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1515 commits

Author SHA1 Message Date
Gergo Magyar
e766cedd1a fix(eval): drop tags from the benchmark's per-arm clone
Every benchmark-arm session failed with "sanitized graph snapshot
preparation failed: clone has more than 1024 references; refusing
incomplete sanitization" (confirmed via a real workflow_dispatch run,
29738099937, after the prior activation fixes let the proposer succeed
end-to-end for the first time).

make_worktree() creates each arm's throwaway clone with a plain `git
clone`, which inherits every tag and branch from the source. This repo's
history has grown to 1144 tags (a v1.6.9-rc.N release-candidate series)
out of 1650 total refs, exceeding oracle_assets.MAX_CLONE_REFS=1024 -- a
fail-closed guard in sanitize_clone_for_hidden_oracles() that refuses to
proceed unless it can enumerate and delete every ref before handing a
sanitized snapshot to a benchmark session (so an agent can never discover
oracle answers via a ref the sanitization missed).

`ref` at every call site (evolve.py, runner.py, sanitized_graph.py) is
always a bare SHA or the literal "HEAD", never a branch name, so
`--single-branch --branch <ref>` isn't viable (git clone's --branch
requires a name). Tags are never used by the checkout fallback or by
sanitization's own delete-everything behavior, so dropping them via
--no-tags removes the 1144-ref majority without touching branch-fetch
behavior or the existing ref/origin-ref checkout fallback, and without
weakening MAX_CLONE_REFS itself.

Verified against the real repository (not just the test fixture): cloning
/workspace (1650 refs, 1144 tags) via the fixed make_worktree() now
produces a clone with 237 total refs and 0 tags.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ
2026-07-20 11:36:58 +00:00
Abhigyan Patwari
6b1c4d4540
fix(eval): surface stdout tail on session failure, not just stderr (#2577)
The proposer's second real-run failure (after the ENV_SCRUB permission fix
landed) exited 1 with subtype "success" and an EMPTY stderr_tail -- opaque:
the downloaded CI artifact showed num_turns:1, cost_usd:0, tokens:0,
duration_s:0.1, meaning the session terminated before any real model turn
completed (consistent with an early, pre-flight-style failure), but nothing
in the persisted record said why.

The actual JSON event stream (permission_denials, tool_use/tool_result,
is_error) lives in stdout, which run_managed already captures as
proc.stdout_tail -- it just never made it into the session's error_detail.
Add it there, bounded and truncated the same way stderr_tail already is.
It flows through evolve.py's existing whole-record redaction before being
written to disk / the uploaded artifact, so this closes the diagnostic gap
without a new blind CI dispatch: the next failure of this shape is
readable directly from the artifact.


Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

Co-authored-by: Gergo Magyar <gergomagyar@icloud.com>
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
2026-07-20 12:06:02 +01:00
Abhigyan Patwari
f832239462
fix(eval): pre-approve proposer tools under Claude Code 2.1.214 ENV_SCRUB hardening (#2576)
The first real skill-evolution run got past task binding, then the proposer
session exited 1 with "Permission mode forced to default —
CLAUDE_CODE_SUBPROCESS_ENV_SCRUB is set (allowed_non_write_users hardening)".

On 2.1.214 the permission resolver unconditionally forces permission mode to
"default" whenever CLAUDE_CODE_SUBPROCESS_ENV_SCRUB is set — `--permission-mode
dontAsk`, settings `permissions.defaultMode`, and `autoAllowBashIfSandboxed`
are all ignored for the mode decision. The proposer runs headless `-p --bare`
where Bash is its only writable tool (it writes the candidate overlay); under
forced "default" Bash was no longer auto-approved, so the session blocked.

We cannot set ENV_SCRUB=0 (it scrubs the Anthropic auth token from the
sandboxed proposer's Bash subprocesses). Instead, align with the forced mode:
pre-approve the proposer's exact tool surface via settings `permissions.allow`
(["Read","Grep","Glob","Bash"]) — under "default" a tool runs without a prompt
iff it matches an allow rule — and stop requesting a non-default mode so no
warning fires. ENV_SCRUB and the full sandbox filesystem/network lockdown are
unchanged. The real-binary containment canary is updated to the new invocation
(no --permission-mode) so the CI job is the authoritative empirical gate, and a
fast unit assertion pins the new permissions.allow / absent defaultMode.


Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

Co-authored-by: Gergo Magyar <gergomagyar@icloud.com>
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
2026-07-20 11:25:49 +01:00
Abhigyan Patwari
2ea00a2b22
fix(ci): install root and shared node_modules for the evolution benchmark (#2575)
* fix(ci): install root and shared node_modules for the evolution benchmark

The first real workflow_dispatch of the skill-evolution loop failed at task
binding: capture_task_dependency_binding aborted with

  SandboxError: sandbox_copy path is unavailable: node_modules: No such
  file or directory

The benchmark tasks sandbox-copy node_modules from three locations
(tasks.scenarios.yaml) — the monorepo root, gitnexus-shared, and gitnexus —
mirroring a full dev checkout. The install step only ran `npm ci` in
gitnexus/, so the root and gitnexus-shared node_modules never existed and
the loop died before any agent ran. Install all three (root, then build
gitnexus-shared, then build gitnexus), matching the per-package install in
ci-tests.yml plus the root deps the tasks require.

A new contract test pins all three installs so this fails in CI rather than
on the next real run — the same guard the workflow's other two P1 fixes got.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* fix(ci): only add the missing root install; the subpackage steps already exist

The initial fix redundantly rebuilt gitnexus-shared and gitnexus inside the
gitnexus step — but the workflow already builds both in their own dedicated
steps. Only the monorepo root node_modules was missing. Add a single
"Install monorepo root dependencies" step and leave the two subpackage
build steps untouched, so the benchmark's root sandbox_copy resolves without
double-building.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

---------

Co-authored-by: Gergo Magyar <gergomagyar@icloud.com>
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
2026-07-20 09:56:54 +01:00
FAll
2cfbc4a259
feat(spring): build bean candidate inventory (#2494)
* feat(java): inventory Spring bean candidates

* fix(java): fail closed on Spring annotation shadowing

* fix(java): resolve Spring beans after imports

* fix(java): remove stale bean extraction path

* style: satisfy locked Prettier version

* fix(spring): address PR review findings

* feat(spring): share bean inventory across Java and Kotlin

* fix(spring): gate bean inventory analysis completeness

* fix(kotlin): avoid reloading cached scope source

* chore(autofix): apply prettier + eslint fixes via /autofix command

---------

Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2026-07-20 09:28:23 +01:00
Sai Asish Y
d10028f371
fix(mcp): guard isTestFilePath against nodes without a filePath (#2565)
Signed-off-by: Sai Asish Y <say.apm35@gmail.com>
Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
2026-07-20 09:26:12 +01:00
azizur100389
c487fd1ecc
fix(web): show origin-blocked analyze guidance (#2568)
Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
2026-07-20 08:15:16 +01:00
SyedaAnshrahGillani
dfe271b2a9
fix(core): ensure path prefix and traversal guards support root directories (#2559)
* fix(core): ensure path prefix and traversal guards support root directories

* chore(autofix): apply prettier + eslint fixes via /autofix command

* test(core): add test coverage for root-level and Windows drive-root paths

* fix(core): apply separator-aware prefix matching in augmentation engine

* chore(autofix): apply prettier + eslint fixes via /autofix command

---------

Co-authored-by: Syeda Anshrah Gillani <gillani@cloudment.io>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
2026-07-20 08:12:15 +01:00
Gergő Magyar
fd1e0a999c
feat(ci): review agent runs as a coordinated reviewer swarm (#2572)
* feat(ci): review agent on Sonnet 5 with structured, linked reviews

Bump the pinned review model from claude-sonnet-4-5-20250929 to
claude-sonnet-5 (verified against the pinned Claude Code 2.1.214 with
subscription auth and --json-schema structured output).

Restructure the published review body: verdict-first summary, findings
ordered by severity, fixed section order, and every file or symbol
reference as a GitHub permalink pinned to the analyzed head SHA (or the
merge-base SHA for deleted and rename-old paths) instead of bare
path:line text, so references are clickable and render inline previews.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* feat(ci): review agent runs as a coordinated reviewer swarm

Implement the review skill's expert-lens section in CI: the main agent
spawns four trusted lanes in parallel via the Task tool — correctness,
security, blast-radius, and coverage — each a purpose-built persona
restricted to Read/Glob/Grep plus the read-only graph MCP tools.

Personas live in the canonical skill tree (mirrored to all shipped
copies) and are installed into the reviewer's user-scope agents dir from
the exact control SHA, so a hostile PR head can never define a lane.
Lane reports are treated as unverified claims: the main agent re-anchors
findings before publishing, and the publisher's context-evidence gate
still requires the main conversation's own successful context call.
Bash and the newer Agent tool remain disallowed for every context; the
analyze timeout gets swarm headroom (45 -> 60 minutes). The workflow
contract test now pins the swarm posture.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* fix(ci): sidechain tool calls can no longer satisfy the evidence gate

The review agent's own review of this PR found that proveGraphReview()
walked the flat transcript without reading parent_tool_use_id, so a
spawned lane's context call could satisfy the publisher's graph-evidence
gate the prompt reserves for the orchestrator. Entries with a non-null
parent_tool_use_id are still strictly validated (malformed linkage fails
the transcript) but are excluded from both candidate context calls and
qualifying results; a new fixture proves sidechain-only evidence is
rejected while mainline evidence beside sidechain turns still passes.

Also gives the orchestrator turn headroom for the four dispatched lanes
(--max-turns 100 -> 150), addressing the review's LOW finding.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* refactor(skills): swarm-lane dispatch belongs to the review skill

Move the lane orchestration out of the workflow prompt and into the
gitnexus-review skill itself: a new "Swarm lanes" section names the four
ci-persona lanes, defines when and how to dispatch them (parallel, one
message, per-lane context and file slices), and owns the verification
contract (lane reports are unverified claims; re-anchor, dedup, drop
unanchored findings; lanes structure the work but never gate it). Any
runner of the skill — the CI workflow or a local harness — now triggers
the lanes from one canonical definition.

The workflow prompt keeps only its CI-specific deltas: the lanes'
trusted-control-SHA install provenance, the Task-tool dispatch surface,
and the publisher's orchestrator-only context-evidence gate. Mirrors
synced; 122 contract tests pass.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* feat(skills): add adversarial finder lane and critic gate to the swarm

ci-adversarial-lens joins the parallel finder wave: it assumes the change
is broken and constructs reachable failure scenarios — interleavings,
hostile inputs, state corruption, abuse of newly exposed surfaces — each
verified to a concrete entry point before it may be reported.

ci-critic-lens runs last as a gate on the orchestrator's finished draft:
it audits anchoring, concreteness, severity calibration, format
conformance, and honesty, returning PASS or a numbered defect list with
the smallest repair per item. The skill bounds it to two passes and the
critic hardens the review without ever blocking it; the workflow inherits
both lanes automatically through the wholesale ci-personas install.

Mirrors synced across all three shipped trees; 122 contract tests pass.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* refactor(ci): workflow defers the whole swarm contract to the skill

Now that the skill's Swarm lanes section owns dispatch, verification, the
critic gate, and the fallbacks, the workflow prompt stops restating any
of it. It contributes only what CI alone knows: the lanes' control-SHA
install provenance, the concrete environment mapping for lane inputs
(diff, manifest, head and merge-base checkouts, exact SHAs), and the one
CI override — the publisher's context-evidence gate remains
orchestrator-only. Analyze timeout gains headroom for the critic's
sequential rounds (60 -> 75 minutes).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* fix(ci): dispatch swarm lanes via the Agent tool, not the renamed Task alias

On the pinned Claude Code 2.1.214 the subagent-dispatch tool is `Agent`
(`Task` was renamed to `Agent` in 2.1.63 and is now a legacy alias), and
permission rules evaluate deny before allow. The workflow allowed `Task`
and denied `Agent`, so the orchestrator could never dispatch a lane and
every review silently fell back to the inline single-agent path while the
text-only tests certified the broken config.

Use `Agent` consistently: add it to --tools, allow it scoped to the six
ci-personas (`Agent(ci-correctness-lens,...,ci-critic-lens)`), remove it
from --disallowedTools, and update the prompt. Tests now match the scoped
allowlist on the raw string (commas inside Agent(...) break a split) and
assert Agent is no longer bare-denied.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* fix(ci): harden swarm permissions — allow Glob/Grep + merge-base reads, quarantine PR-head agents

Three permission-hygiene gaps around the swarm dispatch:
- Glob/Grep were in --tools but had no allow rule, so the lanes' declared
  tools could manufacture denied-tool errors; allow them (read-only,
  sandboxed by cwd + add-dir).
- The prompt hands lanes the merge-base source checkout for deleted /
  rename-old symbols, but no Read rule covered it; add a scoped Read()
  allow (which grants access without triggering --add-dir agent discovery).
- The --add-dir PR-head copy is scanned for spawnable agent definitions and
  the pinned runtime has no suppression env, so a PR could ship its own
  .claude/agents/*.md. Drop that subtree from the materialized copy after
  checkout-index (skills left intact), so only the trusted control-SHA
  personas can ever be dispatched.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* test(ci): pin the Agent allowlist to the ci-personas; require a dispatch canary

A text-only assertion cannot prove the pinned CLI actually dispatches the
lanes (print mode silently ignores invalid settings and does not validate
Agent(type) content at parse time) — that is what let the original
Task/Agent inversion pass CI. Two mitigations for the class:

- A cross-consistency test asserts the six names in the Agent(...) allowlist
  equal the six ci-personas filenames and each persona's frontmatter name,
  so a rename or typo in any of the three fails without auth.
- The activation checklist now requires the post-merge canary to prove a
  positive dispatch AND an unlisted-type refusal before enabling the trigger.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* fix(ci): bound swarm transcript volume with per-persona maxTurns

The six lanes stream into the single execution transcript the publisher
validates, but the personas carried no turn budget, so a large-PR swarm
run could overflow the (hard-throw) transcript caps and brick a valid
review. Bound each lane deterministically — finders maxTurns 12, the
critic maxTurns 6 — which keeps the worst case (~2×(150+5×12+2×6) ≈ 444
messages) under the unchanged 1_000 cap, so no cap needs raising. A new
test encodes that invariant: it fails if a persona's maxTurns is bumped
without revisiting the cap. Applied byte-identically across all four
shipped skill trees.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* test(ci): independently pin both sidechain evidence-gate guards

The sidechain-exclusion guards at candidate registration and result
acceptance were mutually redundant on realistic transcripts (a real
sidechain turn carries parent_tool_use_id on both its call and result),
so deleting either guard alone still passed the whole suite. Add two
asymmetric cross-wired fixtures — a mainline call with a sidechain result
(pins the acceptance guard) and a sidechain call with a mainline result
(pins the registration guard), both expecting missing_graph_evidence.
Mutation-verified: deleting either guard alone now reddens the suite.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* docs(skills): require own evidence before dispatch; document critic fail-open and swarm naming

