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)

docs/design/callback-edge-synthesis.md

@@ -1,12 +1,19 @@
 # Design + status: general callback / observer edge synthesis
 
-**Status:** Phases 1–3 implemented & validated as a **prototype, uncommitted on `main`**
-(as of 2026-05-22). This doc is the handoff for continuing the work.
+**Status:** SHIPPED (the synthesizer in `callback-synthesizer.ts` is merged and on
+`main`). This doc records the original design.
 **Motivation:** close the dynamic-dispatch hole that static extraction leaves for
 observer / event-emitter / signal patterns, where a *dispatcher* invokes callbacks
 registered elsewhere through a shared store — so flows like "how does an update
 reach the screen" actually exist in the graph.
 
+> **Update (2026-06-01):** the `codegraph_trace` and `codegraph_context` MCP tools
+> were since **removed** — `codegraph_explore` is the single surfacing tool now. Its
+> "Flow" section (`buildFlowFromNamedSymbols`) and the `codegraph_node` trail surface
+> these synthesized edges; the `trace(a, b)` notation below means "the a→b flow,"
+> which you now verify with `codegraph_explore` / `probe-explore.mjs` (the
+> `probe-trace.mjs` / `probe-context.mjs` dev probes went away with the tools).
+
 ---
 
 ## TL;DR for a new session
@@ -35,11 +42,11 @@ rm -rf /tmp/codegraph-corpus/excalidraw/.codegraph
 sqlite3 /tmp/codegraph-corpus/excalidraw/.codegraph/codegraph.db \
   "select s.name||' → '||t.name||'  '||coalesce(e.metadata,'') from edges e \
    join nodes s on e.source=s.id join nodes t on e.target=t.id where e.provenance='heuristic';"
-# end-to-end trace (uses the dev probes):
-node scripts/agent-eval/probe-trace.mjs /tmp/codegraph-corpus/excalidraw triggerUpdate triggerRender
+# end-to-end flow (the synthesized edge shows up in explore's Flow section + node trail):
+node scripts/agent-eval/probe-explore.mjs /tmp/codegraph-corpus/excalidraw "triggerUpdate triggerRender"
 ```
 Probe scripts (dev-only, in `scripts/agent-eval/`): `probe-node.mjs` (symbol + trail),
-`probe-trace.mjs` (call path), `probe-context.mjs`, `probe-explore.mjs`. EventEmitter
+`probe-explore.mjs` (relevant source + the flow among named symbols). EventEmitter
 fixture lives at `/tmp/cb-fixture/bus.js` (ephemeral — recreate or move into `__tests__/`).
 
 ---
@@ -172,8 +179,9 @@ This is one half of closing dynamic-dispatch coverage. The other artifacts on `m
   pre-filter in `resolution/index.ts`) + django ORM resolver (`frameworks/python.ts`,
   `_iterable_class` → `ModelIterable.__iter__`).
 - **Retrieval/UX changes** (separate from coverage): `explore` whole-small-file + glue
-  fixes, `node`-with-trail, `codegraph_trace`, `context` call-paths — all in
-  `src/mcp/tools.ts` / `src/context/index.ts`.
+  fixes, the `explore` Flow section (`buildFlowFromNamedSymbols`), and `node`-with-trail
+  — all in `src/mcp/tools.ts`. (`codegraph_trace` / `codegraph_context` were later
+  removed; explore is the one surfacing tool.)
 - **Full investigation context + findings:** auto-memory
   `project_codegraph_read_displacement` (why coverage — not prompting/hooks/new-tools —
   is the lever for getting agents to use codegraph over Read).

docs/design/dynamic-dispatch-coverage-playbook.md

@@ -9,6 +9,14 @@ each one the same way, so cross-symbol *flows* exist in the graph everywhere.
 > synthesizer) is in [`callback-edge-synthesis.md`](./callback-edge-synthesis.md).
 > Full investigation context + findings: auto-memory `project_codegraph_read_displacement`.
 
+> **Update (2026-06-01):** the `codegraph_trace` and `codegraph_context` MCP tools were
+> **removed** — `codegraph_explore` is the single surfacing tool now. Its "Flow" section
+> (`buildFlowFromNamedSymbols`) surfaces the synthesized edges this playbook is about, and
+> you validate coverage with `codegraph_explore` / `scripts/agent-eval/probe-explore.mjs`.
+> Where the text below writes `trace(a, b)` or lists `trace`/`context` among the tools,
+> read it as "the a→b flow, now surfaced and verified via explore." The synthesizers and
+> the coverage matrix are unchanged.
+
 ---
 
 ## 1. The goal (why this matters)