Three separate code paths all wrote to the same SQLite state.db with
no deduplication, inflating session transcripts by 3-4x:
1. _log_msg_to_db() — wrote each message individually after append
2. _flush_messages_to_session_db() — re-wrote ALL new messages at
every _persist_session() call (~18 exit points), with no tracking
of what was already written
3. gateway append_to_transcript() — wrote everything a third time
after the agent returned
Since load_transcript() prefers SQLite over JSONL, the inflated data
was loaded on every session resume, causing proportional token waste.
Fix:
- Remove _log_msg_to_db() and all 16 call sites (redundant with flush)
- Add _last_flushed_db_idx tracking in _flush_messages_to_session_db()
so repeated _persist_session() calls only write truly new messages
- Reset flush cursor on compression (new session ID)
- Add skip_db parameter to SessionStore.append_to_transcript() so the
gateway skips SQLite writes when the agent already persisted them
- Gateway now passes skip_db=True for agent-managed messages, still
writes to JSONL as backup
Verified: a 12-message CLI session with tool calls produces exactly
12 SQLite rows with zero duplicates (previously would be 36-48).
Tests: 9 new tests covering flush deduplication, skip_db behavior,
compression reset, and initialization. Full suite passes (2869 tests).
