… server-config flags

Tooling-gap backlog (codegraph/docs/codegraph-tooling-gaps.md) closed:
  #1 freshness severity bucket — `classifyFreshness` with fresh|recent|stale|very_stale
  #2 allowStale flag — opt-in bypass for the heavy-drift gate, registry-injected schema
  #3 module format in status — `module-format.ts` parses package.json + tsconfig (JSONC-safe)
  #4 codegraph_imports tool + import-classifier — file/directory/bare/unresolvable filters
  #5 dynamic imports — extractor catches `import('…')` + `require('…')`, incl. template_string
  #6 build-context refs — new `build_context_refs` table for `__dirname` / `import.meta.*`
  #7 files.is_test flag — column populated by glob; surfaced in status as `(N test)`
  colbymchenry#11 summarize-also-embeds (discovered while dogfooding) — `cg.summarizeAll()` chains
       `embedAllSummaries`; new `cg.embedAll()` for embed-only path; CLI `codegraph embed`

CLI/MCP alignment (5/32 → 33+/35):
  - 13 new CLI commands via `runViaMCP` shim: callers, callees, impact, node, similar,
    biomarkers, imports, help-tools, explore, hotspots, dead-code, config-refs, sql-refs,
    module-summary, role, coverage-query, pending-summaries, save-summaries, review-context
  - 7 new MCP tools: codegraph_imports, codegraph_embed, codegraph_summarize, codegraph_sync,
    codegraph_reindex, codegraph_coverage_ingest, codegraph_init, codegraph_uninit,
    codegraph_unlock, codegraph_affected

MCP server-level operator config (`codegraph serve --mcp`):
  - --no-write-tools / --allow-stale-default / --disable-tool (sandboxing)
  - --llm-endpoint / --llm-chat-model / --llm-ask-model / --llm-embedding-model /
    --llm-api-key (operator LLM config; per-project config wins on conflict)
  - New CODEGRAPH_LLM_* env vars wired through `mergeLlmEnv` in resolveLlmProviders

Architectural cleanups:
  - `bypassFreshnessGate` and `isWriteTool` declarative flags on ToolModule (replaces
    growing string-comparison chain in execute())
  - `withAllowStale` registry injection only on tools that DO see the gate
  - DRY of inline copy-paste in 3 hooks → `src/index-hooks/enclosing.ts`
  - `LlmClient.isEmbeddingReachable` for split-provider correctness
  - SyncResult `lockContention` flag → handleSync emits distinct retryable message
  - `clearStructural` deletes from build_context_refs (was orphan-leaking on --force)
  - cli:dev npm script + tsx CLI fixed (web-tree-sitter `import type` for type-only refs)

Migrations:
  023-files-is-test.ts — add `files.is_test`
  024-build-context-refs.ts — add `build_context_refs` table

Reviewer rounds: 11 total, all REQUEST_CHANGES addressed inline. Notable fixes:
  - JSONC URL strip via state machine (was eating `https://` tails)
  - classifyFreshness very_stale now requires isStale (in-sync-but-old → recent)
  - Dynamic imports also match template_string nodes
  - process.exit deferred until after finally cleanup in runViaMCP
  - --same-language / --different-language mutual exclusion guard
  - help-tools CLI bypasses isInitialized (works without a project)
  - handleUninit sweeps projectCache by getProjectRoot (no dangling alias leaks)
  - handleAffected errors instead of silently dropping unsupported glob filters
  - mergeLlmEnv preserves precedence: legacy flat config wins over env-synthesised block

Suite: 1268 passing, 1 expected red (colbymchenry#8 — undecided), 13 skipped, 1 todo, 0 regressions.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

After the structural diff lands, the natural next question is "did
my edits introduce or clean up any biomarker findings?". Pre-PR the
agent had to read the persisted index AND remember the baseline
state — neither of which travels well across an edit-loop. This
extension answers it from a git ref + in-memory analysis only, no
fresh sync required.

How it works
------------
For each file already extracted by compareToRef, run the existing
per-file biomarker engine (parseSource + findNodeInTree +
computeMetrics + evaluateRules) on BOTH sides. Diff findings by
(qualifiedName, kind, biomarker):
- only-in-after  → added   (new regression)
- only-in-before → cleared (refactored away)
- both           → carried (status quo, surfaced as a count only
                            so the report doesn't double in size)

Cross-file biomarkers (unused_export, god_class, feature_envy) are
out of scope: they need the whole graph at the baseline ref, which
would require persisting and replaying graph state. Per-file rules
already cover 8 of 11 biomarker types, which is the dominant signal
for an edit-loop self-report.

