Clean up orphaned messages when deleting a branch

[Doondi-Ashlesh]

Summary

delete_branch was removing rows from turn_usage and message_structure but leaving behind the corresponding rows in the messages table that belonged exclusively to the deleted branch. Those rows were invisible to any query since get_items joins through message_structure, but they kept accumulating on disk with each branch deletion.

The existing _cleanup_orphaned_messages_sync helper already does the right thing: it finds messages with no remaining references in message_structure and removes them. This just calls it inside the same transaction before the final commit, so shared messages (referenced by other branches) are preserved and exclusive ones are removed atomically.

Test plan

Added test_delete_branch_removes_orphaned_messages which:

• Creates two messages on main and one message exclusively on a side branch
• Verifies all three rows exist in the messages table before deletion
• Deletes the side branch
• Checks only two rows remain (the branch-only message is gone)
• Checks the shared message is still readable from main

All 38 tests in test_advanced_sqlite_session.py pass. No regressions in the wider suite.

Issue number

Closes #3346

Checks

• I've added new tests (if relevant)
• I've added/updated the relevant documentation
• I've run make lint and make format
• I've made sure tests pass