fix(docs): update plugins.md to reflect actual implementation

Address Greptile review comments:
- Clarify that plugin system is in early stage/foundation phase
- Document currently implemented features (basic manifest management)
- Move WASM, capabilities, permissions, hooks, commands to 'Roadmap' section
- Add clear status indicators for implemented vs planned features

The documentation now accurately reflects that:
- Only basic manifest fields (name, version, description, enabled) are supported
- WASM runtime integration is planned but not yet implemented
- Capabilities, permissions, hooks, and commands are roadmap items

Author: echobt