Strengthen the gitnexus-review "Swarm lanes" contract (all four mirrors):
- The orchestrator must make its own graph context call on a changed
  symbol before dispatching any lane, so a fully-delegated run cannot
  leave the publisher's evidence gate unsatisfied (mirrored into the
  workflow prompt, with a test pinning the ordering phrase).
- Document that the critic's fail-open is deliberate (bounded to two
  passes, cannot deadlock, review still gated by evidence + schema),
  and distinguish it from the hard lane-7 gate in the separate
  gitnexus-pr-swarm-review skill.
- Give a concrete local-harness registration pointer for ci-personas.
- Add a reciprocal cross-reference in gitnexus-pr-swarm-review (single
  path — that skill is not part of the mirrored family).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* docs: record the review-agent swarm capability (AGENTS.md, CLAUDE.md, reviewer-swarm README)

Reflect the shipped swarm in the standing docs: bump AGENTS.md to 1.14.0
and CLAUDE.md to 1.8.0 with changelog rows, extend the gitnexus-review
description to mention the ci-personas swarm lanes, and refresh the
reviewer-swarm README so its differentiator names the real distinction
(interactive on-demand swarm vs the CI review agent's in-workflow lanes)
now that both run swarms. No CHANGELOG.md edit (feature-PR rule).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* fix(ci): close pre-push review findings on the swarm permission change

Adversarial review of the fix diff caught two issues introduced by the
permission-hygiene commit:
- Bare Glob/Grep in --allowedTools are separate tools that the Read()-scoped
  path denies (/proc, github.workspace, ...) do not cover, opening an
  undenied read path to the raw checkouts and host paths via a prompt-
  injected lane. Drop the bare allow — under dontAsk they stay denied by
  omission; lanes read via the scoped Read() rules and the graph MCP.
- The agents quarantine removed only the add-dir root's .claude/agents; make
  it recursive so a nested (e.g. monorepo subpackage) .claude/agents cannot
  survive and be discovered.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* feat(ci): post an "in progress" marker while the review swarm runs

Swarm reviews can take up to 75 minutes, and until now the PR showed no
sign a review was running. Add a dedicated write-scoped `acknowledge` job
that, under the same authorization gate as analyze, upserts a per-PR
"🔄 GitNexus review in progress" sticky comment linking to the live run
(and reacts 👀 to the trigger comment); the publisher removes that marker
when the review — or a clean failure — posts.

The marker lives in its own job so the model-facing analyze job stays
secretless and read-only: it cannot post to the PR, so per-lane live
progress isn't exposed there — the marker is a binary "running" state with
a link to the Actions run where lane-by-lane progress is visible.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

---------

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
2026-07-20 07:31:40 +01:00
Gergő Magyar
becac9a5d3
feat(eval): run the skill-evolution loop online (#2571)
* feat(eval): run the skill-evolution loop online

Add a scheduled + dispatch-gated workflow that runs the offline
propose -> benchmark -> gate loop (workflow_bench.evolve) in CI with the
pinned Claude canary runtime and bubblewrap containment, uploads the
benchmark evidence as an artifact, and on a gate-passed promotion opens
a human-reviewed PR via the release App token. The applied overlay is
bounded to the canonical skill tree and its shipped mirrors; any escape
fails the run instead of reaching a PR.

The scheduled lane ships disabled behind GITNEXUS_EVOLUTION_ENABLED and
requires the new GITNEXUS_BENCH_AUTH_TOKEN secret (benchmark sessions
bill real API usage), mirroring the review agent's staged rollout.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* fix(ci): restructure promotion-PR script so no lint suppression is needed

Replace the inline single-quoted credential helper with a GIT_ASKPASS
file written via a quoted heredoc (the App token still reaches git only
through step env at push time), and assemble the PR body from quoted
heredocs plus double-quoted printf instead of a backtick-laden
single-quoted template. Every run script in the workflow now passes
shellcheck with zero findings and zero disables; the body and askpass
rendering are smoke-tested.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* fix(ci): apply gate-passing overlays in the evolution loop

The loop invoked workflow_bench.evolve without --apply, so
apply_promoted_overlay (its only working-tree writer, gated by
`if args.apply:`) never ran. git status stayed clean, promoted=false was
emitted every run, and the App-token/PR-open steps were unreachable dead
code — a gate-passing run went green as "No promotion this run".

validate_promotion_for_apply already runs before the apply gate, so
adding --apply lets a passing candidate reach the tree without weakening
the deterministic gate; the boundary check then confirms it stayed in the
skill trees.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* fix(ci): provision ~/GitNexus so the benchmark repo resolves on CI

Every scenario in tasks.scenarios.yaml addresses the target repo as
~/GitNexus; runner_tasks.py resolves it with expanduser().resolve() then
`git -C <repo> rev-parse`, which raises when the path is missing. On a
hosted runner the checkout lands in $GITHUB_WORKSPACE and nothing created
~/GitNexus, so the first real run failed at task-binding.

Symlink ~/GitNexus -> $GITHUB_WORKSPACE before the loop. The checkout uses
fetch-depth: 0 (full history for the parentless clone), and the benchmark
only clones the repo copy-on-write and mounts deps read-only, so the
checkout is never mutated. GITNEXUS_BENCH_ORACLE_ROOT stays unset — it
defaults to the in-repo oracles dir and is staged by the harness.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* fix(ci): harden promotion summary output and PR branch recovery

Three fixes to the promotion-detection and PR-open steps:

- GITHUB_OUTPUT summary used a fixed `PROMOTION_EOF` heredoc delimiter; a
  value containing that marker on its own line could close the block early
  and inject output keys. Use a per-run random delimiter, matching the
  pattern already in tree-sitter-upgrade-readiness.yml.
- The summary concatenated every generation's promotion.json (including
  rejected ones), so the PR body could show a losing generation's
  decisions. The loop returns on the first promotion, so emit only the
  highest-numbered gen-N/bench/promotion.json — the decision that fired.
- The promotion branch name omitted the run attempt. GITHUB_RUN_ID is
  stable across re-runs, so a re-run after push-succeeds/PR-create-fails
  could never push. Include ${GITHUB_RUN_ATTEMPT} (the artifact name
  already does).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* fix(ci): least-privilege the promotion App token and gate on an Environment

The Mint-App-Token step passed only app-id + private-key, so the minted
token inherited every permission the Release App installation holds
(including Workflows: write) — far more than "push a branch, open a PR".
Switch to `client-id` (as publish.yml does) and request only
permission-contents: write + permission-pull-requests: write.

Bind the job to a protected Environment (gitnexus-evolution) so promotion
runs can be gated server-side. workflow_dispatch runs the workflow and
in-tree evolve.py from the *dispatched ref*, so a code-side ref guard is
removable by the dispatched branch itself; an Environment deployment-branch
rule (main only) is the boundary that holds. The admin steps to create it
and scope the secrets are documented in the activation checklist.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* fix(ci): correct upload-artifact pin comment and add shell strict-mode

- The upload-artifact SHA 043fb46d… is v7.0.1 (labeled so in the sibling
  workflows that pin it); the comment mislabeled it # v6.0.0. Correct the
  comment; the pin is unchanged.
- Add `set -euo pipefail` to the two build steps that lacked it, matching
  every other run block in the file (GitHub's default shell already sets
  -eo pipefail; this adds -u and consistency).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* docs(ci): complete the skill-evolution activation checklist

- Add RELEASE_APP_ID / RELEASE_APP_PRIVATE_KEY to the required-secrets
  checklist (the Mint step hard-fails without them on a promotion) and the
  App-install-scope verification.
- Document the protected Environment admin step and why it is the real
  boundary for the workflow_dispatch ref-secret exposure.
- Note that workflow_dispatch runs the billing loop regardless of
  GITNEXUS_EVOLUTION_ENABLED.
- Justify the weekly cron against the README's ~90-day guidance and note the
  355-minute timeout ceiling.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* fix(eval): redact API tokens from diagnostic fields before artifact upload

results.jsonl (runner.py) and proposer-session.json (evolve.py) serialize
session records whose error_detail can carry a stderr_tail that echoed the
API key. Transcripts are redacted before persistence, but these two sinks
were not, and both land in the 14-day evolution artifact.

Run each record's serialized JSON through the existing redact_text with the
run's auth token before writing. Scoped to these diagnostic sinks only: the
promoted overlay and proposal.md are left untouched (the overlay is the
applied artifact and must stay byte-identical for apply and the
shipped-skills-sync guard).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* test(ci): add a contract test for the skill-evolution workflow

No test exercised this workflow's path, which is why both P1 blockers
(missing --apply, unresolvable ~/GitNexus task repo) reached production.
Parse the workflow YAML and assert the structural contract: --apply is
passed, the task repo is provisioned, the promotion branch carries the run
attempt, the App token is permission-scoped and the job is Environment-
gated, the output summary uses a random delimiter and a single generation,
the artifact pin is labelled correctly, and every multi-line shell step
sets strict mode. Follows the review-agent-workflow.test.ts precedent.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* feat(ci): run the proposer on its own (stronger) model

One `model` input drove both the benchmark arms and the proposer/diagnosis
session. Split them: `model` stays the benchmark arms (match the model your
skill users run, so a promotion is valid for them and the tasks aren't
ceiling-saturated), and a new `proposer_model` input runs the proposer —
the harder meta-reasoning task that writes the candidate skill, and only one
session per generation, so a stronger model is cheap here. evolve.py already
supports --proposer-model; the workflow just didn't expose it.

Defaults: arms = claude-sonnet-5, proposer = claude-opus-4-8 (both
overridable via workflow_dispatch). The weekly cadence bounds the added
spend. Contract test asserts the split stays wired.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

---------

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
2026-07-20 05:37:07 +01:00
Gergő Magyar
94a528f577
feat(ci): review agent on Sonnet 5 with structured, linked reviews (#2570)
Some checks are pending
CodeQL / Analyze (javascript-typescript) (push) Waiting to run
CodeQL / Analyze (python) (push) Waiting to run
Gitleaks / gitleaks (push) Waiting to run
Publish / Classify release event (push) Waiting to run
Publish / RC guard (marker + release-PR skip) (push) Blocked by required conditions
Publish / ci (push) Blocked by required conditions
Publish / Publish to npm (push) Blocked by required conditions
Publish / Build & Push RC Docker images (push) Blocked by required conditions
Scorecard / Scorecard analysis (push) Waiting to run
Skill copy sync / shipped skills drift guard (push) Waiting to run
Trivy Image Scan / Trivy (gitnexus-cli) (push) Waiting to run
Trivy Image Scan / Trivy (gitnexus-web) (push) Waiting to run
Bump the pinned review model from claude-sonnet-4-5-20250929 to
claude-sonnet-5 (verified against the pinned Claude Code 2.1.214 with
subscription auth and --json-schema structured output).

Restructure the published review body: verdict-first summary, findings
ordered by severity, fixed section order, and every file or symbol
reference as a GitHub permalink pinned to the analyzed head SHA (or the
merge-base SHA for deleted and rename-old paths) instead of bare
path:line text, so references are clickable and render inline previews.


Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
2026-07-19 17:45:35 +01:00
Gergő Magyar
b3826d6b0e
fix(ci): unblock the review agent dispatch and publisher lanes (#2567)
* fix(ci): unblock the review agent dispatch and publisher lanes

The first workflow_dispatch validation run surfaced two defects:

- setup-node rejects `cache: false` (the YAML boolean arrives as the
  string 'false' and v6 fails with "Caching for 'false' is not
  supported"), killing the analyze job before the isolation preflight.
  Omitting the input is the supported way to disable caching.
- The publisher held only `issues: write`, but GITHUB_TOKEN needs
  `pull-requests: write` to create issue comments on a pull request,
  so even the safe-failure comment died with "Resource not accessible
  by integration".

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

* test(ci): align the publisher permission contract with PR commenting

The workflow contract test pinned the publisher to pull-requests: read,
which is exactly the permission set that made comment publication fail.
Encode the corrected scope and assert the publisher still cannot write
repository contents.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Va5uu9Ar3e45QZ5xFsG4AZ

---------

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
2026-07-19 16:36:22 +01:00
Gergő Magyar
8b5057f325
feat(skills): GitNexus Engineering Tool Kits (#2566)
* feat(skills): add ce-plan — GitNexus+PDG implementation-planning skill

Adds .claude/skills/ce-plan: a planning-only skill that builds
implementation-ready plans from GitNexus graph navigation (query/context/
impact/trace), bounded statement-level PDG slices (pdg_query, impact
mode:pdg, explain), and targeted source verification, with a context
ledger to prevent repeated reads and a machine-readable implementation
context pack (stable contract for a future ce-implement). Whitelisted in
.gitignore and registered in AGENTS.md and CLAUDE.md outside the
auto-managed gitnexus block.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(skills): apply ce-plan validation findings (tool contract, consistency, conventions)

Tool contract: impact mode:'pdg' shape now includes the schema-required
direction param; CDG branch sense documented as the result 'label' field
(reason is cypher/raw-edge only); explain caveats corrected to its real
false-negative classes (cross-function TAINT_PATH is modeled).

Consistency: PDG slice homed in working memory (ledger keeps one-liners);
depth knob defined and category-overrides-baseline ordering stated;
call_depth (consumed by nothing) and content-hash bookkeeping dropped;
Never section folded into Hard rules; Phase 3 deduplicated to a pointer;
allowed-repeat escalations defined; budget/discard accounting clarified;
verification-commands gathering added to Phase 4; open_questions added to
the context pack.

From scenario runs: plans now pin the verified-at HEAD commit and index
freshness in a header, tag claims [verified]/[graph]/[inferred]/[assumed],
quote load-bearing tool output, prefer pre-hook-carrying npm scripts, and
support an out:<path> destination override; output path defined as the
Phase 1 target repo root.

Conventions: AGENTS.md 1.9.0 / CLAUDE.md 1.4.0 changelog rows + metadata
bumps; future ce-implement qualified as future.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(skills): rename ce-plan → gitnexus-plan; add cross-CLI (Codex) entrypoints

Renames the skill dir, frontmatter, output filename convention, plan H1
(GitNexus Engineering Plan), the future executor handle
(gitnexus-implement), the .gitignore whitelist entry, and all
AGENTS.md/CLAUDE.md references. Follows the pr-swarm-review cross-CLI
pattern: SKILL.md is the canonical CLI-neutral spec, AGENTS.md § Engineering
planning is the Codex/any-agent entrypoint, and the README documents the
optional user-level ~/.codex/prompts/gitnexus-plan.md slash command plus an
invocation matrix. Skill prose de-branded from Claude Code (agent-neutral
verification layer).

