claude-mpm 5.4.96__py3-none-any.whl → 5.6.10__py3-none-any.whl

claude_mpm/cli/commands/run.py

@@ -13,7 +13,7 @@ DESIGN DECISIONS:
 - Support multiple output formats (json, yaml, table, text)
 """
 
-import subprocess
+import subprocess  # nosec B404 - required for process management
 import sys
 from datetime import datetime, timezone
 from typing import Optional
@@ -489,6 +489,18 @@ class RunCommand(BaseCommand):
         if hasattr(args, "claude_args") and args.claude_args:
             claude_args.extend(args.claude_args)
 
+        # Add --resume if flag is set
+        if getattr(args, "resume", False) and "--resume" not in claude_args:
+            claude_args.insert(0, "--resume")
+
+        # Add --chrome if flag is set
+        if getattr(args, "chrome", False) and "--chrome" not in claude_args:
+            claude_args.insert(0, "--chrome")
+
+        # Add --no-chrome if flag is set
+        if getattr(args, "no_chrome", False) and "--no-chrome" not in claude_args:
+            claude_args.insert(0, "--no-chrome")
+
         # Create runner
         runner = ClaudeRunner(
             enable_tickets=enable_tickets,
@@ -553,7 +565,7 @@ class RunCommand(BaseCommand):
                 wrapper_path = get_scripts_dir() / "interactive_wrapper.py"
                 if wrapper_path.exists():
                     print("Starting interactive session with command interception...")
-                    subprocess.run([sys.executable, str(wrapper_path)], check=False)
+                    subprocess.run([sys.executable, str(wrapper_path)], check=False)  # nosec B603 - trusted internal paths
                 else:
                     self.logger.warning(
                         "Interactive wrapper not found, falling back to normal mode"
@@ -907,6 +919,26 @@ def run_session_legacy(args):
         else:
             logger.info("[INFO]️ --resume already in claude_args")
 
+    # Add --chrome to claude_args if the flag is set
+    chrome_flag_present = getattr(args, "chrome", False)
+    if chrome_flag_present:
+        logger.info("📌 --chrome flag detected in args")
+        if "--chrome" not in raw_claude_args:
+            raw_claude_args = ["--chrome", *raw_claude_args]
+            logger.info("✅ Added --chrome to claude_args")
+        else:
+            logger.info("ℹ️ --chrome already in claude_args")
+
+    # Add --no-chrome to claude_args if the flag is set
+    no_chrome_flag_present = getattr(args, "no_chrome", False)
+    if no_chrome_flag_present:
+        logger.info("📌 --no-chrome flag detected in args")
+        if "--no-chrome" not in raw_claude_args:
+            raw_claude_args = ["--no-chrome", *raw_claude_args]
+            logger.info("✅ Added --no-chrome to claude_args")
+        else:
+            logger.info("ℹ️ --no-chrome already in claude_args")
+
     # Filter out claude-mpm specific flags before passing to Claude CLI
     logger.debug(f"Pre-filter claude_args: {raw_claude_args}")
     claude_args = filter_claude_mpm_args(raw_claude_args)
@@ -1044,7 +1076,7 @@ def run_session_legacy(args):
         wrapper_path = get_scripts_dir() / "interactive_wrapper.py"
         if wrapper_path.exists():
             print("Starting interactive session with command interception...")
-            subprocess.run([sys.executable, str(wrapper_path)], check=False)
+            subprocess.run([sys.executable, str(wrapper_path)], check=False)  # nosec B603 - trusted internal paths
         else:
             logger.warning("Interactive wrapper not found, falling back to normal mode")
             runner.run_interactive(context)

claude_mpm/cli/commands/skill_source.py

@@ -11,6 +11,7 @@ for better UX. Handles errors gracefully with actionable messages.
 
 import json
 import logging
+import os
 import re
 
 from ...config.skill_sources import SkillSource, SkillSourceConfiguration
@@ -20,6 +21,33 @@ from ...services.skills.skill_discovery_service import SkillDiscoveryService
 logger = logging.getLogger(__name__)
 
 
+def _get_github_token(source: SkillSource | None = None) -> str | None:
+    """Get GitHub token with source-specific override support.
+
+    Priority: source.token > GITHUB_TOKEN > GH_TOKEN
+
+    Args:
+        source: Optional SkillSource to check for per-source token
+
+    Returns:
+        GitHub token if found, None otherwise
+
+    Security Note:
+        Token is never logged or printed to avoid exposure.
+    """
+    # Priority 1: Per-source token (env var reference or direct)
+    if source and source.token:
+        if source.token.startswith("$"):
+            # Env var reference: $VAR_NAME -> os.environ.get("VAR_NAME")
+            env_var_name = source.token[1:]
+            return os.environ.get(env_var_name)
+        # Direct token (not recommended but supported)
+        return source.token
+
+    # Priority 2-3: Global environment variables
+    return os.environ.get("GITHUB_TOKEN") or os.environ.get("GH_TOKEN")
+
+
 def _test_skill_repository_access(source: SkillSource) -> dict:
     """Test if skill repository is accessible via GitHub API.
 
