Fix: Remove short flags from non-boolean typer.Option definitions

Fixes #48

## Problem
CAM failed to initialize with "TypeError: Secondary flag is not valid
for non-boolean flag" when running any command. The error occurred during
Typer/Click CLI initialization.

## Root Cause
Throughout the codebase, non-boolean typer.Option() definitions incorrectly
included short flags (e.g., -c, -s, -n, -o, -b, -f, -d, -a, -l, -m).

In Click/Typer, only boolean flags can have both a long form (--flag) and
short form (-f). Non-boolean options (strings, paths, integers, etc.) can
only use long-form flags.

## Changes
- Removed short flags from all non-boolean typer.Option definitions across
  12 files in cli/ and mcp/ directories
- Fixed parameter name conflict in prompts_commands.py where 'default'
  parameter conflicted with boolean flag syntax
- Boolean options (with True/False as first argument) retain their short flags

## Affected Files
- cli/agents_commands.py
- cli/app.py
- cli/options.py
- cli/plugins/plugin_discovery_commands.py
- cli/plugins/plugin_install_commands.py
- cli/plugins/plugin_management_commands.py
- cli/plugins/plugin_marketplace_commands.py
- cli/prompts_commands.py
- cli/skills_commands.py
- mcp/cli.py
- mcp/install_commands.py
- mcp/server_commands.py

## Testing
Verified that CLI initializes successfully and no TypeError is raised:
```python
from code_assistant_manager.cli import app
from typer.main import get_command
cmd = get_command(app)  # No error
```

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

Author: Vadiml1024

code_assistant_manager/cli/agents_commands.py

@@ -27,29 +27,20 @@
 )
 AGENT_KEY_ARGUMENT = typer.Argument(..., help="Agent identifier")
 APP_TYPE_OPTION = typer.Option(
-    "claude",
-    "--app",
-    "-a",
-    help="App type(s) to install to (claude, codex, gemini, droid, codebuddy, opencode, all). Comma-separated.",
+    "claude", "--app", help="App type(s) to install to (claude, codex, gemini, droid, codebuddy, opencode, all). Comma-separated.",
 )
 FORCE_OPTION = typer.Option(False, "--force", "-f", help="Skip confirmation")
-OWNER_OPTION = typer.Option(..., "--owner", "-o", help="Repository owner")
-NAME_OPTION = typer.Option(..., "--name", "-n", help="Repository name")
-BRANCH_OPTION = typer.Option("main", "--branch", "-b", help="Repository branch")
+OWNER_OPTION = typer.Option(..., "--owner", help="Repository owner")
+NAME_OPTION = typer.Option(..., "--name", help="Repository name")
+BRANCH_OPTION = typer.Option("main", "--branch", help="Repository branch")
 AGENTS_PATH_OPTION_REPO = typer.Option(
     None, "--agents-path", help="Agents subdirectory path"
 )
 APP_TYPE_OPTION_ALL = typer.Option(
-    None,
-    "--app",
-    "-a",
-    help="App type(s) to show (claude, codex, gemini, droid, codebuddy, opencode, all). Default shows all.",
+    None, "--app", help="App type(s) to show (claude, codex, gemini, droid, codebuddy, opencode, all). Default shows all.",
 )
 APP_TYPE_OPTION_UNINSTALL = typer.Option(
-    ...,
-    "--app",
-    "-a",
-    help="App type(s) to uninstall all agents from (claude, codex, gemini, droid, codebuddy, opencode, all). Comma-separated.",
+    ..., "--app", help="App type(s) to uninstall all agents from (claude, codex, gemini, droid, codebuddy, opencode, all). Comma-separated.",
 )
 from code_assistant_manager.plugins.fetch import parse_github_url
 

