claude-mpm 5.4.22__py3-none-any.whl → 5.6.34__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

@@ -18,7 +18,7 @@ ARCHITECTURE:
 """
 
 import os
-import subprocess
+import subprocess  # nosec B404
 from typing import Optional
 
 from rich.console import Console
@@ -84,6 +84,7 @@ class SkillsManagementCommand(BaseCommand):
                 SkillsCommands.INFO.value: self._show_skill_info,
                 SkillsCommands.CONFIG.value: self._manage_config,
                 SkillsCommands.CONFIGURE.value: self._configure_skills,
+                SkillsCommands.SELECT.value: self._select_skills_interactive,
                 # GitHub deployment commands
                 SkillsCommands.DEPLOY_FROM_GITHUB.value: self._deploy_from_github,
                 SkillsCommands.LIST_AVAILABLE.value: self._list_available_github_skills,
@@ -504,7 +505,7 @@ class SkillsManagementCommand(BaseCommand):
                 # Open in editor
                 editor = os.environ.get("EDITOR", "nano")
                 try:
-                    subprocess.run([editor, str(config_path)], check=True)
+                    subprocess.run([editor, str(config_path)], check=True)  # nosec B603
                     console.print(
                         f"\n[green]Configuration saved to {config_path}[/green]\n"
                     )
@@ -537,7 +538,7 @@ class SkillsManagementCommand(BaseCommand):
             toolchain = getattr(args, "toolchain", None)
             categories = getattr(args, "categories", None)
             force = getattr(args, "force", False)
-            all_skills = getattr(args, "all_skills", False)
+            deploy_all = getattr(args, "all", False)
 
             if collection:
                 console.print(
@@ -548,23 +549,15 @@ class SkillsManagementCommand(BaseCommand):
                     "\n[bold cyan]Deploying skills from default collection...[/bold cyan]\n"
                 )
 
-            # Auto-detect toolchain if not specified and not deploying all
-            if not toolchain and not all_skills:
-                console.print(
-                    "[yellow]No toolchain specified. Use --toolchain to filter by language,[/yellow]"
-                )
-                console.print(
-                    "[yellow]or --all-skills to deploy all available skills (not just agent-referenced).[/yellow]\n"
-                )
-
-            # Selective deployment is enabled by default (deploy only agent-referenced skills)
-            # Use --all-skills to disable selective mode
+            # 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=not all_skills,  # Disable selective mode if --all-skills is set
+                selective=not deploy_all,
             )
 
             # Display results
@@ -577,11 +570,7 @@ class SkillsManagementCommand(BaseCommand):
                     f"(out of {total_available} available)[/cyan]"
                 )
                 console.print(
-                    "[dim]Use --all-skills to deploy all available skills[/dim]\n"
-                )
-            else:
-                console.print(
-                    "[cyan]📦 Deploying all available skills (selective mode disabled)[/cyan]\n"
+                    "[dim]Use 'claude-mpm skills configure' to manually select skills[/dim]\n"
                 )
 
             if result["deployed_count"] > 0:
@@ -606,6 +595,16 @@ class SkillsManagementCommand(BaseCommand):
                     console.print(f"  • {error}")
                 console.print()
 
+            # Show cleanup results
+            cleanup = result.get("cleanup", {})
+            if cleanup.get("removed_count", 0) > 0:
+                console.print(
+                    f"[yellow]🧹 Removed {cleanup['removed_count']} orphaned skill(s):[/yellow]"
+                )
+                for skill in cleanup.get("removed_skills", []):
+                    console.print(f"  • {skill}")
+                console.print()
+
             # Show restart instructions
             if result["restart_instructions"]:
                 console.print(
@@ -677,33 +676,91 @@ class SkillsManagementCommand(BaseCommand):
     def _check_deployed_skills(self, args) -> CommandResult:
         """Check currently deployed skills in ~/.claude/skills/."""
         try:
-            result = self.skills_deployer.check_deployed_skills()
+            # Get deployed skills
+            deployed_result = self.skills_deployer.check_deployed_skills()
+            deployed_names = {skill["name"] for skill in deployed_result["skills"]}
 
