fix(cli): make --no-stats actually omit volatile counts (#1477)

Closes #1477.

The `--no-stats` flag on `gitnexus analyze` was advertised as
"Omit volatile file/symbol counts from AGENTS.md and CLAUDE.md"
but had no effect: every reindex still rewrote the markdown with
fresh count phrases, producing chore-commit churn on every run —
the exact problem the flag was added to solve in #704.

Root cause is commander.js negation-flag semantics. `.option(
'--no-stats', ...)` registers the option under the accessor
`stats` (boolean, default `true`; `false` when the flag is passed),
NOT `noStats`. The two action-handler reads in `analyze.ts`
(lines 414 and 500 pre-fix) read `options?.noStats`, which is
always `undefined`, so the `noStats` payload always reached
`runFullAnalysis` / `generateAIContextFiles` as `undefined`/falsy
and the count branch in the template always fired.

Fixed by replacing `options?.noStats` with `options?.stats === false`
at both reads. The strict `=== false` check (rather than
`!options?.stats`) means absent options or absent `.stats` field
fall through as no-stats=false, preserving the documented default-on
behaviour. Also updated the `AnalyzeOptions` interface to declare
`stats?: boolean` (matching commander's actual output) with a
JSDoc explaining the negation, since the prior `noStats?: boolean`
shape was a static-type misrepresentation of what commander
provides at runtime.

Internal call sites that re-pack `{ noStats: ... }` for
downstream consumers (`run-analyze.ts`, `ai-context.ts`) keep
their existing field name — those interfaces are not commander-
shaped, so `noStats` is the correct name there.

## Regression tests

Two new unit tests in `test/unit/ai-context.test.ts`:

* `omits volatile counts when noStats option is set (#1477)` —
  asserts the count parenthetical is absent from both CLAUDE.md
  and AGENTS.md when `noStats: true` is passed.
* `preserves volatile counts when noStats is not set (default)` —
  documents the default-on path so a future refactor can't
  silently flip the default.

Both call `generateAIContextFiles` directly with distinctive numbers
that would unmistakably leak through if the omit branch is broken.

## Manual verification

* `vitest run test/unit/ai-context.test.ts` → 13/13 pass
  (11 prior + 2 new).
* Verified before-fix behaviour by checking out main, running
  `npx gitnexus analyze --no-stats` against an indexed repo, and
  observing the count phrase still present. Re-running on the fix
  branch with the same flag strips the phrase as documented.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

gitnexus/src/cli/analyze.ts

@@ -117,8 +117,18 @@ export interface AnalyzeOptions {
   verbose?: boolean;
   /** Skip AGENTS.md and CLAUDE.md gitnexus block updates. */
   skipAgentsMd?: boolean;
-  /** Omit volatile symbol/relationship counts from AGENTS.md and CLAUDE.md. */
-  noStats?: boolean;
+  /**
+   * Stats inclusion in AGENTS.md and CLAUDE.md.
+   *
+   * Commander.js represents `--no-stats` as `stats: boolean` (default
+   * `true`; `false` when the user passes `--no-stats`), NOT as
+   * `noStats: boolean`. Reading the negated form would always be
+   * `undefined` and the flag would silently no-op (#1477). Consumers
+   * that want "did the user request --no-stats?" should compare with
+   * `=== false` to distinguish the explicit-off case from the
+   * default-on case.
+   */
+  stats?: boolean;
   /** Index the folder even when no .git directory is present. */
   skipGit?: boolean;
   /**
@@ -411,7 +421,12 @@ export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOption
         dropEmbeddings: options?.dropEmbeddings,
         skipGit: options?.skipGit,
         skipAgentsMd: options?.skipAgentsMd,
-        noStats: options?.noStats,
+        // commander.js `.option('--no-stats', …)` registers the flag as
+        // `options.stats` (boolean, default true; `false` when the user
+        // passed --no-stats). Reading `options?.noStats` here returns
+        // undefined every time, so the flag was a no-op on the markdown
+        // rewrite path before this fix. See #1477.
+        noStats: options?.stats === false,
         registryName: options?.name,
         // Registry-collision bypass — its own CLI flag, intentionally NOT
         // overloading --force. A user who hits the collision guard should
@@ -497,7 +512,9 @@ export const analyzeCommand = async (inputPath?: string, options?: AnalyzeOption
               processes: s.processes,
             },
             skillResult.skills,
-            { skipAgentsMd: options?.skipAgentsMd, noStats: options?.noStats },
+            // See note above (#1477): commander stores --no-stats as
+            // `options.stats === false`, not as `options.noStats`.
+            { skipAgentsMd: options?.skipAgentsMd, noStats: options?.stats === false },
           );
         }
       } catch {

gitnexus/test/unit/ai-context.test.ts

@@ -45,6 +45,57 @@ describe('generateAIContextFiles', () => {
     expect(content).toContain('TestProject');
   });
 
+  it('omits volatile counts when noStats option is set (#1477)', async () => {
+    // Distinct subdir per case so we can assert on a clean slate.
+    const subDir = await fs.mkdtemp(path.join(os.tmpdir(), 'gn-no-stats-test-'));
+    const subStorage = path.join(subDir, '.gitnexus');
+    await fs.mkdir(subStorage, { recursive: true });
+    try {
+      // Stats values picked to be unmistakable if they leak through.
+      const stats = { nodes: 12345, edges: 67890, processes: 99 };
+      await generateAIContextFiles(
+        subDir,
+        subStorage,
+        'NoStatsProject',
+        stats,
+        undefined,
+        { noStats: true },
+      );
+
+      for (const f of ['CLAUDE.md', 'AGENTS.md']) {
+        const content = await fs.readFile(path.join(subDir, f), 'utf-8');
+        expect(content).toContain('NoStatsProject');
+        // The "(N symbols, N relationships, N execution flows)"
+        // phrase MUST NOT appear when noStats=true.
+        expect(content).not.toMatch(
+          /\(\d+\s+symbols,\s+\d+\s+relationships,\s+\d+\s+execution flows\)/,
+        );
+        // And the distinctive numbers must not leak via any other path.
+        expect(content).not.toContain('12345');
+        expect(content).not.toContain('67890');
+      }
+    } finally {
+      await fs.rm(subDir, { recursive: true, force: true });
+    }
+  });
+
+  it('preserves volatile counts when noStats is not set (default)', async () => {
+    const subDir = await fs.mkdtemp(path.join(os.tmpdir(), 'gn-with-stats-test-'));
+    const subStorage = path.join(subDir, '.gitnexus');
+    await fs.mkdir(subStorage, { recursive: true });
+    try {
+      const stats = { nodes: 12345, edges: 67890, processes: 99 };
+      await generateAIContextFiles(subDir, subStorage, 'WithStatsProject', stats);
+      const content = await fs.readFile(path.join(subDir, 'CLAUDE.md'), 'utf-8');
+      expect(content).toContain('WithStatsProject');
+      expect(content).toMatch(
+        /\(12345\s+symbols,\s+67890\s+relationships,\s+99\s+execution flows\)/,
+      );
+    } finally {
+      await fs.rm(subDir, { recursive: true, force: true });
+    }
+  });
+
   it('keeps the load-bearing repo-specific sections in the CLAUDE.md block (#856)', async () => {
     // The trimmed block must still contain everything that is genuinely
     // unique per repo or load-bearing for the agent: the freshness warning,