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

[Vadiml1024]

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, making the tool completely unusable.

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.

Solution

1. Fixed Short Flag Definitions (Commit: af64dfe)

• Removed short flags from all non-boolean typer.Option definitions across 12 files
• Fixed parameter name conflict in prompts_commands.py where the default parameter name conflicted with boolean flag syntax
• Boolean options (with True/False as first argument) retain their short flags as they are allowed

2. Fixed Typer Version Incompatibility (Commit: 2545df3)

During testing, we discovered a second bug: The project required typer>=0.13.0, but short flags for booleans were only added in Typer 0.16.0. This caused an error:

TypeError: Boolean options accept only one no_args_is_help per argument, got: ('False', 'True')

Fix: Upgraded minimum Typer version from >=0.13.0 to >=0.16.0 in pyproject.toml to ensure short flag support works correctly.

Changes

Files Modified (13 total)

• 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
• pyproject.toml (Typer version update)

Example Changes

Before:

CONFIG_FILE_OPTION = typer.Option(None, "--config", "-c", help="Path to config file")
SCOPE_OPTION = typer.Option("user", "--scope", "-s", help="Configuration scope")

After:

CONFIG_FILE_OPTION = typer.Option(None, "--config", help="Path to config file")
SCOPE_OPTION = typer.Option("user", "--scope", help="Configuration scope")

Boolean flags (unchanged):

DEBUG_OPTION = typer.Option(False, "--debug", "-d", help="Enable debug logging")
FORCE_OPTION = typer.Option(False, "--force", "-f", help="Skip confirmation prompt")

Version update in pyproject.toml:

# Before:
typer = ">=0.13.0"

# After:
typer = ">=0.16.0"

Testing

Verified that CLI initializes successfully without errors:

from code_assistant_manager.cli import app
from typer.main import get_command
cmd = get_command(app)  # ✓ No TypeError raised

Impact

• Before: Tool completely unusable - all commands failed on initialization
• After: Tool works as expected, all commands initialize properly

Breaking Changes

Users who were using short flags for non-boolean options will need to switch to long flags:

• -c → --config
• -s → --scope
• -n → --name
• -o → --owner
• etc.

However, since the tool was completely broken before this fix, there are likely no active users relying on these short flags.

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Note: This PR was created with assistance from Claude Code after discovering and documenting the issue in #48. The Typer version incompatibility was discovered during testing and fixed in a follow-up commit.