chore: sort all imports within the repo with uv run isort .

scripts/benchmark_manifest_ops.py

@@ -12,10 +12,10 @@
 """
 
 import os
+import shutil
+import sys
 import tempfile
 import time
-import sys
-import shutil
 from pathlib import Path
 
 # ---------------------------------------------------------------------------

src/apm_cli/adapters/client/codex.py

@@ -6,11 +6,13 @@
 """
 
 import os
-import toml
 from pathlib import Path
-from .base import MCPClientAdapter
+
+import toml
+
 from ...registry.client import SimpleRegistryClient
 from ...registry.integration import RegistryIntegration
+from .base import MCPClientAdapter
 
 
 class CodexClientAdapter(MCPClientAdapter):
@@ -331,6 +333,7 @@ def _process_environment_variables(self, env_vars, env_overrides=None):
         """
         import os
         import sys
+
         from rich.prompt import Prompt
 
         resolved = {}

src/apm_cli/adapters/client/copilot.py

@@ -8,12 +8,13 @@
 import json
 import os
 from pathlib import Path
-from .base import MCPClientAdapter
-from ...registry.client import SimpleRegistryClient
-from ...registry.integration import RegistryIntegration
+
 from ...core.docker_args import DockerArgsProcessor
 from ...core.token_manager import GitHubTokenManager
+from ...registry.client import SimpleRegistryClient
+from ...registry.integration import RegistryIntegration
 from ...utils.github_host import is_github_hostname
+from .base import MCPClientAdapter
 
 
 class CopilotClientAdapter(MCPClientAdapter):
@@ -327,6 +328,7 @@ def _resolve_environment_variables(self, env_vars, env_overrides=None):
         """
         import os
         import sys
+
         from rich.prompt import Prompt
 
         resolved = {}
@@ -406,6 +408,7 @@ def _resolve_env_variable(self, name, value, env_overrides=None):
         import os
         import re
         import sys
+
         from rich.prompt import Prompt
 
         env_overrides = env_overrides or {}
@@ -684,7 +687,7 @@ def _is_github_server(self, server_name, url):
             bool: True if this is a legitimate GitHub MCP server, False otherwise.
         """
         from urllib.parse import urlparse
-        
+
         # Check server name against an allowlist of known GitHub MCP servers
         github_server_names = [
             "github-mcp-server",

src/apm_cli/adapters/client/vscode.py

@@ -8,9 +8,10 @@
 import json
 import os
 from pathlib import Path
-from .base import MCPClientAdapter, _INPUT_VAR_RE
+
 from ...registry.client import SimpleRegistryClient
 from ...registry.integration import RegistryIntegration
+from .base import _INPUT_VAR_RE, MCPClientAdapter
 
 
 class VSCodeClientAdapter(MCPClientAdapter):

src/apm_cli/adapters/package_manager/default_manager.py

@@ -1,8 +1,8 @@
 """Implementation of the default MCP package manager."""
 
-from .base import MCPPackageManagerAdapter
 from ...config import get_default_client
 from ...registry.integration import RegistryIntegration
+from .base import MCPPackageManagerAdapter
 
 
 class DefaultMCPPackageManager(MCPPackageManagerAdapter):
@@ -81,7 +81,7 @@ def list_installed(self):
         try:
             # Import here to avoid circular import
             from ...factory import ClientFactory
-            
+
             # Get client type from configuration (default is vscode)
             client_type = get_default_client()
 

src/apm_cli/bundle/__init__.py

@@ -1,8 +1,8 @@
 """Bundle creation and consumption for APM packages."""
 
-from .packer import pack_bundle, PackResult
+from .packer import PackResult, pack_bundle
 from .plugin_exporter import export_plugin_bundle
-from .unpacker import unpack_bundle, UnpackResult
+from .unpacker import UnpackResult, unpack_bundle
 
 __all__ = [
     "pack_bundle",

src/apm_cli/bundle/lockfile_enrichment.py

@@ -5,7 +5,6 @@
 
 from ..deps.lockfile import LockFile
 
-
 # Authoritative mapping of target names to deployed-file path prefixes.
 _TARGET_PREFIXES = {
     "copilot": [".github/"],

src/apm_cli/bundle/packer.py

@@ -7,10 +7,10 @@
 from pathlib import Path
 from typing import Dict, List, Optional
 