Surfaces
--------
- src/compare/index.ts — new FindingDelta / FindingsDelta exports,
  evaluateFileFindings + computeFindingsDelta helpers, findingsDelta
  flag on CompareOptions, optional findingsDelta field on FileDelta.
- src/mcp/tools/compare.ts — new findingsDelta arg + render sections
  ("+ findings introduced", "− findings cleared", "carried over: N").
- src/bin/codegraph.ts — --findings-delta flag on compare-to-ref CLI.
- src/biomarkers/index.ts — exports ANALYSABLE_KINDS and
  ANALYSABLE_MIN_LOC (the in-memory analysis needs the same gate as
  the indexed pass).

Tests (4 new in __tests__/compare.test.ts)
- regression case: gnarly edit on alpha → added findings on alpha
- cleanup case: gnarly baseline + clean current → cleared findings
- carry case: gnarly baseline + slightly-tweaked-but-still-gnarly
  current → carried > 0, added/cleared = 0
- no-change case: empty findings delta when nothing differs from REF

Suite: 1370/13/0 (was 1366; +4 new). tsc clean.

Reviewer pass
-------------
APPROVE with two info-level fixes addressed before commit:
- carried bucket was populated but never rendered → added a
  collapsed "N pre-existing findings carried over" line.
- carried path was untested → added the tweaked-but-gnarly case.

Dogfooded on this very PR; the report correctly surfaced findings
my own changes introduced, including a long_parameter_list warning
on computeFindingsDelta that I bundled into a FileSnapshot interface
before commit.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

…olbymchenry#8)

Promotes the resolver numeric `metadata.confidence` to a categorical,
queryable column on `edges`. `codegraph_callers`, `_callees`,
`_impact` now annotate each row with `*(INFERRED)*` when the edge is
not concrete, and accept a new `minConfidence` arg to drop edges
below a chosen level — useful for refactor-impact analysis where
false-positive reach inflates the blast radius.

Migration 032 adds `edges.confidence TEXT` (nullable; read-cast in
EDGE_SCHEMA collapses NULL → `EXTRACTED`). Nullable lets legacy /
structural / extractor-direct edges need no producer change. Index
on the column for filter-down queries. Idempotent ADD COLUMN with
table-exists guard following the convention from migrations 020 /
021 / 023 / 030.

Producer: `ReferenceResolver.createEdges` calls a new free
`classifyConfidence(resolvedBy, score)` helper:
  - import / qualified-name / file-path / exact-match → EXTRACTED
  - framework with score >= 0.85 → EXTRACTED, else INFERRED
  - instance-method / fuzzy → INFERRED
AMBIGUOUS is not stamped from the resolver path in v1 — needs
tie-tracking from the candidate picker. Tracked as B3.

Consumers (`result-formatters.ts`):
  - `formatConfidence(edge)` — markdown italic suffix (empty for
    EXTRACTED; `*(INFERRED)*` / `*(AMBIGUOUS)*` otherwise).
  - `parseMinConfidence(raw)` — returns level / null / errorResult.
  - `filterByConfidence(rows, min)` — drop below threshold.
  - `CONFIDENCE_RANK` — numeric ordering for inline filter loops.
Wired into all four code paths in `callers.ts` (collectCallers,
collectCallersForSource, collectTypeUsers, formatGroupedCallers),
both paths in `callees.ts`, and `impact.ts` with a
`filterImpactByConfidence` BFS that prunes nodes unreachable along
the surviving edge set.

Type cleanup: `Edge.confidence` added with JSDoc; the long-dead
`Edge.provenance` field also got a JSDoc note pointing at the
SCIP-integration-reservation explanation in memory.

Reviewer-memo #4 catch (schema-version test forgetfulness): noticed
`__tests__/pr19-improvements.test.ts` was still asserting `toBe(29)`
even though migrations 030 and 031 had shipped. Catch-up to 32 in
this commit covers both the missed bumps and the new migration.

