Fix sync skipping directory spec_paths

plumb/cli.py

@@ -484,13 +484,16 @@ def _run_modify(repo_root: Path, decision_id: str) -> None:
         console.print("  [yellow]No staged changes to modify.[/yellow]")
         return
 
-    # Read spec
+    # Read spec (resolve directories to individual .md files)
     config = load_config(repo_root)
     spec_content = ""
     if config:
         for sp in config.spec_paths:
             spec_file = repo_root / sp
-            if spec_file.is_file():
+            if spec_file.is_dir():
+                for md_file in sorted(spec_file.rglob("*.md")):
+                    spec_content += md_file.read_text()
+            elif spec_file.is_file():
                 spec_content += spec_file.read_text()
 
     decision_branch = find_decision_branch(repo_root, decision_id)

plumb/sync.py

@@ -267,10 +267,19 @@ def sync_decisions(
         )
     decisions_text = "\n".join(decision_lines)
 
+    # Resolve spec paths: directories expand to all .md files within
+    # (matches the resolution logic in parse_spec_files above)
+    resolved_spec_files: list[Path] = []
     for spec_path_str in config.spec_paths:
-        if on_progress:
-            on_progress(f"Updating spec: {spec_path_str}...")
         spec_path = repo_root / spec_path_str
+        if spec_path.is_dir():
+            resolved_spec_files.extend(sorted(spec_path.rglob("*.md")))
+        elif spec_path.is_file():
+            resolved_spec_files.append(spec_path)
+
+    for spec_path in resolved_spec_files:
+        if on_progress:
+            on_progress(f"Updating spec: {spec_path.relative_to(repo_root)}...")
         if not spec_path.is_file():
             continue
 

tests/conftest.py

@@ -43,6 +43,27 @@ def initialized_repo(tmp_repo):
     return tmp_repo
 
 
+@pytest.fixture
+def initialized_repo_dir_specs(tmp_repo):
+    """A tmp_repo with spec_paths pointing to a directory (not individual files)."""
+    ensure_plumb_dir(tmp_repo)
+    cfg = PlumbConfig(
+        spec_paths=["specs/"],
+        test_paths=["tests/"],
+        initialized_at=datetime.now(timezone.utc).isoformat(),
+    )
+    save_config(tmp_repo, cfg)
+    # Create specs directory with multiple spec files
+    specs_dir = tmp_repo / "specs"
+    specs_dir.mkdir(exist_ok=True)
+    (specs_dir / "spec.md").write_text("# Spec\n\n## Features\n\nThe system must do X.\n")
+    (specs_dir / "api.md").write_text("# API\n\n## Endpoints\n\nGET /items returns all items.\n")
+    # Create tests dir
+    (tmp_repo / "tests").mkdir(exist_ok=True)
+    (tmp_repo / ".plumb" / "decisions").mkdir(exist_ok=True)
+    return tmp_repo
+
+
 @pytest.fixture
 def sample_decisions():
     """Return a list of sample Decision objects."""

tests/test_sync.py

@@ -189,6 +189,54 @@ def test_new_requirement_gets_current_timestamp(self, initialized_repo):
         assert result[0]["last_seen_commit"] is None
 
 
+class TestSyncDecisionsDirectorySpecPaths:
+    """Tests for directory-based spec_paths (e.g., spec_paths: ['specs/'])."""
+
+    def test_syncs_when_spec_path_is_directory(self, initialized_repo_dir_specs):
+        """sync_decisions should resolve directory spec_paths to .md files."""
+        d = Decision(
+            id="dec-dir1",
+            status="approved",
+            question="How to authenticate?",
+            decision="Use API keys.",
+            created_at=datetime.now(timezone.utc).isoformat(),
+        )
+        append_decision(initialized_repo_dir_specs, d, branch="main")
+
+        updater_call_count = [0]
+
+        def mock_run(fn, *args, **kwargs):
+            from plumb.programs.spec_updater import WholeFileSpecUpdater
+            if isinstance(fn, WholeFileSpecUpdater):
+                updater_call_count[0] += 1
+                return [{"header": "## Features", "content": "Uses API keys.\n"}], []
+            return []
+
+        with patch("plumb.programs.configure_dspy"), \
+             patch("plumb.programs.run_with_retries", side_effect=mock_run):
+            result = sync_decisions(initialized_repo_dir_specs)
+
+        # Should have called updater for each .md file in the directory
+        assert updater_call_count[0] == 2  # spec.md + api.md
+        assert result["spec_updated"] >= 1
+
+    def test_parses_spec_files_from_directory(self, initialized_repo_dir_specs):
+        """parse_spec_files should find .md files inside directory spec_paths."""
+        mock_reqs = [
+            MagicMock(text="The system must do X.", ambiguous=False),
+        ]
+
+        with patch("plumb.programs.configure_dspy"), \
+             patch("plumb.programs.run_with_retries", return_value=mock_reqs):
+            result = parse_spec_files(initialized_repo_dir_specs)
+
+        # Should parse both spec.md and api.md (2 files × 1 req each = 2, but
+        # same text → same ID → deduped to 1)
+        assert len(result) >= 1
+        req_path = initialized_repo_dir_specs / ".plumb" / "requirements.json"
+        assert req_path.exists()
+
+
 class TestSyncDecisionsWholeFile:
     """Tests for the whole-file spec update path."""