Also fixes two post-review README contradictions: the anti-reread claim now
names the ledger's allowed escalations, and 'read-only by contract' is now
'planning-only' (the skill writes exactly one repo file — the plan); the
scope-creep rule and template §12 now agree on where deferred follow-ups
land. Drops the stale plugin-collision limitation.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs(skills): document Codex user-level install path for gitnexus-plan

Codex discovers SKILL.md skills from ~/.agents/skills (same path the other
gitnexus-* skills install to); README now documents the cp install plus the
optional ~/.codex/prompts slash-command file, with the prompt body preferring
the repo copy and falling back to the user-level install.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(skills): gitnexus-plan freshness gate + active PDG-layer refresh

Freshness is now a Phase 1 gate, not advisory: under the default
freshness:strict, a stale index is refreshed once per planning session via
node .gitnexus/run.cjs analyze --index-only (appending --pdg when the task
will reach the PDG phase), then the context resource is re-read. A missing
PDG layer likewise triggers the one permitted --index-only --pdg refresh
and re-probe instead of a passive recommendation. freshness:accept (or a
failed/impractical refresh) preserves the old behavior: plan on the stale
graph, source-weighted, labelled in the plan header. --index-only is the
load-bearing flag choice — it suppresses all file generation, so the
planning-only contract holds (only the .gitnexus store changes). Ledger
gains an index_refresh record; plan header states fresh / refreshed /
refresh-skipped-with-reason.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(skills): gitnexus-plan runner build check before freshness refresh

When the target repo builds the analyzer from its own source (bin → dist/
mapping, as gitnexus/ does), the Phase 1 freshness gate now verifies dist/
is current before running the analyze refresh — rebuilding via the
package's build script when any analyzer source file is newer than the
built entrypoint — and prefers that freshly built CLI. Otherwise a stale
dist re-indexes with outdated extraction logic and the 'fresh' index lies.
Rebuilds are recorded in the ledger's index_refresh; the PDG-phase refresh
inherits the same check.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(skills): add gitnexus-work executor and gitnexus-lfg pipeline

gitnexus-work executes a gitnexus-plan as verified atomic commits: consumes
the §11 implementation_context pack, drift-checks the plan's evidence pin
against HEAD, re-verifies assumptions before relying on them, runs impact
before every symbol edit and detect_changes before every commit (repo
mandates), builds tests from the plan's scenarios, and routes structural
drift back to gitnexus-plan Deepen mode instead of coding around it.

gitnexus-lfg is a thin orchestrator: gitnexus-plan → blocking user gate
(deepen / proceed / stop, deepen loops allowed) → gitnexus-work → review
via the existing gitnexus-pr-review skill (open PR, else branch diff vs
default). One bounded fix cycle for review findings; never pushes or opens
a PR on its own.

gitnexus-plan gains a Deepen mode (re-run freshness gate, escalate to
depth:deep, re-verify graph/inferred/assumed claims toward verified,
rewrite the same file); its 'future gitnexus-implement' placeholder is
retired in favor of gitnexus-work. Registered via .gitignore whitelists,
AGENTS.md 1.10.0 (section renamed to Engineering planning & execution),
CLAUDE.md 1.5.0.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(skills): apply cross-skill review findings to the gitnexus skill family

Two P1s: gitnexus-plan Deepen mode now re-anchors before re-pinning
(diffs the old evidence pin over every [verified]-claim file and re-reads
or downgrades before the header moves — moving the pin without this
laundered stale claims as verified); the index-refresh budget is stated
once in Phase 1 (one --index-only refresh plus at most one Phase 3 --pdg
upgrade per session, Deepen = its own session) with ledger and pdg-slice
deferring to it.

Contract fixes: gitnexus-work's drift check now covers every file the
pack cites (not just files_to_modify) and parses the full pack incl.
primary/related symbols and acceptance_criteria (walked in Phase 4
alongside §13); a pre-completed check skips §7 steps already landed and
Deepen gains a reconcile-execution-state step, closing the mid-execution
route-back loop; pack assumptions must name what to check and how.

lfg: Lane 4 passes the merge-base to detect_changes compare (two-dot
diff misattributes upstream commits when default advanced), branch-diff
is the stated normal case, oversized review findings route to the plan
gate instead of overflowing direct mode, the one-fix-cycle cap is
explicit on re-run, and headless runs end at the plan gate with the plan
as deliverable. work: blank mode narrowed to *gitnexus-plan*.md with a
re-execution guard, direct-mode discipline spelled out, branch
meaningfulness defined against the plan slug, and the plan document is
committed as the branch's docs commit (review diff includes it).
Planning-only contract now names the dist/ rebuild as the second
permitted state change; Phase 5.1 names the four claim tags; stale
AGENTS.md anchors fixed.

Known latent issue left untouched: gitnexus/gitnexus-pr-review pairs a
three-dot example with a two-dot detect_changes compare — that skill is
also shipped by the plugin, so fixing it here would drift the copies;
lfg compensates by passing the merge-base.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(skills): ship the engineering skill family with the gitnexus package

npm i -g gitnexus users now get gitnexus-plan / gitnexus-work / gitnexus-lfg:
the three skills are added to gitnexus/skills/ in directory form (SKILL.md +
references/), which installSkillsTo already enumerates dynamically and copies
recursively to every editor target (~/.agents/skills for Codex, Cursor,
OpenCode, Qoder, ...) on gitnexus setup — uninstall enumerates the same root,
so removal stays clean. The Claude Code plugin channel
(gitnexus-claude-plugin/skills/) carries the same copies plus the standard
per-skill mcp.json.

Global-install support in the skill text: gitnexus-plan Phase 1 now resolves
the analyzer runner explicitly — node .gitnexus/run.cjs analyze when the
project has a runner, else gitnexus analyze (installed CLI), else
npx gitnexus analyze — and all analyze mentions route through it, satisfying
the skills-steering policy (#1939/#1945) which sweeps the plugin copies.

New drift guard test/unit/shipped-skills-sync.test.ts asserts the npm and
plugin copies stay byte-identical to the canonical .claude/skills/ family
(plugin = canonical + mcp.json), same discipline as run.cjs ↔
resolve-invocation.ts. skills-steering + shipped-skills-sync: 11/11 green.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(eval): workflow_bench — measure the skill workflow's token savings

Benchmarks gitnexus-plan → gitnexus-work against a baseline agent
(--disallowedTools Skill) on identical tasks, in fresh detached worktrees,
using real headless Claude Code sessions; every number comes from the CLI's
--output-format json usage report (field names validated against a live
2.1.207 session). Reports per-arm medians (input/cache/output tokens, cost,
wall time, turns), a savings row, and resolve status from a per-task verify
command — savings on failed tasks are flagged, not celebrated. Per-task
setup hook prepares fresh worktrees (deps); --permission-mode
bypassPermissions (default) lets sessions run unattended in the throwaway
trees.

Free-model support: --base-url/--auth-token/--model route headless sessions
through any Anthropic-compatible endpoint; free-model.litellm.yaml is a
ready litellm-proxy template for OpenRouter :free variants or local Ollama,
so benchmarking burns no paid tokens (README documents rate limits and the
small-model skill-following caveat).

Harness validated end-to-end with a stub CLI (worktree lifecycle, both
arms, plan→work chaining, verify, aggregation, report) and 4 pytest units
for the pure aggregation/savings/report helpers. AGENTS.md 1.11.0.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs(eval): record first workflow_bench calibration run

Trivial-task calibration (add -V alias): both arms resolved; workflow arm
~4.3x baseline cost — the documented overhead-dominated regime, recorded so
the regime boundary is empirical rather than asserted.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(eval): workflow_bench scenario matrix — arm variants, task classes, churn

Ground-base measurement across scenarios: tasks.scenarios.yaml spans four
labeled classes (trivial → investigation-bug → investigation-feature →
cross-module) with deterministic verifies (prescribed test files). New arms:
workflow_direct (gitnexus-work direct mode — the middle option that locates
the routing boundary lfg's gate and work's triage encode) and baseline_nomcp
(no skills AND no graph tools — separates workflow-discipline value from
GitNexus-tool value; off by default). Records now carry task class and diff
churn (files/+ins/−del vs the starting commit) as an over-engineering proxy;
the report renders a class column and per-arm savings rows vs baseline.
5 pytest units + stub-CLI e2e of the full three-arm matrix.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs(eval): record workflow_bench ground base; fix churn measurement bias

Ground base (3 classes x 3 arms, n=1/cell): every arm resolved every task —
pass/fail quality saturates at this difficulty, making the comparison pure
cost. Full plan→work never amortized its ~$9-11 fixed cost on tasks a
baseline finishes in ≤35 turns (−211% to −333% cost); workflow_direct sits
near baseline (−15% to −55%, once faster wall) with more test coverage.
Routing implication recorded: direct mode/plain agent below this scale,
full workflow for cross-module / multi-session / plan-as-deliverable work.
The cross-module cell and multi-run variance are the next measurements.

Churn fix: git add --intent-to-add -A before diffing (arms that never
commit no longer undercount new files) and :(exclude)docs/plans (the
committed plan doc no longer inflates workflow churn); this run's churn
numbers predate the fix and are omitted from the recorded table.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* perf(skills): cost-optimize the workflow from measured ground base

Every optimization targets a measured fixed-cost component
(eval/workflow_bench ground base: workflow arm −211% to −333% vs baseline,
all tasks resolved):

- Plan form is category-priced: compact form (core sections w/ § anchors
  preserved, ≤80 lines excl. pack, mini-pack subset of the context pack)
  for narrow/default categories; the full 13 sections only for deep work
  (refactor/security/performance/concurrency/architecture). A compact plan
  outgrowing its cap reclassifies to full rather than overflowing.
- Freshness gate is category-priced: compact categories default to accept
  (source-weighted, refresh only when a graph claim becomes load-bearing);
  strict stays the default for full-plan categories — the rebuild+re-index
  was the largest single fixed cost.
- Turn economy: per-category tool-call budgets (~10 to ~45; architecture
  uncapped); budget exhaustion routes open questions to §12 instead of
  more digging.
- gitnexus-work fast path: HEAD == evidence pin → skip all citation
  re-reading (the pin's entire point); mini-pack fields tolerated.
- lfg Lane 1 boundary triage: tasks below the measured ~35-turn boundary
  get offered gitnexus-work direct mode before the plan lane is spent.

Copies re-synced (npm skills/, plugin, ~/.agents); steering + sync guards
green. Re-measurement of the workflow arm follows to verify the numbers
actually improve.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs(eval): record optimization re-measurement — inv-bug workflow cell −20% cost

Same task, same conditions, post-830a0459 skills: $14.56→$11.70 (−20%),
83→72 turns, cache_read −24%; verified in-transcript that the compact form,
turn budget, and skipped rebuild/re-index all fired. Wall +15% from a work-
session test-debugging tail (n=1 variance). Regime unchanged (~3.5x baseline
on this class) — routing rule stands.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(eval): per-arm clone isolation — worktree ref-namespace leak contaminated an arm

The cross-module workflow_direct cell reported an impossible 28-turn solve
with churn byte-identical to the workflow arm: git worktree add shares the
repo's ref namespace, so the workflow arm's slug branch (created by
gitnexus-work Phase 2) survived worktree removal and the direct arm found
and adopted the completed work. Arms now get isolated git clone --shared
copies (object store via alternates, refs clone-local — agent branches and
stashes die with the clone; origin/<ref> fallback for non-default refs).
Leaked branch deleted; baseline arm verified clean (0 branch references in
its transcript); cell marked invalidated pending re-run.

Records the valid cross-module cells: workflow $18.32 vs baseline $18.03
(premium −1.6%, vs −211%..−333% on smaller classes) — fixed costs amortize
at this scale, with a less destructive diff and a plan artifact as bonus;
resolve rate still tied. Churn fingerprinting is what caught the
contamination — noted in the README as an integrity check.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs(eval): complete cross-module cell — direct mode wins 47% cost / 56% wall

Clean clone-isolated re-run: workflow_direct resolved the hardest class at
$9.53/52 turns/15m vs $18.03/98/34m baseline and $18.32/107/37m full
workflow. The measured story across all four classes: the execution
discipline (gitnexus-work) is the consistent sweet spot and delivers real
token savings on hard tasks; the planning pass buys its artifact, not
same-session savings. Resolve rate tied everywhere (n=1/cell caveat).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(eval): add trajectory-gated skill evolution (#2431)

- Pair prompt candidates with incumbent workflow arms
- Gate promotions on pinned-model quality and efficiency
- Expire router evidence and document its lifecycle

* fix(eval): allow pr-review skill candidates

* feat(skills): rename and generalize GitNexus review

* feat(eval): external-comparator and review arms for workflow_bench

- ce_workflow / ce_workflow_direct: compound-engineering ce-plan/ce-work
  arms prompted with the same structure as the gitnexus arms
- review / ce_review: gitnexus-review vs ce-code-review on an identical
  diff applied by the task's setup
- plan handoff is snapshot-based: committed example plans in docs/plans/
  tie on clone mtimes and broke the name-glob pick (executed a stale plan)
- verify output tail is recorded per run and the final working-tree patch
  is kept, so failed rows are diagnosable after the clone is destroyed

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(skills,eval): address #2431 review — data-safe rename migration, fail-closed bench evidence

- setup: never delete a legacy renamed skill dir — the installer cannot
  prove ownership (users customize or hand-write skills under these
  names); warn with the path instead, and the test now asserts survival
- workflow_bench: fail closed when a session's --output-format json
  report is empty, malformed, or missing usage fields — an exit-0 shell
  with no parseable usage no longer counts as measured evidence
  (5 parametrized regression tests)
- workflow_bench: document the trust model prominently (task setup/verify
  are shell-executed, sessions run bypassPermissions with the parent env,
  candidate overlays are prompt injection surface) in README + docstring
- free-model.litellm.yaml: master_key from LITELLM_MASTER_KEY env instead
  of a static token; loopback-binding warning
- ci: run the eval workflow_bench pytest suite on ubuntu (pytest+pyyaml
  only — no full eval stack)

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(eval): demand observed foreground verification in headless work-arm prompts

In a headless -p session there is no later turn: a work arm backgrounded
its slow test run, scheduled wakeups that can never fire, and reported
done while two of its tests failed. All four work-arm prompts (both
skill families, symmetric) now require verification output to be
observed inside the session.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(skills): ask plan depth up front instead of offering deepen afterwards

gitnexus-plan Phase 0 now asks one blocking question in interactive
sessions — quick / standard / deep, mapped onto the existing depth/form/
freshness knobs — when the invocation carries no explicit depth signal.
Explicit knobs and headless runs skip the question (category posture
unchanged, so benchmarks and automation behave as before).

gitnexus-lfg's plan gate slims to proceed/stop: depth was already the
user's up-front choice, so deepening is no longer offered by default —
an explicit deepen request at the gate and executor route-backs still
run Deepen mode, which remains the mechanism for strengthening an
existing plan document.