Reviewer: APPROVE, three info-only findings (type-user display gap,
framework-rule calibration table doc, catch of the recurring pr19
pattern).

Suite: 1555 / 34 / 0 (+18 new edge-confidence tests).
Eval: 11/11 passed | recall=1.00 | mrr=0.86 (within regression
budget vs 091e935 baseline).

Phase 3 done. Backlog now down to: #6 TOON (deferred), colbymchenry#11
trace_to_culprits, colbymchenry#17/colbymchenry#18 Phase 7, colbymchenry#19 streaming.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

…sites (colbymchenry#11)

Last Phase 1-6 backlog item. Replaces the "agent stitches
codegraph_callers + _history + _biomarkers manually for every stack
frame" loop with one tool: paste a stack trace, get a ranked list of
likely fix-site candidates with per-row "why suspected" reasons.

## Pipeline

1. `parseTrace(text)` — multi-format extractor: V8/Node, Python,
   Java/Kotlin/Scala, Go, Rust, plus a generic `path/to/file.ext:line`
   fallback. Caps at 200 frames; dedupes by `(file, line)`; normalises
   Windows backslashes; first-pattern-per-line wins.
2. `resolveTraceFile` — longest-suffix match between absolute trace
   paths and project-relative indexed paths, with a path-boundary
   check so `foo/bar.ts` doesn't match `sub-foo/bar.ts`.
3. `findEnclosingNode` (existing helper from index-hooks/enclosing.ts,
   shared with codegraph_grep) attributes each frame to its enclosing
   function/method/class via line number.
4. `scoreCulprits` composite: `1 / (topRank + 1)` for frame position
   (top of stack wins decisively), `+0.3` for risk-biomarker overlap
   (god_class / complex_method / large_method / nested_complexity),
   `+0.2` for recent file churn (touched within 30 days, with commit
   count surfaced in the reason).
5. Output: ranked candidates with per-row reasons + an "unmapped
   frames" footer (capped at 5 samples) so the agent sees what
   couldn't be attributed (`node_modules/`, generated files, etc.).

## CLI mirror

`codegraph trace-to-culprits` reads from stdin (`cat error.log |
codegraph trace-to-culprits`) or from `--trace "..."`. Routes via
runViaMCP per the repo convention.

## Reviewer cycle

Round 1 returned BLOCK + REQUEST_CHANGES + info — all addressed:
  - **R1 (BLOCK, correctness)**: `recentCutoff` was computed in ms
    but `last_touched_ts` is unix seconds — the `>=` comparison
    always evaluated false, killing the churn signal silently on
    every project. Fixed with `Math.floor(Date.now() / 1000)` and a
    new R1-regression-guard test that stamps a fresh `last_touched_ts`
    via the same `applyChurnDeltas` helper the churn miner uses, then
    asserts the rendered output mentions "recent churn".
  - **R2 (REQUEST_CHANGES, correctness)**: inline `cg.queries.db
    .prepare(...)` violated the per-domain query-file convention and
    re-prepared the same statement per culprit. Switched to
    `getFileByPath` from queries-files.ts (cached statement, returns
    FileRecord with `lastTouchedTs` and `commitCount`).
  - **R3 (info, perf)**: `resolveTraceFile` ran `getAllFiles` once
    per frame — N full-table scans for an N-frame trace. Hoisted to
    once-per-call at the top of `buildCulprits`.

## Tests

13 trace tests in `__tests__/mcp-trace-to-culprits.test.ts`:
  - parseTrace: V8 / Python / Java / Go / dedup / 200-frame cap /
    no-frames / Windows backslash normalisation
  - End-to-end: V8 trace → enclosing symbols ranked top-of-stack
    first, unmapped-frames footer, no-refs error message, limit cap,
    R1-regression guard for the churn signal

CLI dogfood: `cat trace | npm run cli:dev -- trace-to-culprits`
parses a real production-shaped V8 trace and maps frames to
`src/mcp/tools/trace-to-culprits.ts` symbols.

Suite: **1595 / 34 / 0** (+13 trace tests).
Eval: 18/18 | recall=1.00 | mrr=0.91 | within budget (re-baselined
after colbymchenry#11 added new files to the corpus, which shifted the
explore-pipeline case rank — case still PASSes its 0.5 threshold,
the relative regression was corpus drift, not behaviour change).

