fix(analyze): address review — rename --no-git to --skip-git, fix stale cache

Addresses all review items from @magyargergo and Copilot:

1. **Rename --no-git to --skip-git**: Commander.js treats --no-X flags
   as negation of --X (stores as options.git = false, not options.noGit).
   --skip-git maps correctly to options.skipGit.

2. **Fix false " Already up to date\ on non-git folders**: When
 currentCommit is empty string, skip the cache check — we cannot
 detect changes without git, so always rebuild.

3. **Replace isGitRepo() with hasGitDir()**: Use filesystem check
 (statSync on .git) instead of shelling out to git CLI. Consistent,
 faster, and works when git is not installed.

4. **Fix misleading warning**: Message now only fires when .git
 directory is actually absent (not when git CLI fails).

5. **Add CLI integration tests**: Verify Commander maps --skip-git
 correctly and that non-git folders are rejected without the flag.

gitnexus/src/cli/analyze.ts

@@ -15,7 +15,7 @@ import { initLbug, loadGraphToLbug, getLbugStats, executeQuery, executeWithReuse
 // versions whose ABI is not yet supported by the native binary (#89).
 // disposeEmbedder intentionally not called — ONNX Runtime segfaults on cleanup (see #38)
 import { getStoragePaths, saveMeta, loadMeta, addToGitignore, registerRepo, getGlobalRegistryPath, cleanupOldKuzuFiles } from '../storage/repo-manager.js';
-import { getCurrentCommit, isGitRepo, getGitRoot, hasGitDir } from '../storage/git.js';
+import { getCurrentCommit, getGitRoot, hasGitDir } from '../storage/git.js';
 import { generateAIContextFiles } from './ai-context.js';
 import { generateSkillFiles, type GeneratedSkillInfo } from './skill-gen.js';
 import fs from 'fs/promises';
@@ -49,7 +49,7 @@ export interface AnalyzeOptions {
   skills?: boolean;
   verbose?: boolean;
   /** Index the folder even when no .git directory is present. */
-  noGit?: boolean;
+  skipGit?: boolean;
 }
 
 /** Threshold: auto-skip embeddings for repos with more nodes than this */
@@ -89,26 +89,26 @@ export const analyzeCommand = async (
   } else {
     const gitRoot = getGitRoot(process.cwd());
     if (!gitRoot) {
-      if (!options?.noGit) {
-        console.log('  Not inside a git repository.\n  Tip: pass --no-git to index any folder without a .git directory.\n');
+      if (!options?.skipGit) {
+        console.log('  Not inside a git repository.\n  Tip: pass --skip-git to index any folder without a .git directory.\n');
         process.exitCode = 1;
         return;
       }
-      // --no-git: fall back to cwd as the root
+      // --skip-git: fall back to cwd as the root
       repoPath = path.resolve(process.cwd());
     } else {
       repoPath = gitRoot;
     }
   }
 
-  const repoHasGit = isGitRepo(repoPath);
-  if (!repoHasGit && !options?.noGit) {
-    console.log('  Not a git repository.\n  Tip: pass --no-git to index any folder without a .git directory.\n');
+  const repoHasGit = hasGitDir(repoPath);
+  if (!repoHasGit && !options?.skipGit) {
+    console.log('  Not a git repository.\n  Tip: pass --skip-git to index any folder without a .git directory.\n');
     process.exitCode = 1;
     return;
   }
   if (!repoHasGit) {
-    console.log('  Warning: no .git directory found — commit-tracking and incremental updates disabled.\n');
+    console.log('  Warning: no .git directory found \u2014 commit-tracking and incremental updates disabled.\n');
   }
 
   const { storagePath, lbugPath } = getStoragePaths(repoPath);
@@ -124,8 +124,11 @@ export const analyzeCommand = async (
   const existingMeta = await loadMeta(storagePath);
 
   if (existingMeta && !options?.force && !options?.skills && existingMeta.lastCommit === currentCommit) {
-    console.log('  Already up to date\n');
-    return;
+    // Non-git folders have currentCommit = '' — always rebuild since we can't detect changes
+    if (currentCommit !== '') {
+      console.log('  Already up to date\n');
+      return;
+    }
   }
 
   if (process.env.GITNEXUS_NO_GITIGNORE) {
@@ -329,8 +332,8 @@ export const analyzeCommand = async (
   await saveMeta(storagePath, meta);
   await registerRepo(repoPath, meta);
   // Only attempt to update .gitignore when a .git directory is present.
-  // Use hasGitDir (filesystem check) rather than isGitRepo (shells out to git)
-  // so we skip correctly for --no-git folders even if git CLI is available.
+  // Use hasGitDir (filesystem check) rather than git CLI subprocess
+  // so we skip correctly for --skip-git folders even if git CLI is available.
   if (hasGitDir(repoPath)) {
     await addToGitignore(repoPath);
   }

gitnexus/src/cli/index.ts

@@ -28,7 +28,7 @@ program
   .option('-f, --force', 'Force full re-index even if up to date')
   .option('--embeddings', 'Enable embedding generation for semantic search (off by default)')
   .option('--skills', 'Generate repo-specific skill files from detected communities')
-  .option('--no-git', 'Index a folder without requiring a .git directory')
+  .option('--skip-git', 'Index a folder without requiring a .git directory')
    .option('-v, --verbose', 'Enable verbose ingestion warnings (default: false)')
    .addHelpText('after', '\nEnvironment variables:\n  GITNEXUS_NO_GITIGNORE=1  Skip .gitignore parsing (still reads .gitnexusignore)')
    .action(createLazyAction(() => import('./analyze.js'), 'analyzeCommand'));

gitnexus/test/unit/skip-git-cli.test.ts

@@ -0,0 +1,38 @@
+import { describe, it, expect } from 'vitest';
+import { execSync } from 'child_process';
+import path from 'path';
+import os from 'os';
+import fs from 'fs';
+
+describe('--skip-git CLI flag', () => {
+  it('Commander maps --skip-git to options.skipGit (not --no-git inversion)', () => {
+    // Verify the CLI defines --skip-git, not --no-git
+    const helpOutput = execSync('node dist/cli/index.js analyze --help', {
+      cwd: path.resolve(__dirname, '../..'),
+      encoding: 'utf8',
+      timeout: 10000,
+    });
+
+    expect(helpOutput).toContain('--skip-git');
+    expect(helpOutput).not.toContain('--no-git');
+  });
+
+  it('rejects non-git folder without --skip-git', () => {
+    const tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gn-no-git-'));
+    fs.writeFileSync(path.join(tmpDir, 'test.ts'), 'export const x = 1;');
+
+    try {
+      execSync(`node dist/cli/index.js analyze "${tmpDir}"`, {
+        cwd: path.resolve(__dirname, '../..'),
+        encoding: 'utf8',
+        timeout: 10000,
+      });
+      // Should not reach here
+      expect.unreachable('Should have exited with non-zero');
+    } catch (err: any) {
+      expect(err.stdout || err.stderr || '').toContain('--skip-git');
+    } finally {
+      fs.rmSync(tmpDir, { recursive: true, force: true });
+    }
+  });
+});