@@ -58,7 +86,13 @@ def _test_skill_repository_access(source: SkillSource) -> dict:
         # Test GitHub API access
         api_url = f"https://api.github.com/repos/{owner_repo}"
 
-        response = requests.get(api_url, timeout=10)
+        # Build headers with authentication if token available
+        headers = {"Accept": "application/vnd.github+json"}
+        token = _get_github_token(source)
+        if token:
+            headers["Authorization"] = f"token {token}"
+
+        response = requests.get(api_url, headers=headers, timeout=10)
 
         if response.status_code == 200:
             return {"accessible": True, "error": None}
@@ -68,9 +102,14 @@ def _test_skill_repository_access(source: SkillSource) -> dict:
                 "error": f"Repository not found: {owner_repo}",
             }
         if response.status_code == 403:
+            error_msg = "Access denied (private repository or rate limit)"
+            if not token:
+                error_msg += (
+                    ". Try setting GITHUB_TOKEN environment variable for private repos"
+                )
             return {
                 "accessible": False,
-                "error": "Access denied (private repository or rate limit)",
+                "error": error_msg,
             }
         return {
             "accessible": False,
@@ -263,6 +302,15 @@ def handle_add_skill_source(args) -> int:
 
         # Create new source
         enabled = not args.disabled
+        token = getattr(args, "token", None)
+
+        # Security warning for direct tokens
+        if token and not token.startswith("$"):
+            print("⚠️  Warning: Direct token values in config are not recommended")
+            print("   Consider using environment variable reference instead:")
+            print("   --token $MY_PRIVATE_TOKEN")
+            print()
+
         source = SkillSource(
             id=source_id,
             type="git",
@@ -270,6 +318,7 @@ def handle_add_skill_source(args) -> int:
             branch=args.branch,
             priority=args.priority,
             enabled=enabled,
+            token=token,
         )
 
         # Determine if we should test

claude_mpm/cli/commands/skills.py

@@ -538,6 +538,7 @@ class SkillsManagementCommand(BaseCommand):
             toolchain = getattr(args, "toolchain", None)
             categories = getattr(args, "categories", None)
             force = getattr(args, "force", False)
+            deploy_all = getattr(args, "all", False)
 
             if collection:
                 console.print(
@@ -548,14 +549,15 @@ class SkillsManagementCommand(BaseCommand):
                     "\n[bold cyan]Deploying skills from default collection...[/bold cyan]\n"
                 )
 
-            # Selective deployment is ALWAYS enabled (deploy only agent-referenced skills)
-            # This ensures only skills linked to deployed agents are deployed
+            # Use selective deployment unless --all flag is provided
+            # Selective mode deploys only agent-referenced skills
+            # --all mode deploys all available skills from the collection
             result = self.skills_deployer.deploy_skills(
                 collection=collection,
                 toolchain=toolchain,
                 categories=categories,
                 force=force,
-                selective=True,  # Always use selective deployment
+                selective=not deploy_all,
             )
 
             # Display results

claude_mpm/cli/executor.py

@@ -127,6 +127,14 @@ def execute_command(command: str, args) -> int:
         result = handle_verify(args)
         return result if result is not None else 0
 
+    # Handle commander command with lazy import
+    if command == "commander":
+        # Lazy import to avoid loading unless needed
+        from .commands.commander import handle_commander_command
+
+        result = handle_commander_command(args)
+        return result if result is not None else 0
+
     # Handle skill-source command with lazy import
     if command == "skill-source":
         # Lazy import to avoid loading unless needed
@@ -206,27 +214,33 @@ def execute_command(command: str, args) -> int:
             "status": show_status,
         }
 
-        # Get handler and invoke
+        # Get handler and call it with argument list (same pattern as autotodos)
         handler = handlers.get(subcommand)
         if handler:
-            # Build Click context programmatically
-            import click
-
-            ctx = click.Context(command=handler)
+            try:
+                # Build argument list for Click command based on subcommand
+                click_args = []
 
