Two unrelated-to-shim-removal pre-existing flakes surfaced during baseline `make ci` verification and blocked the shim-removal lode. Both are test-only fixes. test_entity_intelligence was depending on a gitignored, shared tests/fixtures/journal/indexer/journal.sqlite whose contents were only populated if an earlier test happened to run scan_journal against that fixture first. Replaced the autouse fixture with the repo-standard journal_copy + scan_journal(..., full=True) pattern so each test builds its own deterministic index. test_cortex_client::test_wait_for_agents_missed_event_recovery had a race between unlinking {use_id}_active.jsonl and writing {use_id}.jsonl. Under make ci's coverage overhead, wait_for_uses() could observe the gap and return empty completed. Reordered the two ops so the terminal file exists before the active marker is removed — matches the real production invariant relied on by _find_use_file(). Co-authored-by: Codex <codex@openai.com>