             console.print("\n[bold cyan]Claude Code Skills Status:[/bold cyan]\n")
-            console.print(f"[dim]Directory: {result['claude_skills_dir']}[/dim]\n")
+            console.print(
+                f"[dim]Directory: {deployed_result['claude_skills_dir']}[/dim]\n"
+            )
+
+            # Fetch available skills from GitHub to get full list
+            try:
+                available_result = self.skills_deployer.list_available_skills()
+                all_skills = available_result.get("skills", [])
+            except Exception as e:
+                console.print(
+                    f"[yellow]Warning: Could not fetch available skills: {e}[/yellow]\n"
+                )
+                all_skills = []
 
-            if result["deployed_count"] == 0:
-                console.print("[yellow]No skills currently deployed.[/yellow]")
+            # Combine deployed and available skills
+            skill_map = {}
+
+            # Add available skills
+            for skill in all_skills:
+                skill_name = skill.get("name", "")
+                if skill_name:
+                    skill_map[skill_name] = {
+                        "name": skill.get("display_name")
+                        or skill_name.replace("-", " ").title(),
+                        "skill_id": skill_name,
+                        "source": "MPM Skills",
+                        "is_deployed": skill_name in deployed_names,
+                    }
+
+            # Add any deployed skills not in available list (local/custom skills)
+            for skill in deployed_result["skills"]:
+                skill_name = skill["name"]
+                if skill_name not in skill_map:
+                    skill_map[skill_name] = {
+                        "name": skill_name.replace("-", " ").title(),
+                        "skill_id": skill_name,
+                        "source": "Local",
+                        "is_deployed": True,
+                    }
+
+            if not skill_map:
+                console.print("[yellow]No skills available.[/yellow]")
                 console.print(
                     "[dim]Use 'claude-mpm skills deploy-github' to deploy skills.[/dim]\n"
                 )
                 return CommandResult(success=True, exit_code=0)
 
-            console.print(
-                f"[green]{result['deployed_count']} skill(s) deployed:[/green]\n"
+            # Create table matching agent management format
+            table = Table(show_header=True, header_style="bold cyan")
+            table.add_column("#", style="bright_black", width=6, no_wrap=True)
+            table.add_column(
+                "Skill ID", style="bright_black", no_wrap=True, overflow="ellipsis"
             )
+            table.add_column(
+                "Name", style="bright_cyan", no_wrap=True, overflow="ellipsis"
+            )
+            table.add_column("Source", style="bright_yellow", no_wrap=True)
+            table.add_column("Status", style="bright_black", no_wrap=True)
 
-            # Create table for deployed skills
-            table = Table(show_header=True, header_style="bold cyan")
-            table.add_column("Skill Name", style="green")
-            table.add_column("Path", style="dim")
+            # Sort skills by name for consistent display
+            sorted_skills = sorted(skill_map.values(), key=lambda s: s["skill_id"])
 
-            for skill in sorted(result["skills"], key=lambda s: s["name"]):
-                table.add_row(skill["name"], skill["path"])
+            for idx, skill in enumerate(sorted_skills, 1):
+                status = (
+                    "[green]Installed[/green]" if skill["is_deployed"] else "Available"
+                )
+                table.add_row(
+                    str(idx), skill["skill_id"], skill["name"], skill["source"], status
+                )
 
             console.print(table)
             console.print()
 
+            # Show summary
+            deployed_count = sum(1 for s in skill_map.values() if s["is_deployed"])
+            console.print(
+                f"[dim]Showing {len(skill_map)} skills ({deployed_count} installed, "
+                f"{len(skill_map) - deployed_count} available)[/dim]\n"
+            )
+
             return CommandResult(success=True, exit_code=0)
 
         except Exception as e:
@@ -1226,6 +1283,99 @@ class SkillsManagementCommand(BaseCommand):
             console.print(f"[dim]{traceback.format_exc()}[/dim]")
             return CommandResult(success=False, message=str(e), exit_code=1)
 
