Remove `LocalDatabase` after oxidation

[FirelightFlagboy]

Remove the python class LocalDatabase after oxidation of the last classes that where using it.

Depend on

• #3168
• #3169

TODOs

• [ ] Remove the class LocalDatabase
• [ ] Rewrite the suite tests test_disk_full at tests/core/fs/test_disk_full.py
• [ ] Rewrite the test test_workspace_manifest_access_while_speculative at tests/core/fs/test_bootstrap.py
• [ ] Rewrite the fixture persistent_mockup at tests/conftest.py

Reminder the goal of the rewrite is to not have the class LocalDatabase defined in the python code base.