-            # Prepare keyword arguments from args
-            kwargs = {}
-            if hasattr(args, "format"):
-                kwargs["format"] = args.format
-            if hasattr(args, "hook_type"):
-                kwargs["hook_type"] = args.hook_type
-            if hasattr(args, "yes"):
-                kwargs["yes"] = args.yes
+                # list command: --format, --hook-type
+                if subcommand == "list":
+                    if hasattr(args, "format") and args.format:
+                        click_args.extend(["--format", args.format])
+                    if hasattr(args, "hook_type") and args.hook_type:
+                        click_args.extend(["--hook-type", args.hook_type])
+                # clear command: --hook-type, -y
+                elif subcommand == "clear":
+                    if hasattr(args, "hook_type") and args.hook_type:
+                        click_args.extend(["--hook-type", args.hook_type])
+                    if hasattr(args, "yes") and args.yes:
+                        click_args.append("-y")
+                # diagnose command: hook_type (positional argument)
+                elif subcommand == "diagnose":
+                    if hasattr(args, "hook_type") and args.hook_type:
+                        click_args.append(args.hook_type)
+                # status and summary commands: no options
 
-            try:
-                # Invoke handler with arguments
-                with ctx:
-                    handler.invoke(ctx, **kwargs)
+                # Call Click command with argument list and standalone_mode=False
+                handler(click_args, standalone_mode=False)
                 return 0
             except SystemExit as e:
                 return e.code if e.code is not None else 0
@@ -346,6 +360,7 @@ def execute_command(command: str, args) -> int:
         CLICommands.SKILLS.value: manage_skills,
         "debug": manage_debug,  # Add debug command
         "mpm-init": None,  # Will be handled separately with lazy import
+        "commander": None,  # Will be handled separately with lazy import
     }
 
     # Execute command if found

claude_mpm/cli/parsers/base_parser.py

@@ -297,6 +297,16 @@ def add_top_level_run_arguments(parser: argparse.ArgumentParser) -> None:
         action="store_true",
         help="Force refresh agents and skills from remote repos, bypassing ETag cache",
     )
+    run_group.add_argument(
+        "--chrome",
+        action="store_true",
+        help="Enable Claude in Chrome integration (passed to Claude Code)",
+    )
+    run_group.add_argument(
+        "--no-chrome",
+        action="store_true",
+        help="Disable Claude in Chrome integration (passed to Claude Code)",
+    )
 
     # Dependency checking options (for backward compatibility at top level)
     dep_group_top = parser.add_argument_group(
@@ -492,6 +502,13 @@ def create_parser(
     except ImportError:
         pass
 
+    try:
+        from .commander_parser import add_commander_subparser
+
+        add_commander_subparser(subparsers)
+    except ImportError:
+        pass
+
     # Add uninstall command parser
     try:
         from ..commands.uninstall import add_uninstall_parser

claude_mpm/cli/parsers/commander_parser.py

@@ -0,0 +1,83 @@
+"""
+Commander parser module for claude-mpm CLI.
+
+WHY: This module provides the commander subcommand for interactive instance management
+and chat interface.
+
+DESIGN DECISION: Uses subparser pattern consistent with other commands (run, agents, etc.)
+to provide a clean interface for Commander mode.
+"""
+
+import argparse
+from pathlib import Path
+
+
+def add_commander_subparser(subparsers: argparse._SubParsersAction) -> None:
+    """
+    Add commander subcommand parser.
+
+    WHY: Provides interactive mode for managing and chatting with multiple Claude instances.
+
+    Args:
+        subparsers: The subparsers object to add the commander parser to
+    """
+    commander_parser = subparsers.add_parser(
+        "commander",
+        help="Interactive Commander mode for managing multiple Claude instances",
+        description="""
+Commander Mode - Interactive Instance Management
+
+Commander provides an interactive REPL interface for:
+- Starting and stopping Claude Code/MPM instances in tmux
+- Connecting to instances and sending natural language commands
+- Managing multiple concurrent projects
+- Viewing instance status and output
+
+Commands:
+  list, ls, instances   List active instances
+  start <path>          Start new instance at path
+    --framework <cc|mpm>  Specify framework (default: cc)
+    --name <name>         Specify instance name (default: dir name)
+  stop <name>           Stop an instance
+  connect <name>        Connect to an instance
+  disconnect            Disconnect from current instance
+  status                Show current session status
+  help                  Show help message
+  exit, quit, q         Exit Commander
+
+Natural Language:
+  When connected to an instance, any input that is not a built-in
+  command will be sent to the connected instance as a message.
+
+Examples:
+  claude-mpm commander
+  > start ~/myproject --framework cc --name myapp
+  > connect myapp
+  > Fix the authentication bug in login.py
+  > disconnect
+  > exit
+        """,
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+
+    # Optional: Port for internal services
+    commander_parser.add_argument(
+        "--port",
+        type=int,
+        default=8765,
+        help="Port for internal services (default: 8765)",
+    )
+
+    # Optional: State directory
+    commander_parser.add_argument(
+        "--state-dir",
+        type=Path,
+        help="Directory for state persistence (optional)",
+    )
+
+    # Debug mode
+    commander_parser.add_argument(
+        "--debug",
+        action="store_true",
+        help="Enable debug logging",
+    )