+    def _select_skills_interactive(self, args) -> CommandResult:
+        """Interactive skill selection with topic grouping.
+
+        This command provides a two-tier selection interface:
+        1. Select topic groups (toolchains) to explore
+        2. Multi-select skills within each topic group
+
+        Features:
+        - Groups skills by toolchain (universal, python, typescript, etc.)
+        - Shows skills auto-included by agent dependencies
+        - Displays token counts for each skill
+        - Updates config and runs reconciliation
+
+        Returns:
+            CommandResult with success/failure status
+        """
+        try:
+            from ...cli.interactive.skill_selector import run_skill_selector
+            from ...core.unified_config import UnifiedConfig
+            from ...services.agents.deployment.deployment_reconciler import (
+                DeploymentReconciler,
+            )
+
+            console.print("\n[bold cyan]Interactive Skill Selector[/bold cyan]\n")
+
+            # Run skill selector
+            selected_skills = run_skill_selector()
+
+            if selected_skills is None:
+                console.print("\n[yellow]Skill selection cancelled[/yellow]")
+                return CommandResult(success=True, exit_code=0)
+
+            # Update config with selected skills
+            config = UnifiedConfig()
+            config.skills.enabled = selected_skills
+
+            # Save config
+            try:
+                config.save()
+                console.print(
+                    f"\n[green]✓ Saved {len(selected_skills)} skills to configuration[/green]"
+                )
+            except Exception as e:
+                console.print(f"\n[red]Failed to save configuration: {e}[/red]")
+                return CommandResult(success=False, message=str(e), exit_code=1)
+
+            # Run reconciliation to deploy skills
+            console.print("\n[cyan]Running skill reconciliation...[/cyan]")
+            reconciler = DeploymentReconciler(config)
+
+            try:
+                from pathlib import Path
+
+                project_path = Path.cwd()
+                result = reconciler.reconcile_skills(project_path)
+
+                if result.deployed:
+                    console.print(
+                        f"  [green]✓ Deployed: {', '.join(result.deployed)}[/green]"
+                    )
+                if result.removed:
+                    console.print(
+                        f"  [yellow]✓ Removed: {', '.join(result.removed)}[/yellow]"
+                    )
+                if result.errors:
+                    for error in result.errors:
+                        console.print(f"  [red]✗ {error}[/red]")
+
+                if result.success:
+                    console.print(
+                        "\n[bold green]✓ Skill deployment complete![/bold green]"
+                    )
+                    return CommandResult(success=True, exit_code=0)
+                console.print(
+                    f"\n[yellow]⚠ Deployment had {len(result.errors)} errors[/yellow]"
+                )
+                return CommandResult(
+                    success=False,
+                    message=f"{len(result.errors)} deployment errors",
+                    exit_code=1,
+                )
+
+            except Exception as e:
+                console.print(f"\n[red]Reconciliation failed: {e}[/red]")
+                return CommandResult(success=False, message=str(e), exit_code=1)
+
+        except Exception as e:
+            console.print(f"[red]Skill selection error: {e}[/red]")
+            import traceback
+
+            console.print(f"[dim]{traceback.format_exc()}[/dim]")
+            return CommandResult(success=False, message=str(e), exit_code=1)
+
 
 def manage_skills(args) -> int:
     """

claude_mpm/cli/executor.py

@@ -66,6 +66,7 @@ def ensure_run_attributes(args):
     args.monitor = getattr(args, "monitor", False)
     args.force = getattr(args, "force", False)
     args.reload_agents = getattr(args, "reload_agents", False)
+    args.force_sync = getattr(args, "force_sync", False)
     # Include dependency checking attributes
     args.check_dependencies = getattr(args, "check_dependencies", True)
     args.force_check_dependencies = getattr(args, "force_check_dependencies", False)
@@ -126,6 +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
@@ -150,6 +159,16 @@ def execute_command(command: str, args) -> int:
         result = summarize_command(args)
         return result if result is not None else 0
 