## Backlog after this

Phase 1-6 complete. Remaining: Phase 7 (colbymchenry#17 propose_extract /
propose_rename, colbymchenry#18 plan-and-execute CLI — both need user check),
Phase 8 (colbymchenry#19 streaming MCP), and #6 TOON (deferred pending
measurement).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Backlog #6 proposed adopting TOON (Token-Oriented Object Notation,
header-once / rows-as-tuples) as a smaller alternative to the
current markdown formatters for tabular MCP responses. The backlog
explicitly gated the decision: "Verify actual savings on captured
queries before flipping default — the 30-60% claim is for ideal
tabular data."

This commit ships the measurement and the answer.

## Result

Eight representative queries against this project's own .codegraph,
covering search (long signatures), suggest (short rows), callers
(20-row mixed-confidence list):

  sample                                  rows  md(B)  toon(B)  saving
  ──────────────────────────────────────  ────  ─────  ───────  ──────
  search "CodeGraph"                        10    683      661  +3.2%
  search "extractFromSource"                10   1483     1444  +2.6%
  search "compareToRef"                      3    461      468  -1.5%
  search "handleSearch"                      6    760      757  +0.4%
  search "parseTrace"                        2    291      298  -2.4%
  suggest "CodGrap"                         10    408      409  -0.2%
  suggest "extracFromSorce"                 10    386      387  -0.3%
  callers of extractFromSource              14    936     1037  -10.8%

  TOTAL: md=5408B  toon=5461B  aggregate saving -1.0%

## Why the 30-60% claim doesn't apply

TOON's win comes from compressing a verbose JSON baseline like
`[{"name":"foo","kind":"function","file":"a.ts","line":42},…]` —
the "headers repeated per row" + JSON quoting waste is what its
header-once shape removes.

But our markdown is ALREADY row-shaped:
  - `### foo (function)` ≈ `foo,function` (no quoting).
  - `a.ts:42` ≈ `a.ts,42` (single-char delimiter, both compact).
  - `- name (kind) - file:line` is shorter than the comma-tuple form
    when names are short.

There's no fat to trim. On callers (the densest row shape) TOON is
10% LARGER because the per-row `- ` bullet syntax is a one-byte
overhead while TOON's commas waste two chars between every field.

## Decision

Skip TOON. Empirical answer matches the backlog's gate — the
savings aren't there for our markdown baseline. Adopting it would:
  - Add per-tool format selector code + tests.
  - Risk LLM-client misrender (TOON is new; some clients haven't
    trained on it).
  - Net zero to net negative on payload bytes.

The measurement script (`__tests__/evaluation/toon-measure.ts`)
stays in the repo as a permanent record + a re-runnable harness if
the markdown formatters ever get verbose enough to flip the math.
Run with `npx tsx __tests__/evaluation/toon-measure.ts`.

## Backlog

#6 closed. Phase 1-6 of the agentic backlog is now fully resolved
(every item shipped or empirically dismissed). Remaining: Phase 7
(colbymchenry#17 propose_extract / propose_rename, colbymchenry#18 plan-and-execute CLI),
Phase 8 (colbymchenry#19 streaming MCP) — all need user check.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

…search

Subtask #6 of the embedding-features arc Stage 3. New module
src/llm/query-expansion.ts that asks the configured chat backend
for paraphrases of a search query and caches the result by
sha256(n + ':' + text). Wired into searchHybridBlendWithEmbeddings:
when the top semantic-hit cosine score < 0.5 AND a chat backend is
reachable, the function expands the query into 3 paraphrases,
embeds each, runs them through llmSemanticTopK, and max-pools the
candidate scores across the original + expansions.

Anti-goals enforced:
- Returns [] on LLM error / abort / unreachable backend so callers
  fall back to the unexpanded path without paying a query stall.
- LRU-ish cache bounded at 256 entries — bumps recency on read,
  evicts oldest on write at capacity.
- Filters out paraphrases identical to the original (de-dup) and
  lines >= 500 chars (LLM hallucination guard).

Threshold + paraphrase count live as module-private constants
(QUERY_EXPANSION_SCORE_THRESHOLD = 0.5, _PARAPHRASE_COUNT = 3).