claude_mpm/cli/parsers/run_parser.py

@@ -85,6 +85,16 @@ def add_run_arguments(parser: argparse.ArgumentParser) -> None:
         action="store_true",
         help="Pass --resume flag to Claude Code to resume the last conversation",
     )
+    run_group.add_argument(
+        "--chrome",
+        action="store_true",
+        help="Enable Claude in Chrome integration (passed to Claude Code)",
+    )
+    run_group.add_argument(
+        "--no-chrome",
+        action="store_true",
+        help="Disable Claude in Chrome integration (passed to Claude Code)",
+    )
 
     # Dependency checking options
     dep_group = parser.add_argument_group("dependency options")

claude_mpm/cli/parsers/skill_source_parser.py

@@ -76,6 +76,10 @@ def add_skill_source_subparser(subparsers) -> argparse.ArgumentParser:
         dest="skip_test",
         help="Skip immediate testing (not recommended)",
     )
+    add_parser.add_argument(
+        "--token",
+        help="GitHub token or env var reference (e.g., ghp_xxx or $PRIVATE_TOKEN)",
+    )
 
     # Remove repository
     remove_parser = skill_source_subparsers.add_parser(

claude_mpm/cli/parsers/skills_parser.py

@@ -167,6 +167,11 @@ def add_skills_subparser(subparsers) -> argparse.ArgumentParser:
         action="store_true",
         help="Force redeployment of already deployed skills",
     )
+    deploy_github_parser.add_argument(
+        "--all",
+        action="store_true",
+        help="Deploy all available skills, not just agent-referenced ones",
+    )
 
     # List available GitHub skills
     list_available_parser = skills_subparsers.add_parser(

claude_mpm/cli/startup.py

@@ -161,7 +161,25 @@ def setup_early_environment(argv):
     # CRITICAL: Suppress ALL logging by default
     # This catches all loggers (claude_mpm.*, service.*, framework_loader, etc.)
     # This will be overridden by setup_mcp_server_logging() based on user preference
-    logging.getLogger().setLevel(logging.CRITICAL + 1)  # Root logger catches everything
+    root_logger = logging.getLogger()
+    root_logger.setLevel(logging.CRITICAL + 1)  # Root logger catches everything
+    root_logger.handlers = []  # Remove any handlers
+
+    # Also suppress common module loggers explicitly to prevent handler leakage
+    for logger_name in [
+        "claude_mpm",
+        "path_resolver",
+        "file_loader",
+        "framework_loader",
+        "service",
+        "instruction_loader",
+        "agent_loader",
+        "startup",
+    ]:
+        module_logger = logging.getLogger(logger_name)
+        module_logger.setLevel(logging.CRITICAL + 1)
+        module_logger.handlers = []
+        module_logger.propagate = False
 
     # Process argv
     if argv is None:
@@ -316,7 +334,7 @@ def deploy_output_style_on_startup():
     Deploys all styles:
     - claude-mpm.md (professional mode)
     - claude-mpm-teacher.md (teaching mode)
-    - claude-mpm-founders.md (founders mode)
+    - claude-mpm-research.md (research mode - for codebase analysis)
     """
     try:
         from ..core.output_style_manager import OutputStyleManager

claude_mpm/cli/utils.py

@@ -107,7 +107,7 @@ def get_agent_versions_display() -> Optional[str]:
                     base_version_tuple
                 )
                 output_lines.append(f"\n  Base Agent Version:  {base_version_str}")
-        except Exception:
+        except Exception:  # nosec B110 - intentional: version display is optional
             pass
 
         # Check for agents needing migration
@@ -173,8 +173,12 @@ def setup_logging(args) -> object:
     if not hasattr(args, "logging") or args.logging is None:
         args.logging = LogLevel.OFF.value
 
