feat(deps): Implement dependency lister tool (deps command)

Adds a new "Dependency Lister" tool, introducing the `contextcraft deps`
command to the CLI.

Core features:
- Parses dependencies from Python projects (pyproject.toml for Poetry/PEP621,
  requirements.txt) and Node.js projects (package.json).
- Supports various dependency groups (main, dev, peer, optional) and
  Python extras.
- Integrates with the configuration manager for a default output filename
  (`default_output_filename_deps`).
- Outputs dependencies in a structured Markdown format suitable for
  console display (via Rich) or saving to a file.
- Includes comprehensive unit tests (`test_dependency_lister.py`) with
  high coverage for the new module.
- Code adheres to project quality standards (Ruff, Mypy, Bandit).

Author: Shorzinator

coverage.xml

@@ -274,8 +274,7 @@ def flatten_command(
             output_file_path=actual_output_path,
             include_patterns=actual_include_patterns,
             exclude_patterns=actual_exclude_patterns,
-            # config_global_include_patterns=config.get("global_include_patterns", []), # For later
-            # config_global_exclude_patterns=config.get("global_exclude_patterns", [])  # For later
+            config_global_excludes=cfg_global_excludes,
         )
     except typer.Exit:
         raise
@@ -335,8 +334,7 @@ def deps_command(
             console.print(f"[dim]Using default output file from config: {actual_output_path.resolve()}[/dim]")
         else:
             warnings.warn(
-                f"Config Warning: 'default_output_filename_deps' should be a string, "
-                f"got {type(cfg_output_filename)}. Outputting to console.",
+                f"Config Warning: 'default_output_filename_deps' should be a string, " f"got {type(cfg_output_filename)}. Outputting to console.",
                 UserWarning,
                 stacklevel=2,
             )

src/contextcraft/main.py

@@ -48,13 +48,7 @@ class DependencyInfo:
         group: Dependency group (e.g., 'dev', 'test', 'main')
     """
 
-    def __init__(
-        self,
-        name: str,
-        version: Optional[str] = None,
-        extras: Optional[List[str]] = None,
-        group: str = "main"
-    ):
+    def __init__(self, name: str, version: Optional[str] = None, extras: Optional[List[str]] = None, group: str = "main"):
         self.name = name
         self.version = version
         self.extras = extras or []
@@ -188,17 +182,17 @@ def _parse_requirement_string(self, req_string: str) -> Tuple[str, Optional[str]
 
         # Extract extras
         extras = []
-        extras_match = re.search(r'\[([^\]]+)\]', req_string)
+        extras_match = re.search(r"\[([^\]]+)\]", req_string)
         if extras_match:
-            extras = [e.strip() for e in extras_match.group(1).split(',')]
-            req_string = req_string.replace(extras_match.group(0), '')
+            extras = [e.strip() for e in extras_match.group(1).split(",")]
+            req_string = req_string.replace(extras_match.group(0), "")
 
         # Extract version constraint
-        version_match = re.search(r'([<>=!~]+.+)', req_string)
+        version_match = re.search(r"([<>=!~]+.+)", req_string)
         version = version_match.group(1) if version_match else None
 
         # Extract package name
-        name = re.sub(r'[<>=!~].*', '', req_string).strip()
+        name = re.sub(r"[<>=!~].*", "", req_string).strip()
 
         return name, version, extras
 
@@ -250,16 +244,16 @@ def parse(self) -> List[DependencyInfo]:
                     line = line.strip()
 
                     # Skip empty lines and comments
-                    if not line or line.startswith('#'):
+                    if not line or line.startswith("#"):
                         continue
 
                     # Skip -r, -f, --find-links, etc. (requirement file options)
-                    if line.startswith('-'):
+                    if line.startswith("-"):
                         continue
 
                     # Remove inline comments
-                    if '#' in line:
-                        line = line.split('#')[0].strip()
+                    if "#" in line:
+                        line = line.split("#")[0].strip()
 
                     if line:
                         try:
@@ -281,32 +275,32 @@ def _determine_group_from_filename(self) -> str:
         """Determine dependency group from filename."""
         filename = self.file_path.name.lower()
 
-        if 'dev' in filename:
-            return 'dev'
-        elif 'test' in filename:
-            return 'test'
-        elif 'prod' in filename or 'production' in filename:
-            return 'production'
+        if "dev" in filename:
+            return "dev"
+        elif "test" in filename:
+            return "test"
+        elif "prod" in filename or "production" in filename:
+            return "production"
         else:
-            return 'main'
+            return "main"
 
     def _parse_requirement_string(self, req_string: str) -> Tuple[str, Optional[str], List[str]]:
         """Parse a requirement string like 'package[extra1,extra2]>=1.0'."""
         req_string = req_string.strip()
 
