refactor: remove legacy compatibility code and unused parameters
Remove ~290 lines of dead code and backwards compatibility shims that are
no longer needed:
**Removed deprecated code:**
- JournalEventWriter class (deprecated, cortex handles logging now)
- test_cortex_agent_logging.py (only tested deprecated class)
- build_index alias (unused, no callers found)
**Removed entity loading fallback:**
- Drop fallback to top-level entities.jsonl when no facet entities exist
- Enforce facet-based architecture for entity management
**Removed unused notification command parameter:**
- Remove --notify-cmd CLI argument from supervisor
- Remove command parameter from send_notification()
- Remove command parameter from alert_if_ready()
- Remove command parameter from handle_runner_exits()
- Remove command parameter from handle_health_checks()
- Remove command parameter from supervise()
- Desktop notifications now use desktop-notifier library directly
**Fixed misleading comments:**
- Remove "legacy patterns" comment from transcript regex (current code)
- Remove "legacy screenshot PNG" comment (still handles both formats)
- Remove "check for legacy path" comments that had no implementation
- Remove "deprecated tests" comment (tests were active, not deprecated)
All tests pass. Remaining compatibility code is actively used and justified.
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Co-Authored-By: Claude <noreply@anthropic.com>