+    # Handle deprecated --verbose flag
+    if hasattr(args, "verbose") and args.verbose and args.logging == LogLevel.OFF.value:
+        args.logging = LogLevel.INFO.value
+
     # Handle deprecated --debug flag
-    if hasattr(args, "debug") and args.debug and args.logging == LogLevel.INFO.value:
+    if hasattr(args, "debug") and args.debug:
         args.logging = LogLevel.DEBUG.value
 
     # Only setup logging if not OFF
@@ -204,7 +208,7 @@ def ensure_directories() -> None:
         from ..init import ensure_directories as init_ensure_directories
 
         init_ensure_directories()
-    except Exception:
+    except Exception:  # nosec B110
         # Continue even if initialization fails
         # The individual commands will handle missing directories as needed
         pass

claude_mpm/commander/__init__.py

@@ -0,0 +1,72 @@
+"""MPM Commander - Multi-Project Orchestration.
+
+This module provides the core infrastructure for managing multiple projects
+with isolated state, work queues, and tool sessions.
+
+Key Components:
+    - ProjectRegistry: Thread-safe project management
+    - Project models: Data structures for state and sessions
+    - TmuxOrchestrator: Tmux session and pane management
+    - Config loading: .claude-mpm/ directory configuration
+    - CommanderDaemon: Main daemon process for orchestration
+    - ProjectSession: Per-project lifecycle management
+    - InstanceManager: Framework selection and instance lifecycle
+    - Frameworks: Claude Code, MPM framework abstractions
+
+Example:
+    >>> from claude_mpm.commander import ProjectRegistry
+    >>> registry = ProjectRegistry()
+    >>> project = registry.register("/path/to/project")
+    >>> registry.update_state(project.id, ProjectState.WORKING)
+"""
+
+from claude_mpm.commander.config import DaemonConfig
+from claude_mpm.commander.config_loader import load_project_config
+from claude_mpm.commander.daemon import CommanderDaemon
+from claude_mpm.commander.frameworks import (
+    BaseFramework,
+    ClaudeCodeFramework,
+    InstanceInfo,
+    MPMFramework,
+)
+from claude_mpm.commander.instance_manager import (
+    FrameworkNotFoundError,
+    InstanceAlreadyExistsError,
+    InstanceManager,
+    InstanceNotFoundError,
+)
+from claude_mpm.commander.models import (
+    Project,
+    ProjectState,
+    ThreadMessage,
+    ToolSession,
+)
+from claude_mpm.commander.project_session import ProjectSession, SessionState
+from claude_mpm.commander.registry import ProjectRegistry
+from claude_mpm.commander.tmux_orchestrator import (
+    TmuxNotFoundError,
+    TmuxOrchestrator,
+)
+
+__all__ = [
+    "BaseFramework",
+    "ClaudeCodeFramework",
+    "CommanderDaemon",
+    "DaemonConfig",
+    "FrameworkNotFoundError",
+    "InstanceAlreadyExistsError",
+    "InstanceInfo",
+    "InstanceManager",
+    "InstanceNotFoundError",
+    "MPMFramework",
+    "Project",
+    "ProjectRegistry",
+    "ProjectSession",
+    "ProjectState",
+    "SessionState",
+    "ThreadMessage",
+    "TmuxNotFoundError",
+    "TmuxOrchestrator",
+    "ToolSession",
+    "load_project_config",
+]

claude_mpm/commander/adapters/__init__.py

@@ -0,0 +1,31 @@
+"""Runtime adapters for MPM Commander.
+
+This package provides adapters for different AI coding tools, allowing
+the TmuxOrchestrator to interface with various runtimes in a uniform way.
+
+Two types of adapters:
+- RuntimeAdapter: Synchronous parsing and state detection
+- CommunicationAdapter: Async I/O and state management
+"""
+
+from .base import Capability, ParsedResponse, RuntimeAdapter
+from .claude_code import ClaudeCodeAdapter
+from .communication import (
+    AdapterResponse,
+    AdapterState,
+    BaseCommunicationAdapter,
+    ClaudeCodeCommunicationAdapter,
+)
+
+__all__ = [
+    # Communication adapters (async I/O)
+    "AdapterResponse",
+    "AdapterState",
+    "BaseCommunicationAdapter",
+    # Runtime adapters (parsing)
+    "Capability",
+    "ClaudeCodeAdapter",
+    "ClaudeCodeCommunicationAdapter",
+    "ParsedResponse",
+    "RuntimeAdapter",
+]