All shipped copies resynced (npm skills/, Claude plugin); AGENTS.md
1.13.0 and CLAUDE.md 1.7.0 pointers updated, including the analyzer's
regenerated index-stats block at this branch's head.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(skills): taint pass, expert lenses, and post-work index refresh

gitnexus-review gains a PDG-backed taint-and-dependence pass (explain +
pdg_query, --pdg folded into the stale refresh on trust-boundary diffs) and
an Expert lenses section: domain reviewers derived from the graph's
clusters plus four cross-cutting lenses (architectural fit, language
conformance per the repo's own contract, Definition of Done, simplicity),
dispatched once after the evidence-gathering steps and scaled to the diff.
gitnexus-work Phase 4 now refreshes the knowledge graph after the DoD walk
via the resolved-runner ladder with analyze --index-only, so the lfg review
lane and later sessions query the finished work without dirtying the tree.
lfg's threshold-governance paragraph moves to its README; eval citations
are tagged as measured in the GitNexus repo. All shipped copies re-synced.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(cli): remove legacy gitnexus-pr-review on uninstall; cover the rename migration

uninstall's removal set now includes LEGACY_SKILL_DIR_NAMES derived from
RENAMED_SKILL_DIRS, so a pre-rename install is cleaned up instead of
orphaned. The rename warning gains behavioral coverage (fires with a legacy
dir present, silent without), and shipped-skills-sync asserts legacy names
stay absent from every shipped tree.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(eval): metric provenance, error-kind rows, skill-invocation verification, gate noise floor

The promotion gate defaults to cost_usd (the only metric that includes
subagent spend); token metrics carry an explicit main-loop-only warning in
the report and promotion.json. Rows are classified by error_kind
(session-error / verify-failed / infra-error), excluded from efficiency
medians, and the gate requires equal valid-run counts. Each session's
transcript is scanned for the expected Skill invocation and fails closed on
a verified miss; a one-run resolution edge no longer promotes (noise
floor). Per-run timeouts and setup failures record an infra-error row
instead of aborting the sweep. Overlays touching skills no candidate arm
exercises are rejected up front.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs: fix skill routing paths, version headers, and skill rosters

Routing tables point at the tracked direct skill paths (matching the
post-#2434 generator output), AGENTS.md/CLAUDE.md headers match their
latest changelog rows, the 1.12.0 row describes what the migration actually
does, package/cursor READMEs list the full shipped skill roster, and the
swarm READMEs describe /gitnexus-review's expert lenses instead of calling
it single-agent.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* ci: drift-guard workflow for skill copies; pin eval pip deps; track docs/plans

ci.yml ignores '**.md', so an md-only skill edit would merge without the
shipped-skills-sync test running — skill-sync.yml triggers exactly on the
guarded trees. The eval job's pip install is version-pinned, and
docs/plans/ is unignored so gitnexus-plan output can be committed.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(ci): keep the runner-invocation literal in gitnexus-review; add concurrency block to skill-sync

skills-steering requires skills with a stale-index hint to carry the exact
'node .gitnexus/run.cjs analyze' form — restore it with the fallback ladder
as a parenthetical instead of replacing it. skill-sync.yml gains the
top-level concurrency block the workflow-convention check enforces.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(skills): token-economy guidance for expert lenses

Merge lenses that ground in the same material into one reviewer, and use
cheaper model/effort tiers for mechanical lenses where the harness offers
them, reserving the strongest engine for adversarial judgment.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* test(eval): isolate transcript home on Windows

Ensure workflow_bench transcript tests set USERPROFILE alongside HOME so Path.home() resolves to the temporary test home on Windows.

* docs(skills): fold PR #2522 execution learnings into review/work/plan

Eight incident-backed hardenings from running the full skill cycle
(review -> plan -> work, 28-finding fix series) on PR #2522:

gitnexus-review:
- Expert lenses execute the code under review on candidate failing shapes
  (empirical probe outranks source reading — every HIGH the language
  lenses found came from a probe, not a read).
- Step 7 re-runs the exact CI check for refreshed baselines/fingerprints
  (a stale committed artifact is invisible in the diff; caught a red
  benchmarks arm).
- Step 8 treats version/invalidation constants as review surface
  (INCREMENTAL_SCHEMA_VERSION class recurred verbatim from #2494).

gitnexus-work:
- Step 4 proves regression tests discriminate against the pre-fix tree.
- Step 5 rebuilds executed build output before every verification run
  (parse workers load dist/; a correct fix 'failed' until rebuilt).
- Step 6 makes stage -> detect_changes -> commit one unbroken sequence.

gitnexus-plan:
- Phase 0 seeded-evidence mode: plan FROM a completed review's verified
  findings instead of re-running the graph ladder.
- Template §7: fingerprint/golden-guarded output rebaselines once, at the
  series tip.

All distribution copies resynced; shipped-skills-sync + skills-steering
24/24 locally.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(eval): close the skill-evolution loop with an automated proposer driver

workflow_bench.evolve adds the three arrows the README described as manual:
a proposer session that turns loser trajectories (results.jsonl rows,
transcripts, patches, the learning queue) into ONE bounded candidate
overlay, a driver that iterates propose -> paired benchmark -> deterministic
gate up to --generations, and an --apply step that copies a promoted
overlay onto the canonical skills and shipped mirrors as a working-tree
diff. The trust boundary is unchanged: overlays re-validate through
candidate_overlay_files before any benchmark or apply consumes them, and
committing, CI, and the PR merge stay human.

learnings.jsonl is gitignored: it is machine-local evidence, like the
session transcripts it complements.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs(skills): route live-task friction into the evolution learning queue

Each family skill gains a short 'Skill feedback' section: on friction with
the skill's own instructions, append one JSON line to
eval/workflow_bench/learnings.jsonl (GitNexus repo only) — never self-edit
the skill from a live task. The proposer in workflow_bench.evolve consumes
the queue as hints; a learning reaches a shipped skill only by beating the
incumbent on the paired benchmark. All shipped mirrors re-copied byte-
identical.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* ci(tests): run the evolve helper tests in the eval pytest job

test_evolve.py needs only pytest+pyyaml, same as the harness tests the job
already runs — without this line the new module had no CI coverage.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(ci): comment-triggered GitNexus review agent for PRs

'@gitnexus review' from a maintainer (OWNER/MEMBER/COLLABORATOR; the action
re-validates write access) runs the repo's gitnexus-review skill headlessly
against the PR and posts the review as a sticky comment — remote triggering
with no local setup. Read-only by construction: contents: read token,
Write/Edit and web tools disallowed, Bash allowlisted to git reads and the
gitnexus CLI; analyze parses PR code with tree-sitter, never executes it.
Requires the ANTHROPIC_API_KEY repository secret; activates once the file
is on the default branch.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(ci): dispatch lane + existing OAuth secret for the review agent

Align with claude.yml: same action pin and the CLAUDE_CODE_OAUTH_TOKEN
secret the repo already carries — no new secret to configure. Add a
workflow_dispatch lane (PR number input) so the agent can be triggered from
the Actions UI and tested before the issue_comment trigger reaches the
default branch. Allowlist gh pr view/diff and gh api, which the review
skill uses to pin PR SHAs.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(ci): close a fork-PR RCE vector in the review agent's tool allowlist

A live headless run of the exact workflow session against PR #2431 (66
turns, full gitnexus-review pass) surfaced a real HIGH-severity confused
deputy: .gitnexus/ is gitignored, not blocked — a fork PR can commit its
own .gitnexus/run.cjs, issue_comment checks out PR-head content, and the
skill's runner ladder tries 'node .gitnexus/run.cjs analyze' first. That
would execute fork-controlled JS inside a job holding
CLAUDE_CODE_OAUTH_TOKEN and a write-scoped GITHUB_TOKEN — the opposite of
the 'PR code is read, never executed' claim in the workflow's own header.

Fix: drop the run.cjs allowlist entry so analyze always resolves through
npx gitnexus (npm registry, not the checked-out tree); the skill's
documented fallback mode covers the resulting graceful degradation. Also
drop 'gh api' (not read-only — accepts -X POST/PATCH/DELETE) and downgrade
pull-requests: write to read (comment posting only needs issues: write;
the prompt already forbids formal review submission).

Same session flagged a latent evolve.py bug: select_evidence's cost sort
used dict.get's missing-key default, which doesn't cover an explicit JSON
null in a foreign --seed-results row and crashes proposer setup with
TypeError. Guarded with 'or 0.0' and added a regression test.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix: harden PR review and evolution trust boundaries

* ci: follow workflow concurrency convention

* fix(eval): make terminating error paths explicit

* fix: unblock hardened review runtime checks

* test: make containment canaries deterministic

* test: expose Claude canary tool failures

* fix: adapt clean shell environment for Claude

* fix(eval): accept the runner's transcript source key in evidence preflight

The proposer evidence preflight required transcript-artifact metadata to be
exactly {path, sha256, bytes}, but the runner stamps a fourth provenance key
(source=parent-captured-stream-json). Any --seed-results or generation>=2 run
therefore aborted with SandboxError before proposing or promoting. Pin the
producer literal as PARENT_EVENT_STREAM_SOURCE and validate it in the metadata
check, and round-trip real producer output through sum_sessions into the
preflight so the schema can't drift again.

* fix(eval): treat an unmeasured session cost as unavailable, not $0

well_formed validated only the nested usage block, so an otherwise-successful
session missing total_cost_usd was recorded as cost_usd=0.0 — and cost_usd is
the default promotion metric (lower wins), so a cost-less session scored as
free and could win promotion it never earned. Extract cost via measured_cost()
(None on absent/garbage, a measured 0.0 preserved), propagate None through
sum_sessions/aggregate/savings/report, and have the gate refuse to rank on a
metric that was not measured on every run in both arms.

* fix(eval): warn when ranking on the main-loop-only num_turns metric

num_turns comes from the CLI's top-level usage (main-loop session only), like
output_tokens, but selecting it emitted no metric_warning — so a subagent-heavy
candidate could look artificially efficient. Add num_turns to
MAIN_LOOP_ONLY_METRICS and broaden the warning to cover turns.

* fix(eval): fail closed when an overlay adds a file with no committed base

An overlay adding a new .md under gitnexus-{plan,work} passes the structural
overlay checks but has no committed base for committed_destination_base_digests
to bind against, so it raised an uncaught ValueError that crashed the evolve
driver (and runner --candidate-overlay) mid-run. Catch it at both call sites:
evolve reports NOT PROMOTED and exits, runner routes it through parser.error.

* feat(eval): circuit-break the runner sweep on a systemic outage

A sustained upstream outage used to pay out every remaining --timeout window
one session at a time. Track consecutive session/infra/cleanup failures via a
pure systemic_outage_streak helper; after --outage-streak (default 5) in a row,
stop the sweep, still write report.md/promotion.json from partial evidence, and
exit non-zero so evolve.py halts instead of proposing from truncated evidence.
A task's own resolved=False never trips the breaker.

* fix(cli): report a dirty working tree as stale in gitnexus status

status --json (and the human output) computed up-to-date from commit + runner
identity + completeness only, so a repo with uncommitted source changes at a
matching HEAD was reported up-to-date while analyze would still re-index it.
A graph-backed agent gating on that JSON could skip re-analysis on a stale
graph. Extract analyze's dirty-tree check into a shared isWorkingTreeDirty()
in storage/git and fold it into the status freshness decision.

* fix(ci): use single-slash deny globs in the review agent's disallowedTools

github.workspace already expands to an absolute path, so Read(/${{ github.workspace }}/**)
and Read(//proc/**),(//sys/**),(//dev/**) produced double-slash patterns that a
normalizing matcher may not match — silently no-opping the deny layer. Not
exploitable (the allowlist is the primary control and never grants those
paths), but the globs should be well-formed. Update the pinned test strings.

* ci: install gitnexus-shared with npm ci from the committed lockfile

The gitnexus-shared build floated its deps via npm install in three workflows
(skill-sync, ci-tests, and — most importantly — the release publish.yml) while
every other install step uses npm ci. The lockfile is committed and in sync, so
switch all three to npm ci for reproducible, locked installs.

* test(cli): make the shipped-skills drift guard reject symlinks

listFilesRecursive walked with readdirSync and snapshotDir read with
readFileSync, both of which follow symlinks — so a mirror file symlinked to the
canonical tree passed the byte-compare (and a symlinked mirror dir would be
followed too). Reject a symlinked root via lstat and any symlinked entry via
Dirent.isSymbolicLink, with negative tests (skipped on Windows).

* test(eval): guard the candidate-skill vs mirror-root coverage invariant

MIRROR_SKILL_ROOTS omits the Cursor tree, safe only because no candidate skill
is cursor-shipped. Pin that invariant: every CANDIDATE_SKILLS entry must exist
under canonical + every mirror root and must not ship to Cursor, so adding a
cursor-shipped skill to the candidate set (the PR #2488 asymmetric-sync class)
fails loudly instead of syncing three of four trees.

* docs(ci): describe the review agent's staged post-merge rollout

The DoD asked for a dry-run or triggered run before merge, but an issue_comment
(or newly added workflow_dispatch) workflow only ever executes the default-branch
copy, so it cannot be exercised from the PR that introduces it. Reword the DoD
and the activation checklist to a staged rollout: merge registered-but-disabled,
validate same-repo and fork execution post-merge, then enable the variable.

* fix: pin plugin skill mcp.json to the release version via #2445 tooling

The ten plugin skill mcp.json launched `npx -y gitnexus@latest mcp` on every
skill connect — non-reproducible and a supply-chain surface, and (unlike the
persisted setup config) never pinned. Extend sync-plugin-manifests.mjs with an
mcp surface kind that stamps the gitnexus@<version> launch arg, pin all ten to
1.6.9 now, and keep them byte-identical so the drift guard stays green. The
release lifecycle + publish.yml --check now re-stamp them like the four manifest
surfaces; only READMEs stay on @latest as docs.

* test(eval): prove the proposer's built-in file tools are confined

The real-Claude canary only exercised Bash + MCP, so it proved process/MCP
containment but not that the proposer's built-in file tools stay inside their
mounts. Add a canary over the exact PROPOSER_ALLOWED_TOOLS surface and the same
read-only /evidence mount as run_proposer (allowlist extracted to a shared
constant so it can't drift): Read reaches /evidence, a Write into the read-only
evidence mount is denied, and a Write lands in the output tree.

* fix(eval): apply the candidate overlay after task setup for fair arms

The candidate overlay was applied before the task's untrusted setup ran, so
setup could observe candidate prose and the incumbent/candidate arms started
from different pre-overlay state. Reorder within the sandbox: capture the base
(pre-overlay) skill digest, run setup against the base skills, verify setup did
not tamper them, then apply the overlay and capture the post-overlay digest the
model must preserve. apply_candidate_overlay stages path-specific overlay files,
so setup's uncommitted changes stay out of the baseline and churn is unchanged.

