fix: Windows shell robustness, project_root detection, and hook stdin safety (#1343)

Address 4 root causes of Windows + Claude Code reliability issues:

1. Workflow shell robustness: add || true guards to informational commands
   (ls, grep, find, cat) that return non-zero on "no results", preventing
   workflow step failures under strict execution models. Guard glob loops
   with [ -e "$var" ] || continue to handle empty glob expansion.

2. Hook stdin handling: replace readFileSync('/dev/stdin') with async
   process.stdin + timeout in agent templates (gsd-verifier.md). Existing
   JS hooks already have timeout guards.

3. project_root detection: fix isInsideGitRepo() to check .git at the
   candidate parent level (not just below it), enabling correct detection
   when .git and .planning/ are siblings at the same directory level —
   the common single-repo case from a subdirectory.

4. @file: handoff: add missing @file: handlers to autonomous.md and
   manager.md workflows that call gsd-tools init but lacked the handler
   for large output payloads.

Fixes #1343

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

tests/core.test.cjs

@@ -1477,6 +1477,38 @@ describe('findProjectRoot', () => {
 
     assert.strictEqual(findProjectRoot(backendDir), backendDir);
   });
+
+  test('walks up from subdirectory when .git is at same level as .planning/ (single-repo)', () => {
+    // Common single-repo layout: .git and .planning are siblings at project root
+    fs.mkdirSync(path.join(projectRoot, '.planning'), { recursive: true });
+    fs.mkdirSync(path.join(projectRoot, '.git'), { recursive: true });
+
+    // User cwd is a subdirectory (e.g., src/)
+    const srcDir = path.join(projectRoot, 'src');
+    fs.mkdirSync(srcDir, { recursive: true });
+
+    // Should detect that parent has .planning/ and .git is at that same level
+    assert.strictEqual(findProjectRoot(srcDir), projectRoot);
+  });
+
+  test('walks up from deep subdirectory when .git is at same level as .planning/', () => {
+    // Single-repo: .git and .planning at root, cwd deep inside
+    fs.mkdirSync(path.join(projectRoot, '.planning'), { recursive: true });
+    fs.mkdirSync(path.join(projectRoot, '.git'), { recursive: true });
+
+    const deepDir = path.join(projectRoot, 'src', 'lib', 'utils');
+    fs.mkdirSync(deepDir, { recursive: true });
+
+    assert.strictEqual(findProjectRoot(deepDir), projectRoot);
+  });
+
+  test('returns startDir when .planning exists at same level (cwd is project root)', () => {
+    // User is already at project root — no parent to walk up to
+    fs.mkdirSync(path.join(projectRoot, '.planning'), { recursive: true });
+    fs.mkdirSync(path.join(projectRoot, '.git'), { recursive: true });
+
+    assert.strictEqual(findProjectRoot(projectRoot), projectRoot);
+  });
 });
 
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