docs: Add comprehensive documentation for plugins, exec mode, and user guide (#6)

* docs: add comprehensive documentation for plugins, exec mode, and user guide

* 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

* fix(docs): improve security warnings and examples in exec-mode.md

- Add stronger warnings for --skip-permissions-unsafe flag
- Quote $file variable in batch processing example
- Add production deployment safeguards and checklist
- Address security audit recommendations

* fix(docs): address additional security review findings

- Quote $SESSION variable in multi-turn session example (exec-mode.md)
- Add security note about reviewing installation scripts (user-guide.md)

Author: echobt