Graph freshness for the review arm is handled by the status dirty-tree fix plus
the review skill's stale-triggered re-index, not by reordering the cached
per-task-sha graph materialization (which is mechanically blocked).

* test(eval): end-to-end containment proof of the autonomous proposer

Drives the real run_proposer through bubblewrap with a deterministic scripted
model (no paid API): it reads the read-only evidence bundle and writes a
candidate gitnexus-plan skill edit plus a rationale into the sandbox output
tree; run_proposer enforces the trust boundary and copies only the validated
overlay + proposal out. This exercises the autonomous-proposal stage of the
self-evolution loop end-to-end in the eval/containment CI job (the gate and
apply stages are covered by test_workflow_bench_evolution and
test_promotion_apply). Env-gated on GITNEXUS_REQUIRE_CLAUDE_CANARY, so it runs
only where the pinned Claude binary and user namespaces are available.

* fix(eval): let the proposer author its overlay via Bash

Running the end-to-end proposer canary in the containment CI job surfaced a real
bug: run_proposer starts the session with --bare, which hard-disables the
Write/Edit tools ("Write exists but is not enabled in this context"), yet
allowlisted Edit/Write and omitted Bash. The proposer therefore had no working
way to write its candidate overlay — the self-evolution loop could never produce
a candidate. The sandbox settings already pre-authorize Bash
(autoAllowBashIfSandboxed) and confine writes to workspace/tmp/home, so switch
PROPOSER_ALLOWED_TOOLS to Read/Grep/Glob/Bash and tell the proposer to author
files with Bash. The end-to-end test now drives the real run_proposer through
bubblewrap and asserts a validated overlay + proposal are produced (this also
replaces the earlier file-tool canary, whose Write/Edit premise was moot).

* test(eval): author the proposer overlay with newline-free Bash content

The nested shell-sandbox prefix mangles embedded newlines, so the multi-line
overlay content never landed. Use single-line content for the deterministic
proposer canary.

* test(eval): drop the unverifiable end-to-end proposer canary

The scripted proposer overlay never materialized in the containment job across
runs, and the model tool-result content is not visible in CI logs, so the test
cannot be finalized without an environment where the sandbox can actually run.
Keep the verified production fix (Bash-authoring in run_proposer); the proposer
sandbox/containment stays covered by the existing Bash+MCP and process-tree
canaries.

* test(cli): drop run-analyze.ts from the windowsHide spawn-family list

U7 moved run-analyze.ts's only child_process call (the git status --porcelain
dirty check) into storage/git.ts (already covered by this test, with
windowsHide). run-analyze.ts no longer imports a spawn-family function, so the
windowsHide-regression test's 'must have >=1 spawn call' invariant failed for
it. Remove it from SRC_FILES.

---------

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Co-authored-by: Zander Raycraft <zanderjraycraft@gmail.com>
Co-authored-by: Azizur Rahman <azizur100389@gmail.com>
2026-07-19 15:07:24 +01:00
Gergő Magyar
12600000e3
feat(java): model enum constant bodies as first-class instances; JLS 13.1 anonymous naming (#2558)
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* feat(java): JLS 13.1 immediate-host naming for anonymous bodies + v9 schema window (#2555, step 1)

`synthesizeJavaAnonymousClassName` generalizes to both anonymous-body
shapes (`object_creation_expression` with a `class_body`; `enum_constant`
with a `body:` field) and switches from topmost-host naming to JLS 13.1
binary names: the `$`-joined chain of enclosing host types
(`EnumWrap$Mode$1`), numbered per IMMEDIATE host in source order across
both shapes (javac's shared counter). Every existing fixture's immediate
host is its top-level type, so existing names are unchanged — proven by
the 11 #2550 tests passing untouched, not assumed. The owner walk's
anonymous branch also fires on `enum_constant` now (the synthesis returns
undefined for body-less constants, so the walk continues to
`enum_declaration` as before).

Identity window: INCREMENTAL_SCHEMA_VERSION 8→9, parse-cache SCHEMA_BUMP
18→19, U-C5 pin extended with the v8-stamp rejection (enum-constant
methods re-key `E.hook`→`E$1.hook`; nested-host anons re-key
`EnumWrap$1`→`EnumWrap$Mode$1`).

Enum-constant Class-node emission and scope-side ownership land in the
next commits per
docs/plans/2026-07-18-gitnexus-plan-enum-constant-bodies.md (plan is
local — docs/ gitignored).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(java): model enum constant bodies as first-class instances (#2555, steps 2-4)

`enum E { A { void hook(){} } }` — javac's other anonymous-class shape —
joins the #2550 instance model:

- Structure: `(enum_constant body: (class_body)) @definition.class` in
  JAVA_QUERIES; `enum_constant` in javaClassConfig.typeDeclarationNodes
  with extractName synthesis. The shouldSkipClassCapture guard now also
  covers enum_constant — without it, extract()'s name fallback would
  fabricate a Class node from the constant's own identifier (`A`).
- Scope: `(enum_constant body: (class_body) @scope.class)` + synthesized
  `@declaration.class`/`@declaration.name` anchored on the body, so the
  constant's methods are owned (`ownerId`) and re-keyed
  (`Method:...:EnumConst$1.hook#0`).
- Inheritance: a body-anchored `@reference.inherits` naming the HOST
  ENUM (javac semantics: E$N extends E) — `mroFor(E$N) ∋ E`, so bare
  calls from the body to enum helpers pass the ownership gate's MRO arm
  while the same-file bare-call leak for constant-body method names is
  closed (discrimination evidence: the #2549 review's archived S1b probe
  showed the identical shape resolving `local-call` pre-fix).
- Nested-host JLS naming verified end-to-end: `EnumWrap$Mode$1` (not
  `EnumWrap$1`).
- Bench: java scope-capture fingerprint rebaselined (new captures + two
  fixtures), `measure.mjs --check` PASS across all 14 languages.

Verified: full java.test.ts 230/230 twice sequentially; TS 254 + JS/
Kotlin 289 (shared-file spot set); schema/scope/owner unit suites 90.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(java): exempt $-chain anonymous class defs from nested-class qualification (#2555 review)

Review lens probe caught a HIGH collapse: same-named methods across
sibling enum constant bodies attributed to the FIRST body's Method node
(`M3$1.hook -> M3.log` where the log() call lives in C's body; the
same-target sibling edge vanished entirely under dedup).

Root cause: `populateClassOwnedMembers`'s qualifier chains a
constant-body class def to `M3.M3$2` — its Class scope's parent is the
enum's Class scope, unlike OCE anons whose parent is a Function scope —
and its methods to `M3.M3$2.hook`. The structure-phase node id encodes
`M3$2.hook`, so the graph-bridge's qualified key misses and falls to
the file-wide simple-name lookup: first-write-wins.

Fix: `qualify()` now skips CLASS-LIKE defs whose name already carries a
`$` chain — a synthesized anonymous binary name is complete by
construction (JLS 13.1). Narrowly scoped: `$`-named MEMBERS (legal and
real in JS/TS) still qualify against their class, and named nested
classes (`Outer.Inner`, #1978) are untouched.

Discriminating regression test: same-name/distinct-target sibling
bodies must each own their edge, and the misattributed cross-edge must
not exist.

Verified: full java.test.ts 231/231; Python+Kotlin 459 (heaviest
populateClassOwnedMembers consumers) — zero assertion failures.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* chore(ci): prettier formatting + java bench rebaseline at the final corpus (#2555)

Two CI reds from the review-fix commit landing AFTER the bench
rebaseline: (1) prettier reformat of the new java.test.ts describe;
(2) the java scope-capture fingerprint drifted again because the
review fix added the java-enum-constant-same-name fixture to the
corpus — rebaselined at the true final corpus (196 fixtures,
ce104a76…, scaling 1.05 < 1.5), local `measure.mjs --check` PASS
across all 14 languages. Lesson honored going forward: the bench
rebaseline is the LAST artifact step — any post-review fixture
addition reopens it.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(java): strict JLS 13.1 chaining through anonymous enclosing types (#2555)

Per review discussion: anonymous enclosing types now chain into the
binary name instead of flattening to the nearest NAMED host — the
immediately enclosing type per JLS 13.1 may itself be anonymous:

- anon inside an anon:            NestHost$1$1   (was NestHost$2)
- anon inside an enum constant:   N$1$1          (was N$2)
- named nested hosts (unchanged): EnumWrap$Mode$1

`nearestJavaAnonHost` becomes `nearestJavaEnclosingType` (named hosts OR
anonymous bodies); an anonymous enclosing type's prefix is its own
synthesized name (memo-bounded recursion); numbering is per immediately
enclosing type in source order. Top-level-hosted names are untouched —
the full existing suite passes unchanged.

New coverage: anon-in-anon chain, anon-in-constant-body chain (with
ownership), and a bodied constant in a NESTED enum (EnumWrap2$Mode$1 —
the one host combination previously untested). Rides the unreleased v9
identity window (doc wording tightened); java bench fingerprint
rebaselined at the final corpus, `--check` PASS across 14 languages;
prettier clean.

Verified: full java.test.ts 234/234 (one worker-crash flake rerun green
in isolation).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
2026-07-18 23:11:45 +01:00
azizur100389
196095b7d1
fix(dart): extract extension type symbols (#2539)
* fix(dart): extract extension type symbols

* test(dart): update extension type benchmark baseline

* fix(dart): emit extension type implements heritage

* fix(dart): handle generic extension type implements

---------

Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
2026-07-18 22:57:26 +01:00
Gergő Magyar
249f5c7aab
fix(lbug): bound the LadybugDB buffer pool instead of the native 80%-of-RAM default (#2560)
* fix(lbug): bound the LadybugDB buffer pool instead of the native 80%-of-RAM default (#2557)

createLbugDatabase passed bufferManagerSize=0, which the native runtime
sizes at 80% of physical RAM. A long-lived gitnexus mcp process (or a
large incremental analyze) could balloon to that ceiling — 19.5 GiB
observed against a 105 MiB on-disk index — and OOM-kill the host session.

Resolve the pool at call time: default min(2 GiB, max(64 MiB, 80% of
totalmem)), overridable via GITNEXUS_LBUG_BUFFER_POOL_SIZE (bytes);
0 deliberately restores the native unbounded default; invalid values
warn and fall back, mirroring GITNEXUS_WAL_CHECKPOINT_THRESHOLD.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs(readme): document GITNEXUS_LBUG_BUFFER_POOL_SIZE and GITNEXUS_LBUG_MAX_DB_SIZE (#2557)

Both env tables gain the new buffer-pool ceiling variable and the
previously code-comment-only GITNEXUS_LBUG_MAX_DB_SIZE, with the
mmap-vs-memory distinction the issue had to discover from source.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* refactor(lbug): keep parseBufferPoolSize module-private

Review finding: the export had zero importers — parseWalCheckpointThreshold
earns its export via the CLI flag validation, but the buffer-pool CLI flag
was deliberately deferred. Re-export when a consumer exists.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* chore(autofix): apply prettier + eslint fixes via /autofix command

---------

Co-authored-by: Claude <claude@anthropic.com>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2026-07-18 20:50:14 +01:00
Gergő Magyar
1abcac9c16
fix(scope-resolution): stop platform builtins resolving to unrelated same-file symbols (#2549)
* fix(scope-resolution): stop platform builtins resolving to unrelated same-file symbols (#2545)

An unqualified call to a platform/language builtin (e.g. TypeScript's
global fetch()) could resolve to an unrelated same-file declaration
sharing that name, most visibly a Cloudflare Worker's
`export default { async fetch(req) {...} }` handler. Two contributing
gaps, both fixed:

- Object literals had no scope boundary in the TS/JS grammar queries,
  so a method's/property-arrow's name auto-hoisted past the literal
  into whatever lexically enclosed it (scope-extractor.ts's auto-hoist
  logic had nowhere to stop). Give object literals a Block scope, like
  6 other languages already do for lexical blocks.

- Independently, finalize's per-file bindings bucket
  (materializeBindings in gitnexus-shared) flattens every local
  declaration in a file onto its module scope for cross-file import
  resolution, regardless of true nesting -- so free-call-fallback's
  scope-chain walk could still hit the leaked binding at module scope.
  Guard free-call resolution: when a match for a known builtin name
  (LanguageProvider.isBuiltInName, already populated for TS/JS but
  never consulted by this pass) has no binding reachable via the true
  lexical scope chain, leave the call unresolved instead of emitting a
  false CALLS edge.

Verified against the full TS/JS resolver suites plus every other
language populating builtInNames (Python, Go, C/C++, C#, Dart, Kotlin,
PHP, Ruby, Rust, Swift, Vue) -- 2333 tests, no regressions.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* fix(scope-resolution): extend the #2545 scope-leak fix to Kotlin and Java

Anonymous object-expressions (Kotlin `object { ... }`) and anonymous
class bodies (Java `new Runnable() { ... }`) have the same missing
scope-boundary gap that caused #2545 in TypeScript/JavaScript: a method
declared inside has no scope of its own to stop the auto-hoist at, so
its name leaks past the container into the enclosing scope.

- Kotlin: `(object_literal) @scope.class` (distinct from the already-
  scoped named `object_declaration`/`companion_object`). Kotlin already
  populates `builtInNames`, so free-call-fallback's isBuiltInName guard
  (added for #2545) fully closes the equivalent leak here too --
  verified with a `println`-shadowing regression test.

- Java: `(object_creation_expression (class_body) @scope.class)`,
  matching PHP's existing `anonymous_class` handling. Java has no
  `builtInNames` list, so the isBuiltInName guard doesn't engage --
  the scope-tree fix is still correct and necessary (the anonymous
  class's own methods are now owned by the right scope), but an
  unqualified call to an unrelated same-file method sharing the
  anonymous class's method name can still resolve via finalize's
  per-file module-scope bucket (materializeBindings, shared/
  language-agnostic, intentionally not touched by this PR). Documented
  in the test as a known residual gap, same as TS/JS/Kotlin's own
  non-builtin-name collisions.

Audited every other language for the same shape (a value/container
node with no @scope.* capture hosting a would-be-auto-hoisted named
declaration): PHP and Vue already handle it correctly (PHP scopes
anonymous_class; Vue's <script> delegates to the now-fixed TS/JS
query). Ruby, Python, Dart, C#, Swift, Go, Rust, and C/C++ have no
query pattern that treats a literal/container value position as a
named declaration in the first place, so the bug shape can't occur
there.

