Overhaul the architectural specification (specification.md) and reorganize
the developer journals to incorporate the new Domain Anchor model. This scopes
sandbox container names, lockfiles, control sockets, and State Anchor persistent
overlay filesystem layers to unique (agent, workspace) hash pairings.
- Add Domain Anchor and Domain Root definitions to glossary and expansion tokens.
- Specify the Ephemeral Session Coordinator pattern with hold-to-bind locking.
- Document Git Sentry nested read-only mount layout replacing the legacy Git Shadow.
- Renamed and reorganized research sub-journals, embedding executable Python logic in-place.
- Include `redb` for embedded transactional state.
