copies the live index
into the temp, applies the incremental delete/writeback to the copy, and
swaps at the end. Off by default because the whole-file copy negates
incremental's speed premise — kept behind a flag pending a benchmark. The
escalation valve also targets the temp so an escalated write stays atomic.
Integration test covers the opt-in incremental path end to end (no temp leak,
the incremental change is reflected after the swap).
* refactor(lbug): centralize the read-pool + bridge open-retry budgets
The lbug-config retry registry documented the open/handle-release/query-time
budgets but the read pool's LOCK_RETRY_* (pool-adapter) and the bridge's
LBUG_OPEN_RETRY_* (group/bridge-db) kept private copies that could drift. Move
both into the registry as exported constants (POOL_OPEN_LOCK_RETRY_*,
BRIDGE_OPEN_RETRY_*) and alias the local names to them — one tuning surface,
no behavior change.
* fix: address CI regressions from the bundled follow-ups
- setQueryTimeout: guard the call so test doubles that don't model the engine
method don't break connection creation.
- atomic swap: skip the rename when the build produced no DB at buildPath (an
empty repo / mocked pipeline) instead of throwing ENOENT.
- #2599: don't wrap the checkpoint error in the driver (it hid the IO signature
the CLI's --wal-checkpoint-threshold hint keys on); name the held-open cause
at the CLI instead, beside that hint, keeping the original error intact.
- retry consolidation: revert to documentation-only — moving the pool/bridge
budgets into lbug-config broke every explicit lbug-config test mock. The
registry now catalogues all budgets with their in-file locations.
- analyze-wal-checkpoint-failure test: block both lbug.wal.checkpoint and
lbug.new.wal.checkpoint, since a full rebuild now checkpoints the temp.
* fix(analyze): publish the swap before stamping meta; identity-gate the reader (#2614 F1)
Review found a HIGH regression: the full-rebuild wrote the freshness stamp
(saveMeta, indexedAt=T_new) BEFORE the atomic swap, so a concurrent MCP reader
that reinited in the saveMeta->swap window opened the OLD inode, recorded
observed=T_new, and then never reinited again (ensureInitialized returns early
on 'current') — serving the pre-rebuild graph indefinitely. The build-into-temp
change inverted the pre-PR invariant that 'meta shows T_new' implied 'lbugPath
holds T_new data'.
Two coordinated fixes:
- run-analyze: move the final saveMeta AFTER the swap, so meta.indexedAt only
becomes visible once lbugPath resolves to the new inode. Verified nothing in
the span reads on-disk meta and registerRepo writes only the registry.
Leaving the dirty flag set across the swap also improves crash-safety.
- local-backend: the reader staleness gate now also compares the lbug file
IDENTITY (ino/mtime/size), reiniting on an inode change even when
meta.indexedAt is unchanged. This closes the swap-window latch and covers the
in-place incremental case — and is what actually makes the pool's dbIdentity
net reachable for the MCP reader (the indexedAt gate otherwise bypassed it).
* fix(lbug/analyze): WAL-aware incremental, residual-sidecar reconcile, Windows opt-in, #2599 anchor (#2614 F2-F4)
Review remediations:
- F3: gate atomic incremental on a CLEAN live index (inspectLbugSidecars) — the
main-file-only copy would drop an orphan .wal's delta; fall back to in-place.
- F4: on the swap, MOVE a residual <buildPath>.wal/.shadow beside the published
index (not orphan it) so a swallowed final checkpoint's delta is replayed.
- F2: record identity on the shared read-only Database and warn when a cached
handle is reused after its on-disk index was rebuilt while another consumer
holds it (unreachable via MCP — one consumer per lbugPath; a complete fix
needs per-inode handles, documented).
- Windows swap: opt-in (GITNEXUS_ATOMIC_WINDOWS_SWAP=1), default off — the
forced real close re-bets an unproven #2264 assumption and can't be verified
without a Windows runner, so the default Windows path stays in-place.
- #2599: anchor isLbugCheckpointBusyError to real held-open wording instead of
isDbBusyError's bare .includes('lock') over a message that embeds the DB path
(a repo under blockchain-app misclassified a disk fault as held-open).
- Docs: corrected retry-catalogue budgets (linear, not exp) and the
checkedOut>0 bound comment (load-bounded, not IDLE_TIMEOUT_MS).
* test(analyze): cover the production close path in the atomic swap (#2614 F5)
Adds a full-rebuild swap test with skipNativeCloseOnExit:true — the close path
the CLI and serve-worker actually ship (build handle left open at swap time),
distinct from the default real-close the other swap tests exercise. Asserts the
POSIX swap still publishes a single consolidated lbug with no .new temp and no
orphan sidecar.
* test(analyze): give the follow-up git commits an inline identity (CI fix)
The end-to-end reopen and atomic-incremental tests' second commits used a bare
`git commit`, which fails on CI runners with no global git identity (empty
ident name). makeRepo's initial commit already passes -c user.name/-c
user.email inline; apply the same to the rename/change commits. No code change.
