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/bin/codegraph.ts

@@ -1073,52 +1073,6 @@ function printFileTree(
   renderNode(root, '', true, 0);
 }
 
-/**
- * codegraph context <task>
- */
-program
-  .command('context <task>')
-  .description('Build context for a task (outputs markdown)')
-  .option('-p, --path <path>', 'Project path')
-  .option('-n, --max-nodes <number>', 'Maximum nodes to include', '50')
-  .option('-c, --max-code <number>', 'Maximum code blocks', '10')
-  .option('--no-code', 'Exclude code blocks')
-  .option('-f, --format <format>', 'Output format (markdown, json)', 'markdown')
-  .action(async (task: string, options: {
-    path?: string;
-    maxNodes?: string;
-    maxCode?: string;
-    code?: boolean;
-    format?: string;
-  }) => {
-    const projectPath = resolveProjectPath(options.path);
-
-    try {
-      if (!isInitialized(projectPath)) {
-        error(`CodeGraph not initialized in ${projectPath}`);
-        process.exit(1);
-      }
-
-      const { default: CodeGraph } = await loadCodeGraph();
-      const cg = await CodeGraph.open(projectPath);
-
-      const context = await cg.buildContext(task, {
-        maxNodes: parseInt(options.maxNodes || '50', 10),
-        maxCodeBlocks: parseInt(options.maxCode || '10', 10),
-        includeCode: options.code !== false,
-        format: options.format as 'markdown' | 'json',
-      });
-
-      // Output the context
-      console.log(context);
-
-      cg.destroy();
-    } catch (err) {
-      error(`Failed to build context: ${err instanceof Error ? err.message : String(err)}`);
-      process.exit(1);
-    }
-  });
-
 /**
  * codegraph serve
  */
@@ -1161,8 +1115,8 @@ program
 }
 `));
         console.error('Available tools:');
+        console.error(chalk.cyan('  codegraph_explore') + '   - Primary: source of the relevant symbols for any question');
         console.error(chalk.cyan('  codegraph_search') + '    - Search for code symbols');
-        console.error(chalk.cyan('  codegraph_context') + '   - Build context for a task');
         console.error(chalk.cyan('  codegraph_callers') + '   - Find callers of a symbol');
         console.error(chalk.cyan('  codegraph_callees') + '   - Find what a symbol calls');
         console.error(chalk.cyan('  codegraph_impact') + '    - Analyze impact of changes');