Add NAVI.md navigation hub and update core docs ...

NAVI.md: lightweight project entry point for Navi — server command,
key paths, doc map with query instructions, tool manual index.
All profiles read this; detailed content stays in docs/.

docs/agent.md: rewrite to cover 3-phase planning, all 10 thinking
mechanics flags, adaptive replan, anti-stall, goal anchoring.

docs/profiles.md: update AgentProfile fields (all flags), correct
profile list (secretary/server_admin/developer), JSON config format,
auto-discovery instead of manual registration.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>