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/index.ts

@@ -681,6 +681,15 @@ export class CodeGraph {
     return this.queries.getNodesByKind(kind);
   }
 
+  /**
+   * Get ALL nodes with an exact name (direct index lookup, not FTS-ranked/capped).
+   * Used to enumerate every overload of a heavily-overloaded name so the specific
+   * definition the caller wants is never dropped below a search cut.
+   */
+  getNodesByName(name: string): Node[] {
+    return this.queries.getNodesByName(name);
+  }
+
   /**
    * Search nodes by text
    */
@@ -692,7 +701,7 @@ export class CodeGraph {
    * Find the project's "primary route file" — the file with the densest
    * concentration of framework-emitted `route` nodes (≥3 routes, ≥30%
    * of all non-test routes). Used to inline the routing config in
-   * `codegraph_context` responses on small realworld template repos
+   * `codegraph_explore` responses on small realworld template repos
    * (rails-realworld, laravel-realworld, drupal-admintoolbar, …) where
    * Glob+Read of `routes.rb`/`urls.py`/etc. otherwise beats codegraph.
    */