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Gergő Magyar 2909b201e0 fix(cli): surface silent finalize-skips so analyze cannot exit 0 without persisting (#1169) (#1237) 
* fix(cli): surface silent finalize-skips so analyze cannot exit 0 without persisting (#1169)

Closes #1169.

On Windows, `gitnexus analyze .` was observed to exit with code 0 after
printing only the "GitNexus Analyzer" banner. `.gitnexus/lbug.wal` was
written but `meta.json` was never persisted and the repo was not added
to `~/.gitnexus/registry.json`, so `gitnexus list` / `status` reported
no indexed repository. The reporter confirmed the same shape on both
LadybugDB (1.6.x) and the pre-LadybugDB KuzuDB build (1.4.1), so the
silent finalize-skip is upstream of the DB engine and indistinguishable
from a healthy index from the user's perspective.

This change makes that state a hard, actionable failure regardless of
the upstream root cause.

Behaviour change

- New `assertAnalysisFinalized()` invariant in `repo-manager.ts` checks
  that meta.json exists at `<repo>/.gitnexus/meta.json` AND that the
  global registry has a canonical-path-matching entry. Throws
  `AnalysisNotFinalizedError` (kind: "AnalysisNotFinalizedError") with a
  diagnostic that names the missing artifact and the storage path the
  user should inspect.
- `analyzeCommand` invokes the invariant on the rebuild path (skipped
  on `alreadyUpToDate`), so a future silent finalize-skip surfaces with
  exit code 1 and a recoverable error instead of a silent exit 0.
- `analyzeCommand` installs idempotent `unhandledRejection` and
  `uncaughtException` handlers that bypass the progress bar's console
  redirection by writing to a stderr handle captured at module load.
  This addresses the secondary symptom where the `barLog` redirection
  visually erased stack traces with `\x1b[2K\r` and stripped them via
  `String(err)`.
- The catch block also writes the failing error's full stack via the
  captured stderr, so failure diagnostics survive any downstream
  monkey-patching of `process.stdout`/`stderr`.

Tests

- `test/unit/repo-manager-finalize-invariant.test.ts` (4 tests): cover
  both `missing="meta"` and `missing="registry-entry"`, the happy path,
  and Windows case-insensitive registry path matching.
- `test/integration/cli-e2e.test.ts` adds a regression test that runs
  the real CLI on a fresh repo copy, asserts exit 0, AND verifies
  `meta.json` plus the matching registry entry are both written —
  catches any future regression of the wiring.

Validation

- `npx tsc --noEmit` passes.
- `npx vitest run --project default` passes for all my touched files
  (89 tests across 4 files). The full default suite reports 7188 pass
  with the known native LadybugDB Windows-worker flake unrelated to
  this change.
- `npx prettier --check` clean on the diff.
- `npx eslint` reports only pre-existing `any` warnings on the file;
  no new warnings introduced.
- Live repro on the issue's two-file Python fixture reproduces a
  successful index after the change: meta.json present (742 B), exit 0,
  `gitnexus list` shows the repo.

Rollback

Strictly additive — the success path is unchanged when `meta.json` is
written and the registry is updated. Reverting the four-file diff is
safe; the previous silent-finalize behaviour returns. No persisted
schema or registry shape changes.

DoD

- [x] Runtime wiring is complete on the affected CLI path.
- [x] Requested behavior is correct and existing contracts are preserved.
- [x] Smallest correct solution — one invariant, one helper, two
      handlers; no speculative abstraction.
- [x] Tests prove the changed behavior at unit AND integration level.
- [x] Required validation for `gitnexus/` was run.
- [x] Repo boundaries respected; no language-specific code, no shared
      ingestion changes, no new injection surfaces.
- [x] Diff contains only the intended change — no unrelated churn.

Made-with: Cursor

* fix(cli): enforce analyze finalization on fast path (#1169)

Address PR review feedback by checking finalization even when analyze reports already up to date, and by making the #1169 E2E guard fail on timeout instead of passing silently.

Made-with: Cursor

* test(cli): fix #1169 regression coverage on CI

Normalize macOS temp paths in the registry assertion and update the analyze worker timeout test mock for the new finalization invariant exports.