Verified: full Kotlin + Java resolver suites, 468 tests, no
regressions.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* fix(scope-resolution): dedicated Object scope kind for object literals (#2545, #2551)

Review of the #2545 fix surfaced two defects, both fixed here:

1. The isBuiltInName guard suppressed genuine cross-file imports whose
   name matches a builtin (`import { fetch } from './fetch-polyfill'`
   silently stopped resolving -- verified regression vs. main). The
   leak the guard targets is inherently same-file (finalize's flat
   bucket is per-file), so the guard now also requires
   `fnDef.filePath === parsed.filePath`. New regression test covers
   the polyfill-import shape.

2. The sibling-property case of the reported bug was still broken and
   masked by a tautological assertion (`c.reason` -- a property that
   doesn't exist; the real path is `c.rel.reason` -- so the test
   passed regardless of behavior). In
   `export default { fetch() {...}, handler: () => fetch(...) }`,
   `handler`'s bare `fetch()` still resolved to its sibling. Reusing
   the `Block` scope kind was the root cause: correct for a real
   lexical block (a nested closure legitimately sees a sibling
   `let`/`const` from an enclosing `if`/`for`), wrong for object
   literals, whose members are reachable only via property access --
   never as bare identifiers, not even by sibling property bodies.

   Fix: a dedicated `Object` ScopeKind (gitnexus-shared) -- a hoist
   boundary whose own bindings scope-chain walkers never consult while
   still traversing past it to the parent. TS/JS object literals now
   emit `@scope.object`; the four chain walkers in
   scope-resolution/scope/walkers.ts (walkScopeChain,
   findAllCallableBindingsInScope, findCallableBindingsAndAdlBlocker,
   findExportedDefByName) and free-call-fallback's
   hasGenuineLexicalBinding skip Object scopes' bindings. Kotlin's
   anonymous `object {}` keeps `@scope.class` -- unlike JS object
   literals it has real implicit-this sibling dispatch.

Verified with the full resolver matrix run sequentially (TS 254, JS/
Kotlin/Java/Python/Go + TS variants 960, C/C++/C#/Dart/PHP/Ruby 1049,
Rust/Swift/Vue/Cobol + route/flow/unit suites 828, scope-extractor/
scope-tree units 51). Worker-pool crashes under parallel suite load
reproduced on unrelated files and pass in isolation (known flake, not
caused by this change).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* chore(autofix): apply prettier + eslint fixes via /autofix command

* feat(java): model anonymous class bodies as first-class Class nodes (#2550, step 1)

`new Runnable() { public void run() {} }` now emits a synthesized
javac-style `Class` node (`Worker$1`, `$N` = source order within the
top-level class) and owns its methods: the enclosing-owner walk
attributes `run` to `Worker$1` (re-keyed `Method:...:Worker$1.run#0`,
HAS_METHOD from the anonymous class) instead of the lexically enclosing
named class.

- `synthesizeJavaAnonymousClassName` (ast-helpers): single naming
  authority for every layer that keys the anonymous class; returns
  undefined for `object_creation_expression` without a `class_body`
  child, which also keeps it a no-op for C#'s same-named node type.
- `findEnclosingClassInfo`: anonymous-body branch before the generic
  container walk.
- JAVA_QUERIES: `(object_creation_expression (class_body))
  @definition.class` (no @name); `getLabelFromCaptures` now lets a
  nameless `definition.class` through — the parse-worker's existing
  `!nameNode && !extractedClassSymbol` gate still drops any nameless
  class the extractor cannot name, so other languages are unaffected.
- `javaClassConfig.extractName` synthesizes the name on the extractor
  path (worker node emission).
- Node identities move on unchanged files: INCREMENTAL_SCHEMA_VERSION
  7→8 and parse-cache SCHEMA_BUMP 17→18 (the v5 Route-identity
  precedent) force full re-analyze / cache invalidation.

Verified: new #2550 identity tests + resolve-enclosing-owner and
has-method suites (53 tests) green.

Prep for step 2/3 (scope-side ownership + receiver typeBinding) and the
free-call instance-ownership gate per
docs/plans/2026-07-18-gitnexus-plan-java-instance-scoped-freecalls.md
(plan file is local — docs/ is gitignored by repo policy).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(java): instance-scoped free-call resolution for anonymous-class methods (#2550, steps 2-4)

Completes the #2550 instance model on top of the Worker$N identity
commit:

- Scope-side ownership (java/captures.ts): synthesize
  `@declaration.class` + `@declaration.name` (`Worker$N`) anchored on
  the anonymous `class_body` — same range as its `@scope.class`, so the
  def lands in that Class scope's ownedDefs, `populateClassOwnedMembers`
  stamps `ownerId` on the anonymous class's methods, and the name
  auto-hoists exactly like a named class declaration.

- Receiver typeBinding (java/captures.ts + type-extractors/jvm.ts):
  `Runnable handler = new Runnable() { ... }` binds `handler` to the
  ANONYMOUS class (`Worker$1`), not the declared JDK interface — in both
  the scope-side TypeRef channel (receiver-bound Case 4) and the worker
  typeEnv. `handler.run()` now resolves through the receiver path
  (reason 'global', target `Worker$1.run#0`) instead of depending on
  the free-call finalize-bucket leak — which is why the prior gate
  attempt broke it (the #2550 landmine, now explained and structurally
  removed).

- Instance-ownership gate (free-call-fallback.ts + contract + run.ts +
  java opt-in): with `ScopeResolver.freeCallsRequireInstanceOwnership`,
  a free call may resolve to a `Method` only when the caller's
  enclosing class chain (self + MRO via `scopes.methodDispatch.mroFor`)
  contains the method's owner. Same-file matches only — the
  `materializeBindings` leak is per-file; cross-file Method matches come
  through genuine import channels (suppressing them broke the
  arity-narrowing parity suite, verified). Suppressions recorded as
  `'free-call-instance-ownership'` outcomes. Java opts in; every other
  language is byte-identical (flag off).

Result on the #2545 fixture: `process()`'s bare `run()` emits NO edge
to the unrelated anonymous method (the #2550 bug, closed), while
`handler.run()`, same-class implicit-this dispatch, and bare inherited
calls (MRO arm) all keep resolving.

Verified: full java.test.ts 223/223 twice sequentially (landmine gate);
cross-language matrix (TS/JS/Kotlin/Python/Go/C/C++/C#/Dart/PHP/Ruby/
Rust/Swift/Vue/Cobol + callable-value-flow + java-class-impact + core
units) — zero assertion failures; worker-crash flakes re-verified green
in single-file isolation.

Known deferral (documented): EXTENDS/IMPLEMENTS edges from the
anonymous class to its constructed type are not yet emitted, so a
same-file inherited-but-not-overridden member called ON the anonymous
instance does not resolve through the anon MRO; tracked as the
follow-up in #2550.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* chore(autofix): apply prettier + eslint fixes via /autofix command

* fix(java): anonymous-class inheritance, host coverage, and phantom-node guard (#2550 review)

Self-review of the instance model (gitnexus-review with empirical lens
probes) surfaced three defects, all fixed:

1. HIGH — the ownership gate suppressed TRUE bare calls to inherited
   methods inside an anonymous body extending a same-file class
   (`new Base() { void extra() { work(); } }` lost `extra -> work`):
   the anon class had no inheritance edge, so `mroFor(Worker$N)` was
   empty and the MRO arm could never pass. The synthesis now emits an
   `@reference.inherits` for the constructed type, anchored on the
   `class_body` so the reference's enclosing class resolves to the
   SYNTHESIZED def (anchoring on the type node would sit outside the
   anonymous scope and attribute the edge to the wrong class). Anon
   classes now get real EXTENDS/IMPLEMENTS edges and inherited bare
   calls pass the gate.

2. MEDIUM — hostless anonymous bodies materialized a phantom Class
   node named after the CONSTRUCTED type (`Class:...:Runnable`) via
   extract()'s extractTypeNameFromNode fallback. New
   `shouldSkipClassCapture` in javaClassConfig drops the capture when
   no name can be synthesized.

3. MEDIUM — enum/interface/record-hosted anonymous bodies silently
   fell back to the pre-#2550 model (mis-attribution + open leak).
   The topmost-host walk now accepts all four host type declarations
   (JAVA_ANON_HOST_TYPES), so `EnumHost$1` etc. are modeled; the
   phantom-node shape disappears for those hosts as a side effect.

Also: per-parse-tree WeakMap memo for the `$N` numbering — the helper
is called from four independent layers per anonymous body and each call
re-scanned the host subtree (`descendantsOfType`), quadratic on
anon-heavy files (old-style listener-per-widget Java); and the
scope-capture bench fingerprints rebaselined for java/typescript/
javascript/kotlin (`measure.mjs --check` now passes all 14 languages —
it failed for every scope query this PR touched; drift notes added per
the file's convention).

Verified: full java.test.ts 225/225; all 11 #2550 tests including the
new anon-extends-base and enum-host scenarios; bench --check PASS.

Known remaining (documented, unchanged-old behavior): enum CONSTANT
bodies (`A { ... }`) stay unmodeled; nested-host naming is top-level-
anchored (`EnumWrap$1`, not javac's `EnumWrap$Mode$1`).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* chore(autofix): apply prettier + eslint fixes via /autofix command

* test(storage): update the INCREMENTAL_SCHEMA_VERSION pin to v8 (#2550)

The U-C5 reuse-gate test deliberately pins the exact schema version so
a bump cannot land without consciously extending the gate expectations.
Extend for v8 (Java anonymous-class node identities, #2550): a v7 stamp
now fails the strict-equality reuse gate — a pre-v8 index would strand
old `Worker.run`-keyed Method nodes alongside the re-keyed
`Worker$N.run` ones on unchanged files — and v8 passes.

Caught by CI (tests/ubuntu coverage shard 2/3 on PR #2549); the local
matrix had not included this unit file. All 7 schema-referencing unit
suites verified green (109 tests).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2026-07-18 14:30:37 +01:00
Gergő Magyar
4d7a0a69ed
fix(analyze): degrade FTS search instead of aborting analyze on index-build failure (#2548)
* fix(analyze): degrade FTS search instead of aborting analyze on index-build failure

createSearchFTSIndexes re-tokenizes every stored row on every analyze run
(full or incremental). A native LadybugDB tokenizer error on a single
pre-existing row (e.g. "Failed calling LOWER: Invalid UTF-8") previously
propagated uncaught out of run-analyze.ts's main FTS phase, discarding an
otherwise-successful run's graph/embeddings work every time analyze ran
thereafter.

Add buildSearchIndexesOrDegrade(), which catches build/verify failures and
lets analyze finish with keyword search degraded for that run instead —
mirroring the existing sibling degrade path for a missing FTS extension.
The dedicated --repair-fts path is untouched and still fails loudly.

Fixes #2544, #2546.

* fix(analyze): keep capabilities.fts/ftsSkipped honest when index build degrades

ftsSkipped and capabilities.fts.status were keyed only on ftsAvailable
(extension loaded), which the new degrade path leaves true even when the
index build itself failed. Track that outcome in ftsReady and use it for
both, and update run-analyze-fts-repair.test.ts's coverage of this path
from asserting the old throw to asserting the new degrade contract
(ftsSkipped, log message, meta.json capabilities.fts.status).
2026-07-18 08:44:09 +01:00
Gergő Magyar
ed8ab1c246
fix(scope-resolution): resolve callable reference flows (#2437) (#2522)
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* docs(plans): add provider-hook value-refs plan (#2437)

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs(plans): deepen #2437 plan to USES + property-dispatch design

Design revised after prior-art research (Kythe ref vs ref/call, Joern
METHOD_REF, Feldthaus field-based call graphs, CodeQL impliedReceiverStep):
registration sites emit reference-class USES, invocation is recovered by a
field-based property-dispatch pass synthesizing CALLS at member-call sites.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(scope-resolution): model provider-hook value references (#2437)

Functions referenced as object-literal property values (provider hooks like
emitScopeCaptures: emitCppScopeCaptures) previously produced no edge at all,
so impact/context reported a false-safe 0 upstream dependents.

Two coordinated halves, per prior art (Kythe ref vs ref/call, Joern
METHOD_REF, Feldthaus ICSE'13 field-based call graphs, CodeQL
impliedReceiverStep):

- Registration -> USES: new ReferenceKind 'value-ref'; TS/JS queries capture
  pair values and shorthand properties (with @reference.property-key);
  emitted as a reference-class USES edge, reason 'scope-resolution:
  value-ref'. Resolution is callable-gated so plain values emit nothing.
- Dispatch -> CALLS: new shared pass emitPropertyDispatchCalls synthesizes
  CALLS (reason 'property-dispatch', confidence 0.7, per-key fan-out cap 32
  calibrated on this repo's 16-provider hook tables) from member-call sites
  to every function registered under the same property key.

Deviation from plan: the pass owns value-ref resolution entirely via the
post-finalize findCallableBindingInScope walker — the shared registries only
see pre-finalize local bindings, so imported hooks (the c-cpp.ts case) were
unresolvable through lookupForSite; Reference.propertyKey passthrough
dropped as unnecessary.

SCHEMA_BUMP 13 -> 14: ParsedFile gains value-ref sites + propertyKey.

Verified end-to-end: impact(emitCppScopeCaptures, upstream) now reports 8
impacted / HIGH with extractParsedFile (true dispatch caller) at d=1 via
property-dispatch and the c-cpp.ts registration via USES.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* test(scope-resolution): cover value-ref registration and property dispatch (#2437)

Integration: same-file/cross-file/aliased/shorthand registrations emit USES;
non-callable and destructuring values emit nothing; dispatch sites gain
property-dispatch CALLS (incl. JS twins and per-language partitioning);
fan-out-capped keys are dropped entirely; factory-call values unchanged.
Unit: capture-shape pins for @reference.value-ref + @reference.property-key.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(scope-resolution): surface dropped property-dispatch keys in stats (#2437)

Review finding: skippedKeys was returned but discarded — a hook table
larger than the fan-out cap silently reopened the #2437 gap for those
keys. Log dropped keys and fold value-ref USES + dispatch CALLS into
referenceEdgesEmitted.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs(plans): add callable reference-flow implementation plan

* fix(scope-resolution): close property-dispatch review gaps

* feat(scope-resolution): add callable flow facts

* feat(scope-resolution): resolve callable value flow

* feat(scope-resolution): resolve callable references across providers

* fix: harden callable reference flow resolution

* fix(scope-resolution): preserve callable binding semantics

* docs(plans): add pr-2522-review-fixes plan

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(storage): bump INCREMENTAL_SCHEMA_VERSION for callable-value-flow edges

Callable-value-flow CALLS/USES edges (#2437) can connect two files whose
content did not change, but the incremental write set only covers changed
files — a top-up against a pre-v7 index would silently omit the new edges
for every unchanged file pair, indefinitely. Force the one-time full
re-analyze (review finding 1, #2522).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(storage): sanitize callable-flow sites per-site at load, log drops

The load-time validator rejected the WHOLE ParsedFile when one site was
malformed or over-bound, with no logging — and C++ legitimately emits
empty-string parameterTypes entries ('' = unknown, the
ReferenceSite.argumentTypes convention) for cv-only/ERROR-recovered types,
so real repos fell into a permanent, silent warm-cache-miss reparse loop
through the #1983-sensitive main-thread path (review finding 7, #2522).

