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)

__tests__/explore-output-budget.test.ts

@@ -27,9 +27,14 @@ describe('getExploreOutputBudget', () => {
     expect(small.maxOutputChars).toBeLessThanOrEqual(20000);
   });
 
-  it('keeps the historical 35k+ ceiling for medium-large projects so existing benchmarks do not regress', () => {
+  it('caps medium-large projects at the inline tool-result ceiling (~24k) so the result is never externalized', () => {
+    // A bigger single response gets externalized by the host to a file the agent
+    // Reads back (a 35k vscode explore did exactly that in the n=4 A/B) — adding a
+    // read AND cache-write cost. So large repos get MORE CALLS (getExploreBudget),
+    // not a fatter single response; the output cap stays under the inline limit.
     const large = getExploreOutputBudget(10000);
-    expect(large.maxOutputChars).toBeGreaterThanOrEqual(35000);
+    expect(large.maxOutputChars).toBeLessThanOrEqual(25000);
+    expect(large.maxOutputChars).toBeGreaterThanOrEqual(20000);
   });
 
   it('uses tier breakpoints matching getExploreBudget so call-count and output-budget agree on a project', () => {
@@ -54,10 +59,13 @@ describe('getExploreOutputBudget', () => {
     const tier3b = getExploreOutputBudget(14999);
     expect(tier3a.maxOutputChars).toBe(tier3b.maxOutputChars);
 
-    // And crossing a breakpoint changes the cap.
-    expect(tier0a.maxOutputChars).not.toBe(tier1a.maxOutputChars);
-    expect(tier1a.maxOutputChars).not.toBe(tier2a.maxOutputChars);
-    expect(tier2a.maxOutputChars).not.toBe(tier3a.maxOutputChars);
+    // Small tiers step up (13k → 18k → 24k); medium and large SHARE the ~24k
+    // inline ceiling — scaling with repo size now lives in the CALL budget
+    // (getExploreBudget), not in a fatter single response.
+    expect(tier0a.maxOutputChars).not.toBe(tier1a.maxOutputChars); // <150 vs <500
+    expect(tier1a.maxOutputChars).not.toBe(tier2a.maxOutputChars); // <500 vs <5000
+    expect(tier2a.maxOutputChars).toBe(tier3a.maxOutputChars);     // <5000 == <15000 (inline cap)
+    expect(getExploreBudget(5000)).toBeGreaterThan(getExploreBudget(4999)); // calls scale instead
   });
 
   it('gates off "Additional relevant files", completeness signal, and budget note on small projects', () => {