Made-with: Cursor
2026-05-03 18:36:45 +08:00
..
call-routing feat(ingestion): language-agnostic heritage extractor with config+factory pattern (#890) 2026-04-17 17:51:17 +01:00
group fix(deps): upgrade @ladybugdb/core to 0.16.0 to resolve native segfaults (#1235) 2026-04-30 17:40:39 +01:00
import-resolution feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
mcp feat: cross-repo impact analysis (#794) — @repo MCP routing + group resources (#984) 2026-04-20 11:55:07 +01:00
model feat(shared): add scope-resolution types + constants (#910, RFC #909 Ring 1) (#949) 2026-04-18 12:55:09 +01:00
named-bindings refactor: SICP-informed LanguageProvider architecture (#488) 2026-03-24 13:42:39 +00:00
scope-resolution fix(go): handle chan T return types and tighten GOPATH suffix resolution 2026-05-01 23:08:20 +08:00
shadow chore(shared): apply Ring 2 SHARED review follow-ups in one diff (#964) 2026-04-18 18:40:29 +01:00
ai-context.test.ts fix(cli): only match <!-- gitnexus:* --> markers at section position (#1041) (#1042) 2026-04-23 07:58:07 +01:00
analyze-api.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
analyze-job.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
analyze-worker-timeout.test.ts fix(cli): surface silent finalize-skips so analyze cannot exit 0 without persisting (#1169) (#1237) 2026-05-03 18:36:45 +08:00
api-graph-streaming.test.ts [codex] fix large repository graph loading (#732) 2026-04-09 17:40:24 +01:00
ast-cache.test.ts fix: guard createASTCache against zero maxSize to prevent LRU cache crash 2026-03-02 08:47:20 +00:00
ast-utils.test.ts feat(embeddings): AST-aware chunking with offset-based splitting (#889) 2026-04-16 22:55:04 +01:00
binding-accumulator.test.ts refactor(pipeline): DAG-based phase architecture + container-logic extraction to LanguageProvider (#809) 2026-04-13 20:31:05 +01:00
bm25-search.test.ts fix(search): create FTS indexes during analyze (#1107) 2026-04-27 11:00:32 +01:00
call-attribution-issue-1166.test.ts fix(ts): attribute calls inside HOF/callback patterns to the right function 2026-04-29 05:33:40 +05:30
call-extraction.test.ts feat(ingestion): language-agnostic call extractor with config+factory pattern (#877) 2026-04-16 11:45:30 +01:00
call-form.test.ts Extract registries into model/ module with SemanticModel interface (#786) 2026-04-12 01:06:55 +01:00
call-processor.test.ts feat(ingestion): TypeScript registry-primary scope resolution (Ring 3) (#1050) 2026-04-26 08:23:08 +01:00
calltool-dispatch.test.ts fix(hook): resolve canonical repo root + guard read-only FTS ensure (#1226) 2026-04-30 18:12:03 +01:00
chunker.test.ts feat(embeddings): structural chunking with data-driven CHUNKING_RULES dispatch (#987) 2026-04-20 08:25:31 +01:00
cli-commands.test.ts fix(swift): use official prebuilt parser runtime (#1130) 2026-04-28 09:57:42 +01:00
cli-index-help.test.ts fix: expose detect-changes in direct CLI (#892) 2026-04-20 17:12:25 +01:00
cobol-copy-expander.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
cobol-preprocessor.test.ts feat: configure eslint with unused import removal (#564) 2026-03-28 15:28:09 +00:00
cohesion-consistency.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
community-processor.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
compatible-stdio-transport.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
cors.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
cross-file-impl.test.ts refactor(pipeline): DAG-based phase architecture + container-logic extraction to LanguageProvider (#809) 2026-04-13 20:31:05 +01:00
cross-file.test.ts refactor(pipeline): DAG-based phase architecture + container-logic extraction to LanguageProvider (#809) 2026-04-13 20:31:05 +01:00
csv-escaping.test.ts refactor: migrate from KuzuDB to LadybugDB v0.15 (#275) 2026-03-15 15:53:01 +00:00
dart-import-resolver.test.ts refactor(ingestion): split ImportSemantics into per-strategy hooks (Strategies 1-4) (#886) 2026-04-16 19:31:44 +01:00