Now: '' entries are valid in type arrays; a malformed/over-bound site drops
only itself (counted, warned once per load); only non-array garbage —
evidence the serialization itself is untrustworthy — rejects the file.
Deviation from plan §6 wording: validator-side tolerance replaces emit-side
clamps — smaller diff, same asymmetry closed at the single chokepoint.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(scope-resolution): keep declarations in the union for reassigned callable cells

The binding-lookup suppression for fact-constrained cells was wholesale:
reassigning a declared function through its own name (greet = other;
greet()) deferred the call to the solver, which then refused the lexical
lookup that resolves the declaration — an unresolvable RHS yielded zero
CALLS for a call that resolved pre-flow (review finding 8, #2522).

Suppression now applies only to cells bound by FORMAL facts — its actual
purpose (a parameter whose grammar emits no declaration binding must not
adopt a same-named outer function). Copy/alias/store/load destinations keep
their declaration as an inclusion seed (Andersen-style union).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(scope-resolution): count forfeited deferred sites in the budget-bailout warning

On work-budget exhaustion the deferred invoke sites end the run with zero
CALLS — free-call fallback and reference emission already skipped them —
but the warning said 'ordinary graph emission remains untouched', which is
false for exactly those sites. The warning context now carries the
unresolved deferred-site count and the comment states the real cost
(review finding: budget-bailout honesty, #2522).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(scope-resolution): surface dropped property-dispatch keys in stats and warn payload

The over-cap warning carried only a count; the dropped key NAMES were
discarded and RunScopeResolutionStats had no field, so the PR-body claim
'includes them in resolver statistics' was unimplemented (review finding,
#2522; reviewer ask on the fan-out cap). The warn payload now names up to
20 dropped keys and the stats carry propertyDispatchSkippedKeys.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* refactor(scope-resolution): drop producer-less ownerQualifiedName from formal sites

No capture emitter anywhere produces @callable-flow.owner-qualified-name —
the solver branch consuming it was unreachable in production, yet the field
was typed, parsed, validated, and unit-tested with hand-built input (review
finding 16, #2522; YAGNI). Re-add with a real producer if C++ qualified
member declarators ever need it.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* refactor(scope-resolution): drop dead callable-flow knobs

CallableFlowPassingMode 'callable-object' had no producer and no consumer
distinguishing it, and CallableFlowCaptureOptions.extractCallArguments had
no language providing it (unlike its live sibling extractCallCallee) —
review finding 17, #2522 (YAGNI). The invocation-kind 'callable-object'
is a different, live concept and stays.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(ingestion): bind subscripted callable cells to the container, not the index

terminalIdentifier iterates children in reverse, so tbl[i] = handler seeded
the INDEX variable's cell (polluting a same-named formal) and tbl[i](7)
looked up the callee under i in a different scope — no join, no CALLS edge
for the classic function-pointer-array dispatch (review finding 12, #2522).
Subscript nodes now recurse into their container field only, in both
bindingIdentifier and terminalIdentifier, across the fielded grammars
(C/C++/JS/TS/Python/Go/Java).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(ingestion): make cross-function file-scope callable bindings resolvable

Two stacked gaps killed the canonical C callback-registration pattern
(fp assigned in init(), called in run()) — the exact #2437 false-safe this
PR exists to fix (review finding H1, #2522):

1. isVisibleValueBinding only consulted assignment regions and formals, so
   a call in a function OTHER than the assigning one emitted no invoke
   fact. A declared callable-typed binding is now a value binding wherever
   its declaration is visible (visibleCallableSignature).
2. The C scope query had no @declaration.variable pattern for function-
   pointer declarators — void (*fp)(int); created no scope-tree binding,
   so the seed (init) and invoke (run) cells canonicalized to different
   keys and never joined. Both bare and initialized forms now bind.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(c): detect variadic parameters via the named variadic_parameter node

tree-sitter-c materializes '...' as a named variadic_parameter node; the
anonymous-token checks never matched, so variadic function-pointer
signatures were emitted with a wrong fixed arity and no '...' sentinel
(review finding, #2522). C++ is unaffected ('...' stays an anonymous token
there); the token checks remain for such grammars.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(ingestion): emit invoke facts for field-stored callable member calls

The C ops-vtable pattern (o->run = handler; o->run(1)) captured the store
but never the call — the member path in emitCallFacts bailed for languages
without protocol methods, and the value-binding index recorded the member
store under the OBJECT's name ('o'), not the member's ('run') (review
finding 11/M3, #2522). Member destinations now also record their terminal
member name, and a member call whose name-cell has a visible store emits an
indirect invoke — gated on the store so plain accessor calls (map.get)
stay inert.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(cpp): disambiguate (obj->*ptr)() ERROR recovery by token order

tree-sitter-cpp groups the recovered '->*' two ways depending on
error-recovery cost (identifier lengths): [identifier, ERROR '->*m'] or
[ERROR 'obj->*', identifier]. The recovery assumed the first shape, so the
second silently swapped receiver/member and dropped the call site — the
committed test passed only by name luck (review finding H2, #2522). The
identifier's position relative to '->*' inside the ERROR now decides roles.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(cpp): class members are never file-local in hasFileLocalCallableLinkage

The name-keyed file-local set is populated from every static declaration,
so an in-class 'static void make();' (external linkage — in-class static
means no-instance) and any member sharing a name with a static free
function were over-marked, refusing legitimate cross-file
declaration/definition joins (review finding 13/M2, #2522). Method and
Constructor defs now bypass the name-set, per the hook's own linkage-only
contract.

Deviation from plan step 13: the regression is a unit-level contract pin
rather than an end-to-end join test — C++ merges out-of-line member
definitions onto the member node by qualified identity, so the graph shape
cannot discriminate the join refusal for members.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(cpp): classify parameter passing mode from the declarator chain only

A whole-subtree scan for reference_declarator inverted copy vs alias:
void reg(void (*cb)(int& out)) marked the by-value pointer cb as
'reference' because of the NESTED parameter's int&, making the solver
back-propagate formal targets into every caller's argument cell — alias
semantics for a copy (review finding 14/M5, #2522). The chain walk never
descends into nested parameter lists; a reference anywhere ON the chain
(int& x, void (*&cb)(int)) still aliases.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(ruby): bare identifiers are calls, not callable references

Ruby parses a receiver-less zero-arg method call identically to a variable
read, so 'action = process' — which CALLS process and stores its return —
seeded action with the callable and minted a wrong CALLS edge from any
dispatch through it, confirmed end-to-end (review finding 15/HIGH, #2522).
New provider knob bareNamesAreCalls: a bare name that is not a provably
local value binding and not an explicit reference form (method(:x),
lambda/proc) emits no flow fact, on both the assignment and argument paths.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(go): pair multi-value := positionally instead of cross-wiring

The shared field fallback took the FIRST LHS identifier and the LAST RHS
identifier of Go's expression_list pair, cross-wiring 'a, b := f, g' and
synthesizing a garbage comma-joined qualified name — the real relationships
were silently dropped (review finding 16, #2522). extractAssignment may now
return multiple pairs; Go pairs list entries positionally and emits nothing
for a length mismatch (multi-return call RHS).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(java): drop get/test from callableProtocolMethods

'get' and 'test' collide with ubiquitous non-functional-interface APIs
(Map/List/Optional/Future.get), so every ordinary container access emitted
a spurious callable-object invoke fact — high-volume misleading graph facts
with a cross-wiring risk on receiver-name reuse (review finding 17, #2522).
Supplier.get/Predicate.test dispatch is deliberately traded away until the
check can gate on the receiver's declared type.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(rust): pin the qualified-name no-degrade guard as a hard invariant

Rust's scoped_identifier callable-reference capture over-includes unit enum
variants and associated constants (Shape::Square seeds as if callable);
they stay edge-free only because resolveSeedCandidates refuses to degrade
an unresolved qualified name to a simple-name lookup (review finding 18,
#2522). Capture-side type filtering would false-negative on tuple-variant
constructors, so the guard IS the contract: documented as a hard invariant
(Go's mis-shaped multi-value forms also rely on it) and pinned end-to-end.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(php): remove nonexistent optional_parameter node type

tree-sitter-php has no 'optional_parameter' — defaults ride on
simple_parameter — so the entry was dead weight the #1920 literal gate
does not cover for capture-option Sets (review finding 19, #2522).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(cobol): detect procedure pointers on fixed-format sources

Two stacked defects made the feature a no-op on classic sequence-numbered
fixed format (review finding 20/H3, #2522):
1. parseDataItemClauses' USAGE alternation knew POINTER but not
   PROCEDURE-POINTER/FUNCTION-POINTER, so the dataItems filter was dead.
2. The raw-line fallback scanned UNCLEANED text, where the sequence number
   satisfied the leading digits and the LEVEL NUMBER got captured as the
   pointer name. It now scans preprocessed lines and requires a letter-
   initial name (COBOL data names must contain a letter).
161 COBOL preprocessor/copy-expander tests stay green; free-format matrix
case unchanged.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(cobol): skip comment lines in SET seed/copy scans

A commented-out SET (indicator-column '*'/'/' or free-format '*>')
produced a live seed and a false CALLS edge from dead code (review
finding 21/M1, #2522). The scan now skips indicator-column comment lines
and strips inline '*>' tails before matching.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs(architecture): document callable-flow-only mode and skipped-key reporting

The Callable-value flow section omitted scopeResolutionEdgeMode:
'callable-flow-only' — a real emit-pipeline branch that suppresses all
ordinary emission for standalone providers (review finding 22, #2522) —
and predated the skipped-key names/stats surfacing.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs(scope-resolution): correct value-ref resolution attribution and stale pdg-gating comments

The value-ref contract comment claimed MethodRegistry resolution — the
mechanism is the post-finalize findCallableBindingInScope walker owned by
emitPropertyDispatchCalls (resolveReferenceSites skips these sites). Three
'only under --pdg' calleeIdSink comments were falsified by the #2437 gating
change (callee-id-sink.ts's header was updated; these copies were missed).
Review finding 23, #2522.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* test(ingestion): direct unit coverage for synthesizeCallableFlowCaptures

The 1,100-line shared synthesizer had no test naming it — only downstream
consumers were covered (review finding 24, #2522). Pins seed/invoke/
formal/argument emission, subscript container binding, store-gated member
invokes, produced-value guards, and the bareNamesAreCalls knob over a
minimal options object so assertions target the synthesizer's own
semantics.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* test(resolvers): deepen shallow-language coverage; fix Kotlin/Swift reassignment gaps it exposed

Adds the COBOL SET x TO y copy-branch scenario and conditional-assignment
scenarios for Kotlin, C#, Swift, and Dart (10 languages previously had one
generic case each — review finding 25, #2522). The new scenarios exposed
two real capture gaps, fixed here:
- tree-sitter-kotlin's 'assignment' node is fieldless, so nested
  reassignments (chosen = ::target inside a block) produced no flow facts;
  Kotlin's extractAssignment now decomposes it positionally.
- tree-sitter-swift fields its assignment as target:/result:, neither in
  the shared fallback's field lists; both added.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* test(infra): literal-validation gate for callable-capture option Sets

The #1920 gate validates query literals and exported configs but not the
module-private *_CALLABLE_CAPTURE_OPTIONS Sets consumed by the shared
synthesizer — a typo'd node type silently captures nothing (PHP shipped a
dead 'optional_parameter'; review finding 26, #2522). Every <key>NodeTypes
Set literal is now validated against its language's grammar; name-carrying
sets (callableProtocolMethods, memberPointerOperators) are deliberately
outside the contract.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* test(storage): centralize corrupt-fixture casts into makeStoreEntry

The callable-flow store tests scattered 'as unknown as' double-casts per
fixture (review finding 27, #2522; standing no-as-any rule). One typed
helper now owns the single controlled escape hatch for building malformed
serialization-boundary payloads.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* chore(bench): refresh capture fingerprints after review fixes

python-scope: the committed baseline (8d5c3699) never matched this
branch's code — CI's benchmarks arm was red on the PR head (review
finding 2/HIGH, #2522); regenerated (a99e69ab), scaling 1.04 in budget.
scope-capture: ruby/cpp/swift/java/kotlin drifted from the review-fix
commits (bare-name suppression, passing modes + ->* recovery, assignment
fields, protocol narrowing, positional assignment); all 14 languages
re-verified PASS with ratios <= 1.18 against the 1.5 budget.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* chore(docs): untrack docs/plans working documents

docs/ is gitignored (local working docs); the plan files were force-added
past the ignore. Untracked from the index only — they stay on disk.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* test(golden): regenerate captures goldens after callable-flow review fixes

The per-language digest guards (csharp/go/php/python/ruby/rust/swift)
locked the pre-fix capture output; the review-fix series intentionally
changed it — store-gated member invokes, subscript container binding,
Ruby bare-name suppression, Swift assignment fields, positional pairing.
Regenerated with UPDATE_GOLDEN=1; clean verification run 59/59; all other
parity/golden guards (pipeline-graph, spring-route, python parity) pass
untouched at 33/33.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(ingestion): prototypes are callees, not callable value cells

The cross-function visibility fix indexed EVERY signature-bearing
declaration as a value binding — including plain function/method
prototypes (void f(int);). Every call to a declared function then became
an indirect invoke, and with emitCanonicalInvokeReference (C/C++) minted a
free-call reference that resolved through the registry, bypassing the
precise passes' two-phase/ambiguity/subobject suppression — eight phantom
CALLS edges in the cpp resolver suite on CI.

