feat(mcp): codegraph_explore as the sole primary tool + store coverage + overload disambiguation (#647)

## Summary

Completes the explore-overhaul arc: `codegraph_explore` becomes the single primary tool an agent reaches for, and its coverage + output shape are tuned so flow/architecture questions resolve with near-zero Read/Grep.

### What changed
- **explore is the sole primary tool** — removed `codegraph_context` (the fuzzy-input Read-trigger) and `codegraph_trace` (under-picked by agents); explore already surfaces the call flow among the symbols you name. A plain natural-language question now works as the query.
- **Store/handler coverage** — functions defined inside object literals (Zustand `create((set, get) => ({ … }))`, Redux/Pinia/MobX, exported handler/route maps) are indexed as real symbols, including calls through `useStore.getState().fn()` and destructured `const { fn } = useStore.getState()`. A general AST rule, not a per-lib hack.
- **Overload disambiguation** — explore leads with the *right* definition when a method name is overloaded across types (a PascalCase type token in the query biases to that type's own def); `codegraph_node` returns *every* overload's body in one call, with an optional `file`/`line` selector to pin one.
- **Method-atomic render** — explore never returns half a method; at the size budget it drops whole methods/files (and lists what it dropped) instead of truncating a body mid-method.
- **Native-read-shaped output** — per-call output is capped to ~24K with a 25K hard ceiling and concentrated into ~150–250-line flow windows, mirroring how the agent natively reads; repo size scales the *call* budget, not the per-call size (a larger response just gets externalized to a file the host Reads back).
- **Blast radius** folded into explore (dependents + covering tests, locations only).

### Benchmark (refreshed on this build)
Re-validated the 7-repo A/B on 2026-06-02 (Opus 4.8, effort=high, median of 4). WITH arm re-measured on this build, WITHOUT reused:

**~16% cheaper · 47% fewer tokens · 22% faster · 58% fewer tool calls** — 0 file reads on 6 of 7 repos (Gin ~1).

The arc trades larger, cache-heavy explore responses for guaranteed near-zero reads, so cost/token margins soften vs the prior build (Excalidraw and Tokio land at cost break-even) while time and tool-calls stay clear wins everywhere — consistent with the project's stated optimization target (latency + tool-calls, not token cost).

### Validation
- Full suite green: **1112 passed, 2 skipped**.
- 28/28 plain WITH runs across the 7 README repos completed clean; reads median 0 on 6/7.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

src/search/query-utils.ts

@@ -340,3 +340,30 @@ export function kindBonus(kind: Node['kind']): number {
   };
   return bonuses[kind] ?? 0;
 }
+
+/**
+ * Whether a query token looks like a code identifier the user deliberately typed
+ * (camelCase / PascalCase-with-internal-caps / snake_case / has a digit) rather
+ * than a plain dictionary word ("flat", "object", "screen").
+ *
+ * Used to decide whether an EXACT name match earns the "the user named this
+ * symbol" exemption from single-term dampening. A common English word that
+ * happens to exact-match an unrelated symbol — the query "flat object" matching
+ * a constant named `FLAT` — must NOT get that exemption, or the +exact-name
+ * bonus floats it to the top of a prose query on its own.
+ *
+ * Classifies the token AS THE USER TYPED IT, not the matched symbol's name:
+ * "flat" (lowercase, descriptive) is non-distinctive even though it matches
+ * `FLAT`. A leading-capital-only word ("Screen", "Zustand") is also treated as
+ * a plain word — sentence-start capitalization and proper nouns aren't reliable
+ * identifier signals.
+ */
+export function isDistinctiveIdentifier(token: string): boolean {
+  if (!token) return false;
+  // snake_case / SCREAMING_SNAKE, or an embedded digit → a deliberate identifier.
+  if (/[_0-9]/.test(token)) return true;
+  // An uppercase letter anywhere AFTER the first char → a camelCase/PascalCase
+  // boundary (setLastEmail, OrgUserStore) or an acronym (REST, HTTP).
+  if (/[A-Z]/.test(token.slice(1))) return true;
+  return false;
+}