dart-type-extractor.test.ts feat: configure eslint with unused import removal (#564) 2026-03-28 15:28:09 +00:00
embedder.test.ts test: add test suite with vitest (unit + integration + fixtures) 2026-03-01 20:07:02 +05:30
embedding-chunking.test.ts feat(embeddings): structural chunking with data-driven CHUNKING_RULES dispatch (#987) 2026-04-20 08:25:31 +01:00
embedding-config.test.ts fix: add platform-aware semantic fallback (#1150) 2026-04-28 12:21:25 +01:00
embedding-pipeline.test.ts fix: add platform-aware semantic fallback (#1150) 2026-04-28 12:21:25 +01:00
entry-point-scoring.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
eval-formatters.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
exact-search.test.ts fix: add platform-aware semantic fallback (#1150) 2026-04-28 12:21:25 +01:00
expo-routes.test.ts feat: add Expo Router file-based route detection (#503) 2026-03-25 11:05:55 +00:00
extract-element-type-from-string.test.ts feat: Phase 6 type resolution — for-loop Tier 1c, pattern matching, container descriptors, 10-language coverage (#318) 2026-03-17 17:10:22 +00:00
extract-generic-type-args.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
fetch-reason-parsing.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
field-extraction.test.ts Extract registries into model/ module with SemanticModel interface (#786) 2026-04-12 01:06:55 +01:00
framework-detection.test.ts fix: detect React component paths before lowercasing (#260) 2026-04-19 07:10:36 +01:00
git-clone.test.ts Fix security issues and critical bugs found in code review (#709) 2026-04-10 05:20:29 +01:00
git-utils.test.ts feat(cli): Fingerprint indexed repos by remote URL to detect sibling-clone graph drift (#982) 2026-04-21 21:58:54 +01:00
git.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
graph.test.ts feat(python): scope-based call resolution + registry-primary flip + perf + generalization (RFC #909 Ring 3) (#980) 2026-04-21 15:50:00 +01:00
group-service-not-found.test.ts fix(group): surface friendly error when group name not found (#903 regression test) (#989) 2026-04-21 15:52:36 +01:00
has-method.test.ts feat: MethodExtractor configs for Python, PHP, Swift, Dart, Rust, Ruby (#624) 2026-04-03 16:11:31 +01:00
heritage-extraction.test.ts feat(ingestion): language-agnostic heritage extractor with config+factory pattern (#890) 2026-04-17 17:51:17 +01:00
heritage-map.test.ts Extract registries into model/ module with SemanticModel interface (#786) 2026-04-12 01:06:55 +01:00
heritage-processor.test.ts Extract registries into model/ module with SemanticModel interface (#786) 2026-04-12 01:06:55 +01:00
hooks.test.ts fix(hook): resolve canonical repo root + guard read-only FTS ensure (#1226) 2026-04-30 18:12:03 +01:00
http-embedder.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
hybrid-search.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
ignore-service.test.ts test(ignore-service): skip EACCES test under uid=0 (root bypasses chmod) (#1108) 2026-04-27 11:06:16 +01:00
impact-batching-grouping.test.ts feat(group): add sync pipeline, CLI, MCP tools, and monorepo fixture 2026-04-02 00:40:31 +03:00
impact-confidence.test.ts feat: METHOD_IMPLEMENTS edges, overload disambiguation, MethodExtractor unification (#574) (#642) 2026-04-04 18:41:47 +01:00
import-processor.test.ts Extract registries into model/ module with SemanticModel interface (#786) 2026-04-12 01:06:55 +01:00
import-resolver-factory.test.ts fix(python): avoid local matches for external dotted imports (#899) 2026-04-17 11:35:59 +01:00
index-repo-command.test.ts feat(cli): Fingerprint indexed repos by remote URL to detect sibling-clone graph drift (#982) 2026-04-21 21:58:54 +01:00
ingestion-utils.test.ts fix(ingestion): two-channel binding lifecycle (closes #1066) + scope-resolution I8 hardening (#1082) 2026-04-26 12:16:09 +01:00
isWriteQuery.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
