fix: #3346 clean up branch-only messages when deleting branches

[Aphroq]

Summary

This pull request fixes AdvancedSQLiteSession.delete_branch() leaving branch-only message rows behind after deleting a branch. After removing the deleted branch's message_structure rows, the method now cleans up message rows for the current session that are no longer referenced by any structure row, using the same lock and transaction while preserving messages still shared by main or other branches.

Test plan

• uv run pytest -q tests/extensions/memory/test_advanced_sqlite_session.py::test_delete_branch_removes_branch_only_messages tests/extensions/memory/test_advanced_sqlite_session.py::test_branching_functionality tests/extensions/memory/test_advanced_sqlite_session.py::test_branch_deletion_with_force
• uv run pytest -q tests/extensions/memory/test_advanced_sqlite_session.py
• bash .agents/skills/code-change-verification/scripts/run.sh

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

[Aphroq]

Pushed follow-up commit to the PR branch with two extra boundary hardenings:

• _cleanup_orphaned_messages_sync() now uses a session-scoped set-based DELETE instead of first materializing every orphan id in Python and building a long IN (...) parameter list. The delete remains scoped to the current session_id, and it preserves any message still referenced by message_structure for that session.
• Added descendant branch coverage: if branch B inherits messages from branch A, deleting branch A does not remove messages still referenced by branch B.
• Added large orphan cleanup coverage: cleaning many orphan rows uses a fixed number of SQL parameters, avoiding SQLite bind parameter limit issues.

[Aphroq]

@codex review

[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. 🚀

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