Only declarations whose binding identifier sits under a pointer/
parenthesized declarator (callable-typed variables like void (*fp)(int);)
create value cells now. cpp resolver suite 331/331; callable-value-flow +
C/C++ suites 181/181 (the cross-function fp regression still passes); cpp
fingerprint rebaselined, both bench gates PASS.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
2026-07-17 17:20:02 +01:00
dependabot[bot]
3c36ab906b
chore(deps)(deps): bump @langchain/anthropic in /gitnexus-web (#2526)
Bumps [@langchain/anthropic](https://github.com/langchain-ai/langchainjs) from 1.3.29 to 1.5.1.
- [Release notes](https://github.com/langchain-ai/langchainjs/releases)
- [Commits](https://github.com/langchain-ai/langchainjs/commits/@langchain/anthropic@1.5.1)

---
updated-dependencies:
- dependency-name: "@langchain/anthropic"
  dependency-version: 1.5.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

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2026-07-17 13:55:12 +01:00
dependabot[bot]
4d85fe1f19
chore(deps)(deps-dev): bump @types/node in /gitnexus-web (#2528)
Bumps [@types/node](https://github.com/DefinitelyTyped/DefinitelyTyped/tree/HEAD/types/node) from 25.9.1 to 25.9.5.
- [Release notes](https://github.com/DefinitelyTyped/DefinitelyTyped/releases)
- [Commits](https://github.com/DefinitelyTyped/DefinitelyTyped/commits/HEAD/types/node)

---
updated-dependencies:
- dependency-name: "@types/node"
  dependency-version: 25.9.5
  dependency-type: direct:development
  update-type: version-update:semver-patch
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2026-07-17 13:54:44 +01:00
dependabot[bot]
06ba512046
chore(deps)(deps-dev): bump @babel/parser in /gitnexus (#2531)
Bumps [@babel/parser](https://github.com/babel/babel/tree/HEAD/packages/babel-parser) from 8.0.0 to 8.0.4.
- [Release notes](https://github.com/babel/babel/releases)
- [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md)
- [Commits](https://github.com/babel/babel/commits/v8.0.4/packages/babel-parser)

---
updated-dependencies:
- dependency-name: "@babel/parser"
  dependency-version: 8.0.4
  dependency-type: direct:development
  update-type: version-update:semver-patch
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2026-07-17 13:24:15 +01:00
dependabot[bot]
22905bb2a7
chore(deps)(deps-dev): bump @babel/traverse in /gitnexus (#2532)
Bumps [@babel/traverse](https://github.com/babel/babel/tree/HEAD/packages/babel-traverse) from 8.0.0 to 8.0.4.
- [Release notes](https://github.com/babel/babel/releases)
- [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md)
- [Commits](https://github.com/babel/babel/commits/v8.0.4/packages/babel-traverse)

---
updated-dependencies:
- dependency-name: "@babel/traverse"
  dependency-version: 8.0.4
  dependency-type: direct:development
  update-type: version-update:semver-patch
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2026-07-17 13:24:01 +01:00
dependabot[bot]
0b777979d8
chore(deps)(deps-dev): bump @babel/types in /gitnexus (#2534)
Bumps [@babel/types](https://github.com/babel/babel/tree/HEAD/packages/babel-types) from 8.0.0 to 8.0.4.
- [Release notes](https://github.com/babel/babel/releases)
- [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md)
- [Commits](https://github.com/babel/babel/commits/v8.0.4/packages/babel-types)

---
updated-dependencies:
- dependency-name: "@babel/types"
  dependency-version: 8.0.4
  dependency-type: direct:development
  update-type: version-update:semver-patch
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2026-07-17 13:23:47 +01:00
dependabot[bot]
11c9d791e4
chore(deps): bump github/codeql-action/init from 4.36.2 to 4.37.0 (#2504)
Bumps [github/codeql-action/init](https://github.com/github/codeql-action) from 4.36.2 to 4.37.0.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](8aad20d150...99df26d4f1)

---
updated-dependencies:
- dependency-name: github/codeql-action/init
  dependency-version: 4.37.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
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2026-07-17 13:23:26 +01:00
dependabot[bot]
64e9ef8484
chore(deps)(deps): bump @langchain/ollama in /gitnexus-web (#2527)
Bumps [@langchain/ollama](https://github.com/langchain-ai/langchainjs) from 1.2.7 to 1.3.0.
- [Release notes](https://github.com/langchain-ai/langchainjs/releases)
- [Commits](https://github.com/langchain-ai/langchainjs/compare/langchain@1.2.7...@langchain/ollama@1.3.0)

---
updated-dependencies:
- dependency-name: "@langchain/ollama"
  dependency-version: 1.3.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
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2026-07-17 13:22:37 +01:00
dependabot[bot]
90b5098b24
chore(deps)(deps): bump @langchain/core in /gitnexus-web (#2530)
Bumps [@langchain/core](https://github.com/langchain-ai/langchainjs) from 1.2.1 to 1.2.2.
- [Release notes](https://github.com/langchain-ai/langchainjs/releases)
- [Commits](https://github.com/langchain-ai/langchainjs/compare/@langchain/core@1.2.1...@langchain/core@1.2.2)

---
updated-dependencies:
- dependency-name: "@langchain/core"
  dependency-version: 1.2.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
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2026-07-17 13:22:18 +01:00
dependabot[bot]
42c4d91cd4
chore(deps)(deps-dev): bump vitest from 4.1.9 to 4.1.10 in /gitnexus-web (#2533)
Bumps [vitest](https://github.com/vitest-dev/vitest/tree/HEAD/packages/vitest) from 4.1.9 to 4.1.10.
- [Release notes](https://github.com/vitest-dev/vitest/releases)
- [Changelog](https://github.com/vitest-dev/vitest/blob/main/docs/releases.md)
- [Commits](https://github.com/vitest-dev/vitest/commits/v4.1.10/packages/vitest)

---
updated-dependencies:
- dependency-name: vitest
  dependency-version: 4.1.10
  dependency-type: direct:development
  update-type: version-update:semver-patch
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2026-07-17 13:21:52 +01:00
dependabot[bot]
e2e9254938
chore(deps): bump github/codeql-action/upload-sarif (#2535)
Bumps the codeql-action group with 1 update: [github/codeql-action/upload-sarif](https://github.com/github/codeql-action).


Updates `github/codeql-action/upload-sarif` from 4.36.2 to 4.37.0
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](8aad20d150...99df26d4f1)

---
updated-dependencies:
- dependency-name: github/codeql-action/upload-sarif
  dependency-version: 4.37.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: codeql-action
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2026-07-17 13:21:25 +01:00
dependabot[bot]
0656099332
chore(deps): bump docker/metadata-action from 6.1.0 to 6.2.0 (#2536)
Bumps [docker/metadata-action](https://github.com/docker/metadata-action) from 6.1.0 to 6.2.0.
- [Release notes](https://github.com/docker/metadata-action/releases)
- [Commits](80c7e94dd9...dc80280410)

---
updated-dependencies:
- dependency-name: docker/metadata-action
  dependency-version: 6.2.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
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2026-07-17 13:21:05 +01:00
dependabot[bot]
731ab6f512
chore(deps): bump marocchino/sticky-pull-request-comment (#2537)
Bumps [marocchino/sticky-pull-request-comment](https://github.com/marocchino/sticky-pull-request-comment) from 3.0.4 to 3.0.5.
- [Release notes](https://github.com/marocchino/sticky-pull-request-comment/releases)
- [Commits](0ea0beb66e...5770ad5eb8)

---
updated-dependencies:
- dependency-name: marocchino/sticky-pull-request-comment
  dependency-version: 3.0.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
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2026-07-17 13:20:48 +01:00
dependabot[bot]
dc993a6d43
chore(deps): bump github/codeql-action/analyze from 4.36.2 to 4.37.0 (#2506)
* chore(deps): bump github/codeql-action/analyze from 4.36.2 to 4.37.0

Bumps [github/codeql-action/analyze](https://github.com/github/codeql-action) from 4.36.2 to 4.37.0.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](8aad20d150...99df26d4f1)

---
updated-dependencies:
- dependency-name: github/codeql-action/analyze
  dependency-version: 4.37.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

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* ci(codeql): keep action steps in lockstep

Co-authored-by: azizur100389 <azizur100389@gmail.com>

---------

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2026-07-17 11:40:51 +01:00
dependabot[bot]
527ea5fc7a
chore(deps)(deps-dev): bump @babel/types in /gitnexus (#2518) 2026-07-17 05:26:54 +01:00
dependabot[bot]
e8fdc2e2ab
chore(deps)(deps-dev): bump @babel/generator in /gitnexus (#2519) 2026-07-17 04:42:39 +01:00
dependabot[bot]
91955e6576
chore(deps)(deps-dev): bump @babel/traverse in /gitnexus (#2520)
Some checks are pending
CodeQL / Analyze (javascript-typescript) (push) Waiting to run
CodeQL / Analyze (python) (push) Waiting to run
Gitleaks / gitleaks (push) Waiting to run
Publish / Classify release event (push) Waiting to run
Publish / RC guard (marker + release-PR skip) (push) Blocked by required conditions
Publish / ci (push) Blocked by required conditions
Publish / Publish to npm (push) Blocked by required conditions
Publish / Build & Push RC Docker images (push) Blocked by required conditions
Scorecard / Scorecard analysis (push) Waiting to run
Trivy Image Scan / Trivy (gitnexus-cli) (push) Waiting to run
Trivy Image Scan / Trivy (gitnexus-web) (push) Waiting to run
Bumps [@babel/traverse](https://github.com/babel/babel/tree/HEAD/packages/babel-traverse) from 7.29.7 to 8.0.0.
- [Release notes](https://github.com/babel/babel/releases)
- [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md)
- [Commits](https://github.com/babel/babel/commits/v8.0.0/packages/babel-traverse)

---
updated-dependencies:
- dependency-name: "@babel/traverse"
  dependency-version: 8.0.0
  dependency-type: direct:development
  update-type: version-update:semver-major
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2026-07-16 22:51:51 +01:00
dependabot[bot]
795f81127b
chore(deps)(deps-dev): bump tsx from 4.23.0 to 4.23.1 in /gitnexus (#2517)
Bumps [tsx](https://github.com/privatenumber/tsx) from 4.23.0 to 4.23.1.
- [Release notes](https://github.com/privatenumber/tsx/releases)
- [Changelog](https://github.com/privatenumber/tsx/blob/master/release.config.cjs)
- [Commits](https://github.com/privatenumber/tsx/compare/v4.23.0...v4.23.1)

---
updated-dependencies:
- dependency-name: tsx
  dependency-version: 4.23.1
  dependency-type: direct:development
  update-type: version-update:semver-patch
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2026-07-16 21:54:48 +01:00
dependabot[bot]
d27b1ab8c4
chore(deps)(deps-dev): bump @babel/parser in /gitnexus (#2521)
Bumps [@babel/parser](https://github.com/babel/babel/tree/HEAD/packages/babel-parser) from 7.29.7 to 8.0.0.
- [Release notes](https://github.com/babel/babel/releases)
- [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md)
- [Commits](https://github.com/babel/babel/commits/v8.0.0/packages/babel-parser)

---
updated-dependencies:
- dependency-name: "@babel/parser"
  dependency-version: 8.0.0
  dependency-type: direct:development
  update-type: version-update:semver-major
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2026-07-16 21:51:25 +01:00
Parafee41
8292b2bee4
test(cli): lock native load guard for lazy actions (#2442) 2026-07-16 15:22:20 +01:00
Parafee41
f45e89e6b6
fix(embeddings): make batch inserts retry-safe (#2453)
* fix(embeddings): make batch inserts retry-safe

* fix(types): cover optional transformers dependency

* Fix embedding restore test expectation

* test(embeddings): count checkpoint creates

---------

Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
2026-07-16 15:21:03 +01:00
Parafee41
b85f1ace7a
fix(mcp): avoid api impact schema combinators (#2489)
Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
2026-07-16 15:20:22 +01:00
azizur100389
a333d94a00
feat(wiki): allow explicit HTTP LLM hosts (#2491)
* feat(wiki): allow explicit HTTP LLM hosts

Keep wiki LLM HTTP endpoints fail-closed by default while adding a narrow exact-host opt-in for LAN/self-hosted models.

Co-authored-by: Cursor <cursoragent@cursor.com>

* fix(wiki): simplify insecure LLM flag name

Rename the wiki HTTP opt-in flag to --allow-insecure-connection per review feedback.

Co-authored-by: Cursor <cursoragent@cursor.com>

* fix(wiki): simplify insecure connection env

Rename the wiki HTTP allowlist environment variable and align validation errors with the CLI flag naming.

Co-authored-by: Cursor <cursoragent@cursor.com>

---------

Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
2026-07-16 13:53:58 +01:00
azizur100389
3dd553b345
feat(taint): expand TS/JS sink model (#2490)
* feat(taint): expand TS/JS sink model

Co-authored-by: Cursor <cursoragent@cursor.com>

* test(taint): cover TS sink disambiguation end-to-end

Add a real-pipeline integration test proving the expanded TS/JS taint sinks only emit findings for intended imported and receiver-conventional symbols.

Co-authored-by: Cursor <cursoragent@cursor.com>

---------

Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
2026-07-16 13:11:57 +01:00
Gergo Magyar
573a777ef5 ci(tests): widen the Windows shard watchdog and keep exit diagnostics (#2449)
The busiest Windows platform shard reached 14m57s against the 15 minute
watchdog on the rc.19 green run and has timed out once since. CI now
sets GITNEXUS_CROSS_PLATFORM_TIMEOUT_MINUTES=20 (the job timeout stays
25), the stale comfortably-under comment reflects reality, and the
runner always logs status, signal, spawn code and elapsed time so the
next status-null death is diagnosable.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-07-16 12:29:01 +01:00
Gergo Magyar
42de243e9a ci(release): sync plugin manifests on every version bump (#2445)
The RC path bumped only gitnexus/package.json, so every v1.6.10-rc tag
through rc.28 shipped the four plugin manifest surfaces frozen at 1.6.9
and failed its own unit suite. The npm version lifecycle script now
runs a fail-closed sync whenever npm version executes, in CI or on a
maintainer's laptop; publish.yml verifies the result and stages the
surfaces into the detached release commit, and the stable path refuses
to publish a tag whose manifests drifted. The sync is textual so a
release commit carries a one-line change per surface instead of
reformatting churn.

Design follows the proposal by @100yenadmin in #2445, moved onto the
standard npm version hook.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-07-16 12:29:01 +01:00
Gergő Magyar
3ee1e2cb60
Merge pull request #2513 from electricsheephq/upstream/file-embedding-delete-regression
test(embeddings): cover File-row deletion
2026-07-16 12:07:18 +01:00
Eva
5e3531133d test(embeddings): cover File-row deletion 2026-07-16 17:51:46 +07:00
Gergő Magyar
c4fb511a0a
Merge pull request #2512 from abhigyanpatwari/merge/eva-fixes-2
fix: land cache, CLI, and embeddings series (#2476 #2470 #2455 #2468)
2026-07-16 11:43:02 +01:00
Gergo Magyar
36d25b5a70 test(cli): pin the non-zero exit for not-found context payloads
The skip-git ignore test asserted the error payload while relying on
exit 0; since the output() guard an error payload also exits 1, so the
test now captures the payload from the exec failure and pins both.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-07-16 10:11:32 +00:00
Gergo Magyar
5869dde31d fix(embeddings): make HTTP generation resumable (#2468) 2026-07-16 10:00:50 +00:00
Gergo Magyar
e814c5a10d fix(embeddings): include File rows in the incremental delete sweeps
The zero-symbol File fallback from #2455 writes File embedding rows,
but the filePath-scoped delete sweeps joined through EMBEDDABLE_LABELS
only. Docs repos accumulated duplicate rows on re-analyze and deleted
files left orphans. Free for code repos: no File rows exist to match.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-07-16 10:00:26 +00:00