code_assistant_manager/cli/app.py

@@ -1113,7 +1113,7 @@ def _create_lazy_tool_command(tool_name: str):
     def tool_command(
         ctx: Context,
         config: Optional[str] = typer.Option(
-            None, "--config", "-c", help="Path to settings.conf configuration file"
+            None, "--config", help="Path to settings.conf configuration file"
         ),
     ):
         """Launch the specified AI code editor."""
@@ -1217,10 +1217,7 @@ def make_placeholder(name):
             def placeholder_cmd(
                 ctx: Context,
                 config: Optional[str] = typer.Option(
-                    None,
-                    "--config",
-                    "-c",
-                    help="Path to settings.conf configuration file",
+                    None, "--config", help="Path to settings.conf configuration file",
                 ),
             ):
                 # Replace this placeholder with the real command
@@ -1255,7 +1252,7 @@ def make_command(name, cls):
         def command(
             ctx: Context,
             config: Optional[str] = typer.Option(
-                None, "--config", "-c", help="Path to settings.conf configuration file"
+                None, "--config", help="Path to settings.conf configuration file"
             ),
         ):
             """Launch the specified AI code editor."""
@@ -1388,7 +1385,7 @@ def doctor(
     ctx: Context,
     verbose: bool = typer.Option(False, "--verbose", "-v", help="Show detailed output"),
     config: Optional[str] = typer.Option(
-        None, "--config", "-c", help="Path to config file"
+        None, "--config", help="Path to config file"
     ),
 ):
     """Run diagnostic checks on the code-assistant-manager installation (alias: d)"""
@@ -1452,7 +1449,7 @@ def upgrade_command(
         False, "--verbose", "-v", help="Enable verbose installer output"
     ),
     config: Optional[str] = typer.Option(
-        None, "--config", "-c", help="Path to config file"
+        None, "--config", help="Path to config file"
     ),
 ):
     """Upgrade CLI tools (alias: u). If not installed, will install."""
@@ -1517,7 +1514,7 @@ def upgrade_alias_cmd(
     ctx: Context,
     target: str = typer.Argument("all", help="Tool to upgrade or 'all'"),
     config: Optional[str] = typer.Option(
-        None, "--config", "-c", help="Path to config file"
+        None, "--config", help="Path to config file"
     ),
 ):
     """Alias for 'upgrade' command."""
@@ -1538,7 +1535,7 @@ def install_command(
         False, "--verbose", "-v", help="Enable verbose installer output"
     ),
     config: Optional[str] = typer.Option(
-        None, "--config", "-c", help="Path to config file"
+        None, "--config", help="Path to config file"
     ),
 ):
     """Install CLI tools (alias: i). Same as upgrade - if not installed, will install. If installed, will try to upgrade."""
@@ -1556,7 +1553,7 @@ def install_alias_cmd(
     ctx: Context,
     target: str = typer.Argument("all", help="Tool to install or 'all'"),
     config: Optional[str] = typer.Option(
-        None, "--config", "-c", help="Path to config file"
+        None, "--config", help="Path to config file"
     ),
 ):
     """Alias for 'install' command."""
@@ -1578,7 +1575,7 @@ def uninstall_command(
         False, "--keep-config", "-k", help="Keep configuration files"
     ),
     config: Optional[str] = typer.Option(
-        None, "--config", "-c", help="Path to config file"
+        None, "--config", help="Path to config file"
     ),
 ):
     """Uninstall CLI tools and backup their configuration files."""
@@ -1603,7 +1600,7 @@ def uninstall_alias(
         False, "--keep-config", "-k", help="Keep configuration files"
     ),
     config: Optional[str] = typer.Option(
-        None, "--config", "-c", help="Path to config file"
+        None, "--config", help="Path to config file"
     ),
 ):
     """Alias for 'uninstall' command."""
@@ -1636,7 +1633,7 @@ def doctor_alias(
     ctx: Context,
     verbose: bool = typer.Option(False, "--verbose", "-v", help="Show detailed output"),
     config: Optional[str] = typer.Option(
-        None, "--config", "-c", help="Path to config file"
+        None, "--config", help="Path to config file"
     ),
 ):
     """Alias for 'doctor' command."""
@@ -1652,7 +1649,7 @@ def doctor_alias(
 @config_app.command("validate")
 def validate_config(
     config: Optional[str] = typer.Option(
-        None, "--config", "-c", help="Path to config file"
+        None, "--config", help="Path to config file"
     ),
     verbose: bool = typer.Option(False, "--verbose", "-v", help="Show detailed output"),
 ):
@@ -1859,10 +1856,10 @@ def set_config(
     ),
     value: str = typer.Argument(..., help="Value to set"),
     app: str = typer.Option(
-        None, "-a", "--app", help="App/tool to operate on (claude, codex, droid, etc.)"
+        None, "--app", help="App/tool to operate on (claude, codex, droid, etc.)"
     ),
     scope: str = typer.Option(
-        "user", "--scope", "-s", help="Configuration scope (user, project)"
+        "user", "--scope", help="Configuration scope (user, project)"
     ),
 ):
     """Set a configuration value for code assistants.
@@ -1951,10 +1948,10 @@ def unset_config(
         ..., help="Configuration key path (e.g., 'model' or 'codex.model')"
     ),
     app: str = typer.Option(
-        None, "-a", "--app", help="App/tool to operate on (claude, codex, droid, etc.)"
+        None, "--app", help="App/tool to operate on (claude, codex, droid, etc.)"
     ),
     scope: str = typer.Option(
-        "user", "--scope", "-s", help="Configuration scope (user, project)"
+        "user", "--scope", help="Configuration scope (user, project)"
     ),
 ):
     """Unset a configuration value for code assistants.
@@ -2070,10 +2067,10 @@ def show_config(
         None, help="Specific config key path to show (optional)"
     ),
     app: str = typer.Option(
-        "claude", "-a", "--app", help="App to show config for (default: claude)"
+        "claude", "--app", help="App to show config for (default: claude)"
     ),
     scope: Optional[str] = typer.Option(
-        None, "--scope", "-s", help="Filter by scope (user, project)"
+        None, "--scope", help="Filter by scope (user, project)"
     ),
 ):
     """Show configuration for an AI editor app in dotted notation format.

