refactor: move data operations into the daemon

[orga-agent]

Summary

• make the daemon the sole application/data host; CLI and MCP use a mandatory protocol-v2 typed Unix-socket API and never open SQLite
• permanently retire remote-cluster PgWire/managed mode, DATABASE_URL routing, capability negotiation, PostgreSQL SQLx features, and managed lifecycle branches
• make remote note creation return the canonical short ID, write the full confirmed row into the local cache, and skip only marker-tagged redundant PowerSync PUTs
• replace cross-process WAL watching with in-process may-write signals while retaining startup CRUD drain and WAL checkpoints
• align with flick-backend PR #399 by removing the retired keyterm domain and safely consuming pre-upgrade queued CRUD
• split the daemon monolith into runtime, connector, upload, storage-maintenance, remote, app-domain, and IPC ownership modules; move private tests beside their owners
• move MCP to the standard Send async stack, remove blocking file reads from daemon async paths, and remove dead/defaulting RPC branches
• permanently enforce too_many_lines, cognitive_complexity, large_futures, and future_not_send through one workspace/all-target/all-feature Clippy command in just, hooks, PR CI, and main CI

Safety and races

• remote create uses stable UUIDs, same-ID create-only retries, and typed unknown/partial outcomes
• marked remote-confirmed inserts never issue a stale backend upsert; malformed or unsupported markers fail closed
• sync-first local races use insert-if-absent; confirmed extraction subsets are committed and reported precisely
• transient upload failures retry without requiring another write trigger
• protocol/version readiness and PID executable identity are checked before lifecycle actions
• existing PowerSync databases preserve project rows while retiring keyterm schema; old queued keyterm CRUD is consumed and retired project fields are stripped

Verification

• cargo fmt --all --check
• cargo clippy --workspace --all-targets --all-features -- -D warnings
• cargo test --workspace --all-features — 318 tests passed
• SQLX_OFFLINE=true cargo check --workspace --all-targets --all-features
• just sqlx-prepare
• just check
• cargo build --workspace
• git diff --check
• lefthook run pre-commit
• lefthook run pre-push

Authorized dev smoke confirmed invalid DATABASE_URL still starts local protocol 2, note add → immediate detail/MCP get, text upload, editor round-trip, project CRUD upload, empty ps_crud, and advancing WAL checkpoint. Test notes/project were archived and the original installed daemon was restored. The dev share endpoint returned an external 404, so live share/unshare could not be completed; application/IPC share contracts remain covered by automated tests.

Observed pre-existing follow-up: an immediate note add against a just-created project can race the project's asynchronous upload and receive backend FK 23503. Recorded as FlickNote deferable #1791; no arbitrary delay or temporary upload barrier was added to this refactor.