Better formatting for attribute inheritance

Use Claude CLI's native mcp add command instead of desktop config file.
This ensures MCP servers are properly registered and store paths stay current.

- Add preHook parameter for running commands before exec
- Update pass tool to use preHook for GPG key import instead of custom wrapper
- Add preHook to passthru for inspection
- Update documentation with preHook examples

- Add flags parameter to makeWrapper for command-line arguments
- Change wrapper parameter to always be a function receiving { exePath, flagsString, envString, env, flags }
- Remove automatic "--" prefix handling for flags (users specify full flag names)
- Improve formatting with proper line breaks and indentation for multi-line commands
- Add passthru for env and flags to make them accessible
- Update tools to use new function-based wrapper syntax:
- tmux: uses flags directly with -f for config file
- pass: uses custom wrapper function for GPG key import
- muchsync: uses custom wrapper function with host detection logic