code_assistant_manager/cli/options.py

@@ -3,9 +3,9 @@
 import typer
 
 # Module-level typer.Option constants to fix B008 linting errors
-CONFIG_FILE_OPTION = typer.Option(None, "--config", "-c", help="Path to config file")
+CONFIG_FILE_OPTION = typer.Option(None, "--config", help="Path to config file")
 CONFIG_OPTION = typer.Option(
-    None, "--config", "-c", help="Path to settings.conf configuration file"
+    None, "--config", help="Path to settings.conf configuration file"
 )
 DEBUG_OPTION = typer.Option(False, "--debug", "-d", help="Enable debug logging")
 ENDPOINTS_OPTION = typer.Option(
@@ -20,10 +20,7 @@
 )
 SHELL_OPTION = typer.Argument(..., help="Shell type (bash, zsh)")
 SCOPE_OPTION = typer.Option(
-    "user",
-    "--scope",
-    "-s",
-    help="Configuration scope (user, project)",
+    "user", "--scope", help="Configuration scope (user, project)",
 )
 TARGET_OPTION = typer.Argument("all", help="Tool to upgrade or 'all'")
 TOOL_ARGS_OPTION = typer.Argument(None, help="Arguments for the editor")

code_assistant_manager/cli/plugins/plugin_discovery_commands.py

@@ -169,10 +169,7 @@ def view_plugin(
         help="Plugin name to view (e.g., 'document-skills' or 'awesome-plugins:document-skills')",
     ),
     app_type: str = typer.Option(
-        "claude",
-        "--app",
-        "-a",
-        help=f"App type ({', '.join(VALID_APP_TYPES)})",
+        "claude", "--app", help=f"App type ({', '.join(VALID_APP_TYPES)})",
     ),
 ):
     """View detailed information about a specific plugin.
@@ -292,10 +289,7 @@ def view_plugin(
 @plugin_app.command("status")
 def plugin_status(
     app_type: Optional[str] = typer.Option(
-        None,
-        "--app",
-        "-a",
-        help=f"App type ({', '.join(VALID_APP_TYPES)}). If not specified, shows status for all apps.",
+        None, "--app", help=f"App type ({', '.join(VALID_APP_TYPES)}). If not specified, shows status for all apps.",
     ),
 ):
     """Show plugin system status for an app, or all apps if none specified."""
@@ -481,10 +475,7 @@ def show_app_info(app: str, show_cam_config: bool = True):
 @plugin_app.command("status")
 def plugin_status(
     app_type: Optional[str] = typer.Option(
-        None,
-        "--app",
-        "-a",
-        help=f"App type ({', '.join(VALID_APP_TYPES)}). If not specified, shows status for all apps.",
+        None, "--app", help=f"App type ({', '.join(VALID_APP_TYPES)}). If not specified, shows status for all apps.",
     ),
 ):
     """Show plugin system status for an app, or all apps if none specified."""