* fix(mcp): route reader reinit through initLbug's active-query guard (#2614 review)
Review found an active-query retirement race: LocalBackend.ensureInitialized
detected an identity/stamp change and called closeLbug(poolKey) DIRECTLY, but
closeOne closes the shared Database at refCount 0 regardless of checked-out
connections. So a reader detecting the new generation could close the Database
a concurrent query is still executing on — a native use-after-free. This
bypassed the checkedOut>0 guard that initLbug itself has.
Fix (delegate, not close directly): initLbug now returns whether it actually
rolled the pool over; ensureInitialized calls initLbug (which serves the
current handle while a query is in flight and reopens only when idle) instead
of closeLbug. The observed IDENTITY is advanced only when the pool actually
reopened — if a query was in flight, the identity stays divergent and the
reopen retries on a later idle check rather than latching on the old handle.
The observed STAMP advances regardless so a same-file stamp change can't loop.
Old generation now stays alive until its in-flight queries drain (lazy
rollover); new requests during the busy window share the old handle until the
pool goes idle, then reopen. No parallel open-both-generations, but no UAF and
no stale latch.
---------
Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
loadIgnoreRules is called once per repo, per language/contract
extractor during group sync -- an N-repo group fans out to 6+
extractors each calling it, turning an uncached execSync per call into
O(extractors x repos) blocking subprocess spawns for the exact
many-repos scenario #2606 describes.
Both getGitInfoExcludePath and getCoreExcludesFilePath resolve to the
same value for the same fromPath for the life of the process, so
memoize by fromPath in a process-lifetime Map. One-shot CLI runs are
unaffected by staleness; the long-lived MCP server would need explicit
invalidation if this becomes a real concern.
The first fully successful real workflow_dispatch run on the self-hosted
runner (https://github.com/abhigyanpatwari/GitNexus/actions/runs/29843028596)
still failed: 17/18 sessions hit error_kind plan-evidence-invalid with
"phase changed unauthorized workspace path(s): .claude/.cc-writes,
.claude/commands, .env, .env.development, ...".
Reproduced directly on the runner (SSM, matching the real sandbox settings
exactly, including enableWeakerNestedSandbox): a single trivial "say OK"
prompt -- no real task, no real API key even -- is enough to make Claude
Code create a synthetic package.json/lockfiles/node_modules, a full set
of .env variants, and .claude/agents, .claude/commands, .claude/.cc-writes
in the workspace on every single session. None of this is something the
model decided to write; it's Claude Code's own internal bootstrap for
running inside an already-sandboxed environment, and it happens
regardless of task or prompt.
enforce_phase_workspace (the planning-phase boundary check: verify the
plan session touched only its one plan doc) already excludes .git for
exactly this class of reason -- harness/tool noise, not substantive diff.
Extends the same exclusion to the empirically-observed bootstrap set.
workspace_snapshot has exactly one use (this check, confirmed via every
caller), so widening its exclusion list can't hide anything in some other
context that actually cares about these paths changing.
Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>
Replace the custom ~/.gitnexus/ignore file with the same two sources
real git itself consults for exactly this purpose (gitignore(5)):
- core.excludesFile: git's own all-repos global ignore file (defaults
to $XDG_CONFIG_HOME/git/ignore when unconfigured)
- $GIT_COMMON_DIR/info/exclude: per-repo, untracked, so it works
without push/commit access to the repo
Precedence mirrors git exactly (lowest to highest): core.excludesFile,
then info/exclude, then .gitignore, then .gitnexusignore -- each later
source can negate an earlier one via a `!pattern` line, same
last-match-wins semantics git itself uses.
Adds getCoreExcludesFilePath and getGitInfoExcludePath to git.ts,
following the same execSync + git-common-dir pattern as
getCanonicalRepoRoot. GITNEXUS_NO_GLOBAL_IGNORE (or noGlobalIgnore)
still skips both global sources, mirroring GITNEXUS_NO_GITIGNORE.
IgnoreService only read per-repo .gitignore/.gitnexusignore, so an
exclusion meant to apply across every indexed repo had to be repeated
per repo or hand-patched into node_modules (wiped on every upgrade).
loadIgnoreRules now also reads a global ignore file at
$GITNEXUS_HOME/ignore (default ~/.gitnexus/ignore), reusing the
existing global directory that already holds registry.json and
config.json. It is added first, so per-repo .gitignore/.gitnexusignore
rules can still negate it, mirroring the .gitignore -> .gitnexusignore
precedence already in place. GITNEXUS_NO_GLOBAL_IGNORE (or
noGlobalIgnore) skips it, mirroring GITNEXUS_NO_GITIGNORE.
GitNexus review-agent finding: stripDynBound's documented Box<dyn Trait>,
Rc/Arc<dyn Trait>, and auto-trait/lifetime bound-list (dyn Trait + Send)
shapes had no test anywhere — only the bare &dyn Trait parameter case was
exercised end-to-end. Add direct unit coverage on normalizeRustTypeName and
(via interpretRustTypeBinding) normalizeRustReturnType for these shapes.
