- Replace all 'Plannotator protocol' with 'stdin/stdout protocol'
- Update README, PROTOCOL.md, source comments, XML docs
- Use generic 'tool' instead of 'Plannotator' where appropriate
- Clarify that the protocol is agent-agnostic, not Plannotator-specific

This makes the documentation describe the protocol itself rather than
framing it as a Plannotator proprietary protocol.