         # Extract extras
         extras = []
-        extras_match = re.search(r'\[([^\]]+)\]', req_string)
+        extras_match = re.search(r"\[([^\]]+)\]", req_string)
         if extras_match:
-            extras = [e.strip() for e in extras_match.group(1).split(',')]
-            req_string = req_string.replace(extras_match.group(0), '')
+            extras = [e.strip() for e in extras_match.group(1).split(",")]
+            req_string = req_string.replace(extras_match.group(0), "")
 
         # Extract version constraint
-        version_match = re.search(r'([<>=!~]+.+)', req_string)
+        version_match = re.search(r"([<>=!~]+.+)", req_string)
         version = version_match.group(1) if version_match else None
 
         # Extract package name
-        name = re.sub(r'[<>=!~].*', '', req_string).strip()
+        name = re.sub(r"[<>=!~].*", "", req_string).strip()
 
         return name, version, extras
 
@@ -381,11 +375,11 @@ def discover_dependency_files(project_path: Path) -> List[Path]:
         "requirements-test.txt",
         "requirements-prod.txt",
         "requirements/*.txt",
-        "requirements/*.in"
+        "requirements/*.in",
     ]
 
     for pattern in requirements_patterns:
-        if '*' in pattern:
+        if "*" in pattern:
             # Handle glob patterns
             for path in project_path.glob(pattern):
                 if path.is_file():
@@ -417,17 +411,15 @@ def create_parser(file_path: Path) -> Optional[PackageManagerParser]:
 
     if filename == "pyproject.toml":
         return PyProjectTomlParser(file_path)
-    elif filename.endswith(('.txt', '.in')) and 'requirements' in filename:
+    elif filename.endswith((".txt", ".in")) and "requirements" in filename:
         return RequirementsTxtParser(file_path)
     elif filename == "package.json":
         return PackageJsonParser(file_path)
 
     return None
 
 
-def format_dependencies_as_markdown(
-    dependency_data: Dict[str, Dict[str, List[DependencyInfo]]]
-) -> str:
+def format_dependencies_as_markdown(dependency_data: Dict[str, Dict[str, List[DependencyInfo]]]) -> str:
     """
     Format dependency data as structured Markdown.
 
@@ -461,7 +453,7 @@ def format_dependencies_as_markdown(
 
             for group, group_deps in grouped_deps.items():
                 if len(grouped_deps) > 1:  # Only show group header if there are multiple groups
-                    group_title = group.replace('_', ' ').title()
+                    group_title = group.replace("_", " ").title()
                     markdown_lines.append(f"#### {group_title} Dependencies\n")
 
                 # Sort dependencies alphabetically
@@ -480,10 +472,7 @@ def format_dependencies_as_markdown(
     return "\n".join(markdown_lines)
 
 
-def list_dependencies_logic(
-    project_path: Path,
-    actual_output_path: Optional[Path]
-) -> None:
+def list_dependencies_logic(project_path: Path, actual_output_path: Optional[Path]) -> None:
     """
     Main logic function for listing project dependencies.
 

src/contextcraft/tools/dependency_lister.py

@@ -152,6 +152,8 @@ def is_path_ignored(
             if relative_path_for_spec:
                 rel_path_str = relative_path_for_spec.as_posix()
                 current_path_obj_for_match = Path(rel_path_str)
+
+                # For directory patterns ending with "/", check if this is a directory
                 if pattern.endswith("/") and path_to_check_abs.is_dir():
                     path_to_match_as_dir = rel_path_str
                     if not path_to_match_as_dir.endswith("/"):
@@ -160,6 +162,17 @@ def is_path_ignored(
                         return True
                     if current_path_obj_for_match.name + "/" == pattern:
                         return True
+
+                # For directory patterns ending with "/", also check if any parent directory matches
+                if pattern.endswith("/"):
+                    # Check if any parent directory of the file matches the pattern
+                    for parent in current_path_obj_for_match.parents:
+                        parent_str = parent.as_posix()
+                        if parent_str + "/" == pattern:
+                            return True
+                        if parent.name + "/" == pattern:
+                            return True
+
                 if current_path_obj_for_match.match(pattern):
                     return True
 
@@ -175,6 +188,8 @@ def is_path_ignored(
             if relative_path_for_spec:
                 rel_path_str_cli = relative_path_for_spec.as_posix()
                 current_path_for_cli_match = Path(rel_path_str_cli)
+
+                # For directory patterns ending with "/", check if this is a directory
                 if pattern.endswith("/") and path_to_check_abs.is_dir():
                     path_to_match_cli_dir = rel_path_str_cli
                     if not path_to_match_cli_dir.endswith("/"):
@@ -183,6 +198,17 @@ def is_path_ignored(
                         return True
                     if current_path_for_cli_match.name + "/" == pattern:
                         return True
+
+                # For directory patterns ending with "/", also check if any parent directory matches
+                if pattern.endswith("/"):
+                    # Check if any parent directory of the file matches the pattern
+                    for parent in current_path_for_cli_match.parents:
+                        parent_str = parent.as_posix()
+                        if parent_str + "/" == pattern:
+                            return True
+                        if parent.name + "/" == pattern:
+                            return True
+
                 if current_path_for_cli_match.match(pattern):
                     return True
 