+from ..core.target_detection import detect_target
 from ..deps.lockfile import LockFile, get_lockfile_path, migrate_lockfile_if_needed
 from ..models.apm_package import APMPackage
-from ..core.target_detection import detect_target
-from .lockfile_enrichment import enrich_lockfile_for_pack, _filter_files_by_target
+from .lockfile_enrichment import _filter_files_by_target, enrich_lockfile_for_pack
 
 
 @dataclass

src/apm_cli/bundle/plugin_exporter.py

@@ -7,18 +7,17 @@
 
 import json
 import os
+import re
 import shutil
 import tarfile
 from pathlib import Path
 from typing import Dict, List, Optional, Set, Tuple
 
 import yaml
 
-import re
-
 from ..deps.lockfile import (
-    LockFile,
     LockedDependency,
+    LockFile,
     get_lockfile_path,
     migrate_lockfile_if_needed,
 )

src/apm_cli/bundle/unpacker.py

@@ -8,7 +8,7 @@
 from pathlib import Path
 from typing import Dict, List
 
-from ..deps.lockfile import LockFile, LOCKFILE_NAME, LEGACY_LOCKFILE_NAME
+from ..deps.lockfile import LEGACY_LOCKFILE_NAME, LOCKFILE_NAME, LockFile
 
 
 @dataclass

src/apm_cli/commands/_helpers.py

@@ -21,8 +21,8 @@
     GITIGNORE_FILENAME,
 )
 from ..utils.console import _rich_echo, _rich_info, _rich_warning
-from ..version import get_build_sha, get_version
 from ..utils.version_checker import check_for_updates
+from ..version import get_build_sha, get_version
 
 # CRITICAL: Shadow Click commands at module level to prevent namespace collision
 # When Click commands like 'config set' are defined, calling set() can invoke the command
@@ -192,8 +192,8 @@ def _check_orphaned_packages():
             return []
 
         try:
-            from ..models.apm_package import APMPackage
             from ..deps.lockfile import LockFile, get_lockfile_path
+            from ..models.apm_package import APMPackage
 
             apm_package = APMPackage.from_apm_yml(Path(APM_YML_FILENAME))
             declared_deps = apm_package.get_apm_dependencies()

src/apm_cli/commands/audit.py

@@ -17,20 +17,19 @@
 
 import click
 
+from ..core.command_logger import CommandLogger
 from ..deps.lockfile import LockFile, get_lockfile_path
 from ..security.content_scanner import ContentScanner, ScanFinding
 from ..security.file_scanner import scan_lockfile_packages
-from ..core.command_logger import CommandLogger
 from ..utils.console import (
+    STATUS_SYMBOLS,
     _get_console,
     _rich_echo,
     _rich_error,
     _rich_success,
     _rich_warning,
-    STATUS_SYMBOLS,
 )
 
-
 # -- Helpers --------------------------------------------------------
 
 
@@ -89,6 +88,7 @@ def _render_findings_table(
     if console:
         try:
             from rich.table import Table
+
             from ..security.audit_report import relative_path_for_report
 
             table = Table(

src/apm_cli/commands/compile/__init__.py

@@ -1,6 +1,6 @@
 """APM compile command."""
 
-from .cli import compile, _display_validation_errors, _get_validation_suggestion
+from .cli import _display_validation_errors, _get_validation_suggestion, compile
 from .watcher import _watch_mode
 
 __all__ = [

src/apm_cli/commands/compile/cli.py

@@ -5,8 +5,8 @@
 
 import click
 
-from ...constants import AGENTS_MD_FILENAME, APM_DIR, APM_MODULES_DIR, APM_YML_FILENAME
 from ...compilation import AgentsCompiler, CompilationConfig
+from ...constants import AGENTS_MD_FILENAME, APM_DIR, APM_MODULES_DIR, APM_YML_FILENAME
 from ...core.command_logger import CommandLogger
 from ...primitives.discovery import discover_primitives
 from ...utils.console import (
@@ -35,6 +35,7 @@ def _display_single_file_summary(stats, c_status, c_hash, output_path, dry_run):
             return
 
         import os
+
         from rich.table import Table
 
         table = Table(

src/apm_cli/commands/compile/watcher.py

@@ -2,8 +2,8 @@
 
 import time
 
-from ...constants import AGENTS_MD_FILENAME, APM_DIR, APM_YML_FILENAME
 from ...compilation import AgentsCompiler, CompilationConfig
+from ...constants import AGENTS_MD_FILENAME, APM_DIR, APM_YML_FILENAME
 from ...core.command_logger import CommandLogger
 