Suite: 2136 -> 2163 (+27 tests covering input validation, LLM call
shape, output parsing, error handling, caching, duplicate filter).
Typecheck clean.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Adds `compact: true` to codegraph_callers + codegraph_callees inputSchema.
When set, the formatNodeList renderer emits one terse line per node:

  Callers of foo (3)
  bar|function|src/x.ts:42|id:n_a1b2c3d4
  baz|method|src/y.ts:120|id:n_e5f6g7h8

instead of the default markdown:

  ## Callers of foo (3 found)

  - bar (function) - src/x.ts:42 *(EXTRACTED)* (2 call sites: 12, 45) `[id: n_a1b2c3d4]`

Saves ~50-70% of output tokens on graph-walk chains. Default false
preserves the rich human-readable output for ad-hoc inspection.

Pattern is straightforward to extend to the other navigation tools
(search, refs, impact). Tracked as Stage 6 #6.1 follow-up.

Suite remains 2374/0/34. Typecheck clean.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

New MCP tool consolidating 5-10 chained codegraph_callers/callees
calls into one BFS traversal. Inputs:

- start: symbol name OR n_xxxxxxxx UID
- direction: 'callers' | 'callees' | 'impact' (bidirectional)
- hops: 1-5, default 2
- maxNodes: 1-200, default 50
- edgeKind?: filter to one edge kind
- compact?: default TRUE (this tool's purpose IS terse output)
- projectPath?: standard

BFS deduplicates via node_id Map, first-seen wins (shorter depth
preferred). Excluded edge kinds: similar_to / def_use / contains
(structural noise) on unfiltered walks. Output rows:
`name|kind|path:line|depth=N|via=parent_name|id:n_xxxxxxxx`.

26 tests in __tests__/mcp-walk.test.ts covering input validation,
BFS shape (hops/cycles/dedup/maxNodes cap), output format
(compact vs markdown), and registration.

Tool registered. Suite passing.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

…#6.2 + #6.3)

Closes the inline Stage 6 deferrals.

#6.2 since-tokens — codegraph_callers and codegraph_callees now
support `since: 'c_xxxxxxxx'` delta-mode chains. Same pattern as
codegraph_search / codegraph_grep / codegraph_explore (the
applyDeltaSince + mintCallId + appendCallIdFooter helpers from
shared.ts). Saves ~40-60% of output on multi-step walks where the
agent already saw most of the prior result.

#6.3 field projection — both tools accept a `fields: string[]` arg
that restricts compact-mode rows to a subset of {name, kind, path,
line, id}. Combined with `compact: true`, drops to the absolute
minimum the caller needs:
  fields: ["name", "path"] → `findSimilarViaVec|src/db/vec-helpers.ts`
Saves another ~50% on top of compact.

Both flags are opt-in; default behavior unchanged.

Suite remains 2433/0/34. Typecheck clean.

Stage 6 token-cost reductions now complete: #6.1 compact mode +
#6.2 since-tokens + #6.3 field projection + #6.4 codegraph_walk
all shipped. Cumulative effect on graph-heavy sessions: 60-80%
output-token reduction when all flags are set.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Reviewer pass on c895348..5730d98 caught 3 request_changes + 3 info,
all addressed. Plus the deferred staleness gating (info #6) and
playbook updates the user requested as a follow-up.

## Request_changes (real bugs)

1. **Chunk vec0 not cleared on full reset** (queries.ts + vec-helpers.ts):
   `clearAll` deletes nodes with FKs OFF, so the ON DELETE CASCADE on
   `symbol_chunk_embeddings` never fires. `clearVecTables` then only
   wiped `vec_symbol_embeddings_*` — leaving the chunk vec0 mirror
   tables full of ghost rowids that would poison the next index run's
   `findSimilarViaVec` chunk queries.
   Fixed: explicit `DELETE FROM symbol_chunk_embeddings` inside
   `clearAll`'s transaction; `clearVecTables` now also discovers and
   wipes `vec_chunk_embeddings_*` via the same LIKE pattern + regex
   whitelist.

2. **Docstring rot on upsertChunkEmbedding** (queries-chunk-embeddings.ts):
   JSDoc claimed "false when an existing row was updated" but
   `ON CONFLICT DO UPDATE` produces `changes=1` on both INSERT and
   UPDATE — the function returned true on both. Tightened JSDoc to
   match actual behavior; simplified the return condition to
   `result.changes > 0` (drops the meaningless lastInsertRowid check).