+    # Handle profile command with lazy import
+    if command == "profile":
+        # Lazy import to avoid loading unless needed
+        from .commands.profile import ProfileCommand
+
+        cmd = ProfileCommand()
+        result = cmd.run(args)
+        # Convert CommandResult to exit code
+        return result.exit_code if result else 0
+
     # Handle auto-configure command with lazy import
     if command == "auto-configure":
         # Lazy import to avoid loading unless needed
@@ -195,35 +214,127 @@ 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
+            try:
+                # Build argument list for Click command based on subcommand
+                click_args = []
+
+                # 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
+
+                # 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
+            except Exception as e:
+                print(f"Error: {e}")
+                return 1
+        else:
+            print(f"Unknown hook-errors subcommand: {subcommand}")
+            return 1
+
+    # Handle autotodos command with lazy import
+    if command == "autotodos":
+        # Lazy import to avoid loading unless needed
+        from .commands.autotodos import (
+            clear_autotodos,
+            inject_autotodos,
+            list_autotodos,
+            list_pm_violations,
+            scan_delegation_patterns,
+            show_autotodos_status,
+        )
 
-            ctx = click.Context(command=handler)
+        # Get subcommand
+        subcommand = getattr(args, "autotodos_command", "status")
+        if not subcommand:
+            subcommand = "status"
 
-            # 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
+        # Map subcommands to functions
+        handlers = {
+            "list": list_autotodos,
+            "inject": inject_autotodos,
+            "clear": clear_autotodos,
+            "status": show_autotodos_status,
+            "scan": scan_delegation_patterns,
+            "violations": list_pm_violations,
+        }
 
+        # Get handler and call it with standalone_mode=False
+        handler = handlers.get(subcommand)
+        if handler:
             try:
-                # Invoke handler with arguments
-                with ctx:
-                    handler.invoke(ctx, **kwargs)
+                # Build argument list for Click command
+                click_args = []
+
+                if subcommand == "list":
+                    fmt = getattr(args, "format", "table")
+                    click_args = ["--format", fmt]
+                elif subcommand == "inject":
+                    output = getattr(args, "output", None)
+                    if output:
+                        click_args = ["--output", output]
+                elif subcommand == "clear":
+                    error_key = getattr(args, "error_key", None)
+                    event_type = getattr(args, "event_type", "all")
+                    if error_key:
+                        click_args.append("--error-key")
+                        click_args.append(error_key)
+                    if event_type != "all":
+                        click_args.append("--event-type")
+                        click_args.append(event_type)
+                    if getattr(args, "yes", False):
+                        click_args.append("-y")
+                elif subcommand == "scan":
+                    text = getattr(args, "text", None)
+                    file = getattr(args, "file", None)
+                    fmt = getattr(args, "format", "table")
+                    save = getattr(args, "save", False)
+
+                    if text:
+                        click_args.append(text)
+                    if file:
+                        click_args.extend(["--file", file])
+                    if fmt != "table":
+                        click_args.extend(["--format", fmt])
+                    if save:
+                        click_args.append("--save")
+                elif subcommand == "violations":
+                    fmt = getattr(args, "format", "table")
+                    if fmt != "table":
+                        click_args.extend(["--format", fmt])
+
+                # 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
             except Exception as e:
                 print(f"Error: {e}")
+                import traceback
+
+                traceback.print_exc()
                 return 1
         else:
-            print(f"Unknown hook-errors subcommand: {subcommand}")
+            print(f"Unknown autotodos subcommand: {subcommand}")
             return 1
 
     # Map stable commands to their implementations
@@ -249,6 +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
@@ -276,6 +388,8 @@ def execute_command(command: str, args) -> int:
         "local-deploy",
         "skill-source",
         "agent-source",
+        "hook-errors",
+        "autotodos",
     ]
 
     suggestion = suggest_similar_commands(command, all_commands)