 

src/apm_cli/commands/config.py

@@ -147,7 +147,7 @@ def get(key):
         apm config get auto-integrate
         apm config get
     """
-    from ..config import get_config, get_auto_integrate
+    from ..config import get_auto_integrate, get_config
 
     logger = CommandLogger("config get")
     if key:

src/apm_cli/commands/deps/__init__.py

@@ -1,17 +1,17 @@
 """APM dependency management commands."""
 
-from .cli import deps, list_packages, tree, clean, update, info
 from ._utils import (
-    _is_nested_under_package,
-    _count_primitives,
     _count_package_files,
+    _count_primitives,
     _count_workflows,
     _get_detailed_context_counts,
-    _get_package_display_info,
     _get_detailed_package_info,
-    _update_single_package,
+    _get_package_display_info,
+    _is_nested_under_package,
     _update_all_packages,
+    _update_single_package,
 )
+from .cli import clean, deps, info, list_packages, tree, update
 
 __all__ = [
     # CLI commands

src/apm_cli/commands/deps/_utils.py

@@ -4,8 +4,8 @@
 from typing import Any, Dict, List, Optional
 
 from ...constants import APM_DIR, APM_MODULES_DIR, APM_YML_FILENAME, SKILL_MD_FILENAME
-from ...models.apm_package import APMPackage
 from ...deps.github_downloader import GitHubPackageDownloader
+from ...models.apm_package import APMPackage
 
 
 def _scan_installed_packages(apm_modules_dir: Path) -> list:

src/apm_cli/commands/deps/cli.py

@@ -1,30 +1,30 @@
 """APM dependency management CLI commands."""
 
-import sys
 import shutil
-import click
+import sys
 from pathlib import Path
-from typing import List, Optional, Dict, Any
+from typing import Any, Dict, List, Optional
+
+import click
 
 # Import existing APM components
 from ...constants import APM_DIR, APM_MODULES_DIR, APM_YML_FILENAME, SKILL_MD_FILENAME
-from ...models.apm_package import APMPackage, ValidationResult, validate_apm_package
 from ...core.command_logger import CommandLogger
+from ...deps.apm_resolver import APMDependencyResolver
 
 # Import APM dependency system components (with fallback)
 from ...deps.github_downloader import GitHubPackageDownloader
-from ...deps.apm_resolver import APMDependencyResolver
-
+from ...models.apm_package import APMPackage, ValidationResult, validate_apm_package
 from ._utils import (
-    _is_nested_under_package,
-    _count_primitives,
     _count_package_files,
+    _count_primitives,
     _count_workflows,
     _get_detailed_context_counts,
-    _get_package_display_info,
     _get_detailed_package_info,
-    _update_single_package,
+    _get_package_display_info,
+    _is_nested_under_package,
     _update_all_packages,
+    _update_single_package,
 )
 
 
@@ -41,9 +41,10 @@ def list_packages():
 
     try:
         # Import Rich components with fallback
-        from rich.table import Table
-        from rich.console import Console
         import shutil
+
+        from rich.console import Console
+        from rich.table import Table
         term_width = shutil.get_terminal_size((120, 24)).columns
         console = Console(width=max(120, term_width))
         has_rich = True
@@ -241,8 +242,8 @@ def tree():
 
     try:
         # Import Rich components with fallback
-        from rich.tree import Tree
         from rich.console import Console
+        from rich.tree import Tree
         console = Console()
         has_rich = True
     except ImportError:
@@ -533,8 +534,8 @@ def info(package: str):
 
         # Display with Rich panel if available
         try:
-            from rich.panel import Panel
             from rich.console import Console
+            from rich.panel import Panel
             from rich.text import Text
             console = Console()