src/contextcraft/utils/ignore_handler.py

@@ -135,7 +135,9 @@ def test_flatten_command_success(mock_flatten_logic, tmp_path: Path):
     """Test flatten command successful execution (mocking actual flattening)."""
     result = runner.invoke(app, ["flatten", str(tmp_path)])
     assert result.exit_code == 0
-    mock_flatten_logic.assert_called_once_with(root_dir_path=tmp_path.resolve(), output_file_path=None, include_patterns=[], exclude_patterns=[])
+    mock_flatten_logic.assert_called_once_with(
+        root_dir_path=tmp_path.resolve(), output_file_path=None, include_patterns=[], exclude_patterns=[], config_global_excludes=[]
+    )
 
 
 @mock.patch("src.contextcraft.tools.flattener.flatten_code_logic")
@@ -147,7 +149,11 @@ def test_flatten_command_with_options(mock_flatten_logic, tmp_path: Path):
     )
     assert result.exit_code == 0
     mock_flatten_logic.assert_called_once_with(
-        root_dir_path=tmp_path.resolve(), output_file_path=output_f.resolve(), include_patterns=["*.py", "*.md"], exclude_patterns=["temp/*"]
+        root_dir_path=tmp_path.resolve(),
+        output_file_path=output_f.resolve(),
+        include_patterns=["*.py", "*.md"],
+        exclude_patterns=["temp/*"],
+        config_global_excludes=[],
     )
 
 
@@ -308,8 +314,7 @@ def test_tree_uses_config_global_excludes(mock_generate_tree, tmp_path: Path):
     config_data = {"global_exclude_patterns": ["*.log", "build/"]}
     create_pyproject_with_config(tmp_path, config_data)
 
-    with runner.isolated_filesystem(temp_dir=tmp_path) as isolated_dir:
-        result = runner.invoke(app, ["tree", str(isolated_dir)])
+    result = runner.invoke(app, ["tree", str(tmp_path)])
 
     assert result.exit_code == 0
     mock_generate_tree.assert_called_once()
@@ -326,8 +331,7 @@ def test_tree_cli_ignore_augments_config_global_excludes(mock_generate_tree, tmp
     create_pyproject_with_config(tmp_path, config_data)
 
     cli_ignore_val = "temp/"
-    with runner.isolated_filesystem(temp_dir=tmp_path) as isolated_dir:
-        result = runner.invoke(app, ["tree", str(isolated_dir), "--ignore", cli_ignore_val])
+    result = runner.invoke(app, ["tree", str(tmp_path), "--ignore", cli_ignore_val])
 
     assert result.exit_code == 0
     mock_generate_tree.assert_called_once()
@@ -345,8 +349,7 @@ def test_flatten_uses_config_global_excludes(mock_flatten_logic, tmp_path: Path)
     config_data = {"global_exclude_patterns": ["__pycache__/", "*.tmp"]}
     create_pyproject_with_config(tmp_path, config_data)
 
-    with runner.isolated_filesystem(temp_dir=tmp_path) as isolated_dir:
-        result = runner.invoke(app, ["flatten", str(isolated_dir)])
+    result = runner.invoke(app, ["flatten", str(tmp_path)])
 
     assert result.exit_code == 0
     mock_flatten_logic.assert_called_once()
@@ -362,8 +365,7 @@ def test_flatten_cli_exclude_augments_config_global_excludes(mock_flatten_logic,
     create_pyproject_with_config(tmp_path, config_data)
 
     cli_exclude_val = "*.css"
-    with runner.isolated_filesystem(temp_dir=tmp_path) as isolated_dir:
-        result = runner.invoke(app, ["flatten", str(isolated_dir), "--exclude", cli_exclude_val])
+    result = runner.invoke(app, ["flatten", str(tmp_path), "--exclude", cli_exclude_val])
 
     assert result.exit_code == 0
     mock_flatten_logic.assert_called_once()
@@ -429,6 +431,8 @@ def test_flatten_integration_with_config_excludes(tmp_path: Path):
     assert "# --- File: utils.py ---" in content
     assert "print('utils')" in content
 
-    assert "ignored.py" not in content
-    assert "docs/index.md" not in content  # Check full path or unique content
-    assert "# Docs" not in content
+    # Check that the actual ignored files are not included (check for file headers)
+    assert "# --- File: ignored.py ---" not in content
+    assert "# --- File: docs/index.md ---" not in content
+    assert "print('ignored')" not in content  # Content from ignored.py
+    assert "# Docs" not in content  # Content from docs/index.md