Enhanced Hook System with Per-Command Timeouts

The hook execution system now supports individual timeout configurations for each command within a hook. Previously, all commands shared a single global timeout, but now each command can specify its own timeout value.

Usage Example: When configuring hooks, you can now specify a timeout for individual commands:

{
  "hook_event_name": "pre-commit",
  "commands": [
    {
      "command": "npm test",
      "timeout": 30  // 30 seconds timeout
    },
    {
      "command": "npm run lint",
      "timeout": 10  // 10 seconds timeout
    }
  ]
}