feat(mcp): relevance scoring overhaul for explore — kill incidental name-collision matches (CG-10, #1500)

Explore's per-file relevance awarded +50/+10/+3/+1 by match class and admitted
anything scoring >= 3. Neither half held up: the tier said HOW a symbol reached
us, never whether the match was evidence, and an absolute floor admits noise on
any repo where the top file scores 50+. Three scripts/agent-eval/*.mjs harnesses
took 63% of this repo's own "how does explore allocate its output budget" answer
on nothing but an unused `const explore` and a `const BUDGET`.

Four levers:

- KIND WEIGHT (RELEVANCE_KIND_WEIGHT): callables and types 1.0, members ~0.5,
  variable/constant/parameter 0.15-0.35. A weak-kind symbol with no usage edge
  anywhere in the graph (`contains` excluded — nesting is not usage) drops to
  0.08. Only weak kinds in the top two tiers pay for the DB probe; the subgraph's
  own edges answer most cases free. No measurable latency change (210 vs 211
  ms/call, n=12 interleaved).

- PERIPHERAL CAP: nodes >=2 hops from any match accumulate into a bucket capped
  at 5. Uncapped they added a flat +1 each, so a file grew more relevant by being
  bigger — parse-session.mjs reached 22 off one constant plus twelve unrelated
  symbols.

- RANK PENALTY: generated files x0.3, low-value x0.5, applied to the score AND
  the graph mass. Score alone would not have fixed #1500 — the generated CRUD
  carries MORE graph mass than the hand-written use-case, and graph mass outranks
  score in the comparator. Self-normalizing, never a hard exclusion.

- RELATIVE FLOOR: clamp(topScore * 0.2, 1, 10). Capped at one full-strength
  direct match so concentration elsewhere can never exclude one (without it a
  named-seed-heavy file pushed the floor to 21 and dropped a file the agent had
  named by class name). Backfills to 3 candidates when it would leave fewer, and
  drops the evidence requirement rather than return nothing at all.

excludeLowValueFiles was dead config — declared per tier, read nowhere; the
test/spec exclusion has been unconditional for a while. Removed. The real gap was
the detector: `isLowValue` anchored on a leading `/`, so a repo-ROOT `test/` dir
(express, cobra, most of npm and Go) never matched — express's routing question
spent 59% of its envelope on three test files. Anchored at `^` too, and the
filter now runs before the floor and judges "are there other candidates?" on the
whole gather.

Measured before/after on the same indexes (baseline bd86ad2):
- payroll-go fixture: generated 57.4% -> 23.5%; answer 25.6% -> 61.5%; cycle.go
  delivered 0 -> 38.9%. Generated ranks #3/#4, was #1/#2.
- self-query fixture: eval scripts 72% -> 0%; tools.ts ranks #1.
- express "route a request": 59% to test/* -> lib/application.js + lib/response.js
- cobra x3, codegraph "indexing pipeline": byte-identical (control)

Diagnostic gains a per-file penalty multiplier and NodeKind mix, so "why did this
file score X" is legible. Selection stages reordered to match the pipeline.

CG-6's gates flip from it.fails to live regressions except the byte-split ones,
which stay open for CG-12 (allocation still follows file size within the ranked
set).

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

CHANGELOG.md

@@ -17,6 +17,8 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ### Fixes
 
+- `codegraph_explore` no longer spends its answer on files that merely share a word with your question. A file whose only connection to the query was an unused local variable or constant of the same name — an eval script with a `const explore` in it, say — used to count as strongly as the file that actually implements the thing, and being small enough to include whole, it could take most of the response while the real answer got trimmed. Matches are now weighted by what was matched (a function, class or route counts for far more than a local variable, and a variable nothing else references counts for almost nothing), and a file has to score within reach of the best match rather than clear a fixed low bar. Generated files are down-weighted throughout the ranking instead of only breaking ties, so a generated CRUD layer no longer outranks the hand-written workflow beside it. Test and spec files in a top-level `test/` or `spec/` directory are now recognized and kept out, which they weren't before. (#1500)
+
 - A CodeGraph process that gets force-killed — by the stuck-process watchdog, a crash, or the OS — no longer leaves the database's write-ahead log behind to grow without bound. Previously each killed session stacked more data onto the same log file and nothing ever shrank it, which on machines where sessions were killed regularly could quietly eat tens of gigabytes of disk. The log is now capped, and any oversized leftover is reclaimed automatically the next time the project is opened. Thanks @tiendungdev for the exceptional Windows report that pinned this down. (#1431)
 - The background server's watchdog no longer kills a healthy server that is just waiting on a slow disk: like indexing already does, it now checks whether the database files are still making progress before concluding the process is stuck. Fewer spurious kills also means fewer leftover write-ahead logs. (#1431)
 - `codegraph status` now shows the write-ahead log's size next to the database size and warns when killed sessions have left it oversized, and every line in the background server's log now carries a timestamp so kills and restarts can be placed in time. (#1431)