Add direct tool access and repository watching

[wesen]

Adds the ability to interact with tools directly without starting a server, plus
automatic repository watching for live updates.

Key changes:

• New server tools command group for direct tool interaction
  • list shows available tools with schemas
  • call executes tools directly
• Automatic repository watching for live updates when tools change
• Refactored tool provider creation into dedicated server layer
• Improved error handling and configuration loading
• Added graceful shutdown handling

Breaking changes:

• Moved server settings into dedicated parameter layer
• Tool provider creation now requires explicit watch flag