fix(tests): stabilize two pre-existing flakes under full-suite load
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>