REST config schemas missing newer config keys

[zicochaos]

Found during review of PR #12 (pre-existing, not caused by the merge).

• extra_agent_dirs is accepted by the file config but absent from both REST config schemas: packages/kap-server/src/protocol/rest-config.ts and packages/protocol/src/rest/config.ts.
• secondary_model is present in packages/kap-server/src/protocol/rest-config.ts but missing from packages/protocol/src/rest/config.ts.

Impact: clients validating against @moonshot-ai/protocol (or the kap-server REST surface) cannot round-trip these keys over REST even though the engine supports them.