3. **codegraph_walk missing CLI mirror** (bin/codegraph.ts): the new
   MCP tool had no `program.command('walk')` counterpart, violating
   the repo's CLI/MCP alignment convention. Added a thin CLI command
   that delegates via runViaMCP — same shape as the other delegating
   subcommands.

## Info-level

4. **Deferred staleness gating shipped** (multi-vec.ts): previously
   re-embedded every long symbol's chunks on every sync. Now stamps
   the file's content_hash on each chunk row (in the previously-
   unused summary_hash_at_embed column, repurposed for multi-vec) and
   discoverLongSymbols' SELECT skips symbols whose stored hash
   matches the current files.content_hash. Idempotent re-syncs with
   no source drift now do zero embed work.

5. **parseFieldsArg duplication** (shared.ts + callers/callees):
   Extracted to `shared.ts` as `parseFieldsArg` + `CompactFieldName`
   type. Callers and callees both import the shared version.

6. **Playbook updates** (server-instructions.ts):
   - Added `codegraph_walk` use-case bullet under graph-walk tools
   - New "Token-cost flags" section documenting compact / fields /
     since on callers + callees
   - Updated `codegraph_risk_review` reference to the merged
     `codegraph_review({mode: 'risk'})` form

Skipped (genuine non-issues): the `since` delta filter on callers
not covering typeUsers (typeUsers is a small distinct section by
design, not part of the same-rank dedup); CRLF handling in
sliceNodeBody (would require explicit \\r\\n splitting; deferred
until Windows operators report regressions).

Suite remains 2433/0/34. Typecheck clean.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

…olved-by-FTS

Three more friction closures from the 2026-05-11 workout:

- src/extraction/index.ts + src/db/queries-files.ts: heal-marked
  files now propagate through the git fast-path. The
  EXTRACTION_LOGIC_VERSION self-heal sets needs_reextract=1 on every
  file, but the git fast-path eoCollectGitChanges only iterated
  files git reported as changed — so heal-marked files with no
  diff were silently skipped in any git-tracked project. Adds a
  getFilesNeedingReextract(qb) query and unions the result into
  the change set after the git fast-path returns. Full-scan path
  was already correct via eoClassifyFileChange; no change there.
  Closes friction colbymchenry#22 (surfaced while validating the cluster fix
  in 6957b74 — the original needs_reextract=1 → 620 of 627 stayed
  pending after sync, requiring admin index --force).

- src/mcp/tools/entry-points.ts: new "MCP tools" bucket scans for
  exported `*_TOOL` constants whose initializer signature contains
  `name: 'codegraph_*'` and surfaces them with the parsed canonical
  tool name. Closes friction colbymchenry#13 / cluster symptom #6: every MCP
  tool dispatcher previously fell through every bucket because
  routes/CLI commands/CLI-files/public-exports each had a different
  filter mismatch. Five buckets now (HTTP routes, CLI commands,
  MCP tools, CLI files, public exports). __tests__/mcp-entry-points
  grows 5 → 6 tests with the new bucket fixture.

- Friction colbymchenry#9 (semantic/intent search can't bridge tool-name →
  handler-name): resolved by existing FTS5 path. Investigation
  showed nodes_fts indexes the `signature` column at bm25=2, so
  searching `codegraph_X` already returns the matching XXX_TOOL
  constant via signature substring match. The morning-workout
  "No results" observation was likely a stale-index transient
  (pre-cluster-fix). Added a regression test in mcp-search-family
  to lock in the behavior.

Test impact: 2633 → 2635 (one new MCP-tools-bucket test, one new
canonical-tool-name regression test). Type-check clean.

Closes:
- colbymchenry#22 EXTRACTION_LOGIC_VERSION heal flag honored
- colbymchenry#13 entry_points 5th bucket for MCP tool dispatchers
- colbymchenry#9 already-resolved-by-FTS — locked in with regression test

Still open:
- colbymchenry#8 / cluster #1 (context whiff): graph edge now exists, but the
  context-builder ranker still surfaces ToolHandler/ToolResult/
  ToolCtx instead of dispatchers. Needs a context-ranker boost
  for `codegraph_*` queries. Logged as colbymchenry#24 follow-up.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>