docs: restructure README — story over catalog, move reference to docs/

README now tells the story in three layers (kernel, emergent behavior,
colony) instead of cataloging every feature. Roughly one-third the
original length. All reference material preserved:
- docs/words.md — complete 309-word reference
- docs/protocol.md — S-expression wire format and mesh details
- docs/operations.md — monitoring, goals, trust, persistence, swarm

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: DavidLiedle