code_assistant_manager/cli/plugins/plugin_install_commands.py

@@ -373,16 +373,10 @@ def install_plugin(
         help="Plugin name or marketplace:plugin-name. Examples: 'code-reviewer' or 'awesome-plugins:code-reviewer'",
     ),
     marketplace: Optional[str] = typer.Option(
-        None,
-        "--marketplace",
-        "-m",
-        help="Marketplace name (alternative to marketplace:plugin-name format)",
+        None, "--marketplace", help="Marketplace name (alternative to marketplace:plugin-name format)",
     ),
     app_type: str = typer.Option(
-        "claude",
-        "--app",
-        "-a",
-        help=f"App type to install to ({', '.join(VALID_APP_TYPES)})",
+        "claude", "--app", help=f"App type to install to ({', '.join(VALID_APP_TYPES)})",
     ),
 ):
     """Install a plugin from available marketplaces.
@@ -490,10 +484,7 @@ def uninstall_plugin(
     plugin: str = typer.Argument(..., help="Plugin name to uninstall"),
     force: bool = typer.Option(False, "--force", "-f", help="Skip confirmation"),
     app_type: str = typer.Option(
-        "claude",
-        "--app",
-        "-a",
-        help=f"App type to uninstall from ({', '.join(VALID_APP_TYPES)})",
+        "claude", "--app", help=f"App type to uninstall from ({', '.join(VALID_APP_TYPES)})",
     ),
 ):
     """Uninstall an installed plugin.
@@ -615,10 +606,7 @@ def _remove_plugin_from_settings(handler, plugin: str) -> bool:
 def enable_plugin(
     plugin: str = typer.Argument(..., help="Plugin name to enable"),
     app_type: str = typer.Option(
-        "claude",
-        "--app",
-        "-a",
-        help=f"App type ({', '.join(VALID_APP_TYPES)})",
+        "claude", "--app", help=f"App type ({', '.join(VALID_APP_TYPES)})",
     ),
 ):
     """Enable a disabled plugin."""
@@ -657,10 +645,7 @@ def enable_plugin(
 def disable_plugin(
     plugin: str = typer.Argument(..., help="Plugin name to disable"),
     app_type: str = typer.Option(
-        "claude",
-        "--app",
-        "-a",
-        help=f"App type ({', '.join(VALID_APP_TYPES)})",
+        "claude", "--app", help=f"App type ({', '.join(VALID_APP_TYPES)})",
     ),
 ):
     """Disable an enabled plugin."""
@@ -699,10 +684,7 @@ def disable_plugin(
 def validate_plugin(
     path: str = typer.Argument(..., help="Path to plugin or marketplace to validate"),
     app_type: str = typer.Option(
-        "claude",
-        "--app",
-        "-a",
-        help=f"App type ({', '.join(VALID_APP_TYPES)})",
+        "claude", "--app", help=f"App type ({', '.join(VALID_APP_TYPES)})",
     ),
 ):
     """Validate a plugin or marketplace manifest."""

code_assistant_manager/cli/plugins/plugin_management_commands.py

@@ -35,28 +35,16 @@ def list_plugins(
         help="Show all plugins from marketplaces (not just enabled). Deprecated: use without marketplace argument instead.",
     ),
     app_type: Optional[str] = typer.Option(
-        None,
-        "--app",
-        "-a",
-        help=f"App type to show plugins for ({', '.join(VALID_APP_TYPES)}). Shows all apps if not specified.",
+        None, "--app", help=f"App type to show plugins for ({', '.join(VALID_APP_TYPES)}). Shows all apps if not specified.",
     ),
     query: Optional[str] = typer.Option(
-        None,
-        "--query",
-        "-q",
-        help="Filter plugins by name or description",
+        None, "--query", help="Filter plugins by name or description",
     ),
     category: Optional[str] = typer.Option(
-        None,
-        "--category",
-        "-c",
-        help="Filter plugins by category",
+        None, "--category", help="Filter plugins by category",
     ),
     limit: int = typer.Option(
-        50,
-        "--limit",
-        "-n",
-        help="Maximum number of plugins to show",
+        50, "--limit", help="Maximum number of plugins to show",
     ),
 ):
     """List installed and available plugins from configured marketplaces.
@@ -428,17 +416,14 @@ def _print_repo(name: str, repo: PluginRepo, is_user: bool = False):
 
 @plugin_app.command("add-repo")
 def add_repo(
-    owner: str = typer.Option(..., "--owner", "-o", help="Repository owner"),
-    name: str = typer.Option(..., "--name", "-n", help="Repository name"),
-    branch: str = typer.Option("main", "--branch", "-b", help="Repository branch"),
+    owner: str = typer.Option(..., "--owner", help="Repository owner"),
+    name: str = typer.Option(..., "--name", help="Repository name"),
+    branch: str = typer.Option("main", "--branch", help="Repository branch"),
     description: Optional[str] = typer.Option(
-        None, "--description", "-d", help="Repository description"
+        None, "--description", help="Repository description"
     ),
     repo_type: str = typer.Option(
-        "marketplace",
-        "--type",
-        "-t",
-        help="Repository type (plugin or marketplace)",
+        "marketplace", "--type", help="Repository type (plugin or marketplace)",
     ),
     plugin_path: Optional[str] = typer.Option(
         None, "--plugin-path", help="Plugin path within the repository"