jcl-parser.test.ts feat: configure eslint with unused import removal (#564) 2026-03-28 15:28:09 +00:00
language-skip.test.ts fix(swift): use official prebuilt parser runtime (#1130) 2026-04-28 09:57:42 +01:00
lazy-action.test.ts Improve MCP startup compatibility and lazy-load CLI commands (#207) 2026-03-07 07:47:09 +00:00
lbug-embedding-hashes.test.ts feat(embeddings): AST-aware chunking with offset-based splitting (#889) 2026-04-16 22:55:04 +01:00
lbug-extension-loader.test.ts fix(deps): upgrade @ladybugdb/core to 0.16.0 to resolve native segfaults (#1235) 2026-04-30 17:40:39 +01:00
lbug-readonly-error.test.ts fix(hook): resolve canonical repo root + guard read-only FTS ensure (#1226) 2026-04-30 18:12:03 +01:00
local-backend-maxbuffer.test.ts fix: ENOBUFS in detect_changes by setting maxBuffer on git/rg execFileSync (#957) 2026-04-18 15:58:31 +01:00
max-file-size.test.ts feat(ingestion): make large-file skip threshold configurable (#1044) 2026-04-23 11:07:37 +01:00
method-extraction.test.ts fix(swift): use official prebuilt parser runtime (#1130) 2026-04-28 09:57:42 +01:00
method-props.test.ts feat: same-arity overload disambiguation via type-hash suffix (#651) (#658) 2026-04-05 21:51:55 +01:00
mro-processor.test.ts feat(python): scope-based call resolution + registry-primary flip + perf + generalization (RFC #909 Ring 3) (#980) 2026-04-21 15:50:00 +01:00
noise-filter.test.ts refactor: split global BUILT_IN_NAMES into per-language provider fields (#523) 2026-03-26 12:15:29 +00:00
parse-diff-hunks.test.ts fix: map diff hunks to symbol line ranges in detect_changes (#779) 2026-04-11 11:29:52 +01:00
parse-impl-fallback.test.ts refactor(pipeline): DAG-based phase architecture + container-logic extraction to LanguageProvider (#809) 2026-04-13 20:31:05 +01:00
parser-loader.test.ts fix(swift): use official prebuilt parser runtime (#1130) 2026-04-28 09:57:42 +01:00
parsing-worker-fallback.test.ts fix: recover worker parse stalls (#1121) 2026-04-27 20:07:03 +01:00
phase-timer.test.ts feat(search): per-phase timing instrumentation for the query pipeline (#953) 2026-04-18 16:30:07 +01:00
pipeline-exports.test.ts test: add test suite with vitest (unit + integration + fixtures) 2026-03-01 20:07:02 +05:30
pipeline-runner.test.ts refactor(pipeline): DAG-based phase architecture + container-logic extraction to LanguageProvider (#809) 2026-04-13 20:31:05 +01:00
platform-capabilities.test.ts fix: add platform-aware semantic fallback (#1150) 2026-04-28 12:21:25 +01:00
process-processor.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
receiver-extraction.test.ts Fix HTTP client vs Express route detection and Spring interface attribution (#780) 2026-04-11 11:24:47 +01:00
registry-primary-flag.test.ts feat(go): promote Go to MIGRATED_LANGUAGES 2026-05-02 00:00:06 +08:00
rel-csv-split.test.ts test(gitnexus): stabilize rel-csv-split stream teardown on Windows (expect.poll) (#1052) 2026-04-23 20:11:54 +01:00
repo-manager-finalize-invariant.test.ts fix(cli): surface silent finalize-skips so analyze cannot exit 0 without persisting (#1169) (#1237) 2026-05-03 18:36:45 +08:00
repo-manager.test.ts feat(cli): gitnexus remove <target> to unindex a registered repo by name or path (#664) (#1003) 2026-04-21 11:52:59 +01:00
resolve-enclosing-owner.test.ts feat(ingestion): language-agnostic heritage extractor with config+factory pattern (#890) 2026-04-17 17:51:17 +01:00
resources.test.ts feat: cross-repo impact analysis (#794) — @repo MCP routing + group resources (#984) 2026-04-20 11:55:07 +01:00
route-tool-detection.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
ruby-self-call.test.ts feat(ingestion): language-agnostic heritage extractor with config+factory pattern (#890) 2026-04-17 17:51:17 +01:00
run-analyze.test.ts feat(analyze): preserve existing embeddings by default; --force regenerates them; add --drop-embeddings opt-out (CLI + HTTP API) (#1055) 2026-04-24 13:07:40 +01:00
schema.test.ts feat(ingestion): language-agnostic variable extractor with config+factory pattern (#878) 2026-04-16 13:57:25 +01:00
security.test.ts feat: METHOD_IMPLEMENTS edges, overload disambiguation, MethodExtractor unification (#574) (#642) 2026-04-04 18:41:47 +01:00
semantic-chunk-search.test.ts feat(embeddings): AST-aware chunking with offset-based splitting (#889) 2026-04-16 22:55:04 +01:00
sequential-language-availability.test.ts fix(ingestion): Log skipped sequential parser languages (#1021) 2026-04-23 08:50:38 +01:00
server.test.ts feat: configure eslint with unused import removal (#564) 2026-03-28 15:28:09 +00:00
setup-codex.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
setup-jsonc.test.ts refactor(setup): migrate all config I/O to mergeJsoncFile (#1031) 2026-04-24 07:33:35 +01:00
setup.test.ts refactor(setup): migrate all config I/O to mergeJsoncFile (#1031) 2026-04-24 07:33:35 +01:00
shape-check.test.ts fix: shape_check false positives — quoted keys, DOM leaks, errorKeys (#501) 2026-03-26 05:43:37 +00:00
shared-type-extractors.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
sibling-clone-drift.test.ts feat(cli): Fingerprint indexed repos by remote URL to detect sibling-clone graph drift (#982) 2026-04-21 21:58:54 +01:00
skill-gen.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
skip-git-cli.test.ts feat: added skip-agents-md cli flag (#517) 2026-03-28 21:23:59 +00:00
staleness.test.ts feat(group): add group infrastructure and contract matching 2026-04-02 00:39:43 +03:00
stdout-silence.test.ts fix(mcp): unify stdout silencing to prevent embedder/pool-adapter conflicts (#645) 2026-04-04 11:56:49 +01:00
structure-processor.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
suffix-index-ambiguity.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
symbol-resolver.test.ts refactor(pipeline): DAG-based phase architecture + container-logic extraction to LanguageProvider (#809) 2026-04-13 20:31:05 +01:00
symbol-table.test.ts feat(ingestion): language-agnostic heritage extractor with config+factory pattern (#890) 2026-04-17 17:51:17 +01:00
text-generator.test.ts feat(embeddings): structural chunking with data-driven CHUNKING_RULES dispatch (#987) 2026-04-20 08:25:31 +01:00
tool-direct-cli.test.ts fix: expose detect-changes in direct CLI (#892) 2026-04-20 17:12:25 +01:00
tool-process-linking.test.ts fix(mcp): project tool_map flows from handlers (#1113) 2026-04-27 17:13:02 +01:00
tools.test.ts feat: cross-repo impact analysis (#794) — @repo MCP routing + group resources (#984) 2026-04-20 11:55:07 +01:00
topological-sort.test.ts refactor(pipeline): DAG-based phase architecture + container-logic extraction to LanguageProvider (#809) 2026-04-13 20:31:05 +01:00
transitive-include-closure.test.ts fix: resolve C/C++ cross-file calls through transitive #include chains (#816) 2026-04-14 09:39:17 +01:00
tree-sitter-queries.test.ts feat(ingestion): language-agnostic variable extractor with config+factory pattern (#878) 2026-04-16 13:57:25 +01:00
type-env.test.ts fix(swift): use official prebuilt parser runtime (#1130) 2026-04-28 09:57:42 +01:00
utils.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
variable-extraction.test.ts feat(ingestion): language-agnostic variable extractor with config+factory pattern (#878) 2026-04-16 13:57:25 +01:00
vue-sfc-extractor.test.ts feat(vue): Vue SFC support + destructured call result tracking (#604) 2026-04-03 14:18:55 +05:30
web-ui-serving.test.ts fix(serve): serve web UI at root path instead of 404 (#1048) 2026-04-27 13:17:40 +01:00
wiki-flags.test.ts feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
wiki-llm-client.test.ts fix(wiki): Azure OpenAI compat and HTML viewer script injection (#618) 2026-04-01 21:30:43 +05:30
wildcard-synthesis.test.ts refactor(pipeline): DAG-based phase architecture + container-logic extraction to LanguageProvider (#809) 2026-04-13 20:31:05 +01:00
worker-pool-options.test.ts fix: recover worker parse stalls (#1121) 2026-04-27 20:07:03 +01:00