[Imkkey]

Configuration.reload() rereads YAML sources with dict.update(), so keys removed from a file remain in memory. Deleted overrides continue to mask lower-priority defaults, and empty files or deleted optional files retain all previous settings. Reordering a file also leaves the old key order in place.

Clear the source after successfully loading and validating the replacement mapping, then populate it with the new contents. Keep the same source object and metadata. Parse errors, invalid non-mapping documents, and missing required files still leave the previous contents intact.

Add regression coverage for deleted overrides falling back to defaults, removal of keys without defaults, empty documents, optional-file deletion and recreation, key order, source identity and metadata, and preserving existing data on failed reloads. In-memory configuration sources remain unchanged.

Validation on Python 3.12.14:

• The original six regression cases fail on unchanged upstream. The follow-up adds five invalid-root regressions that fail on the previous head, plus explicit null/~ controls; all 16 added cases pass on c523030.
• All 36 YAML tests and 315 core tests pass.
• Full suite: 316 passed, one existing failure in test_bump_version_applies_sequential_changelog_updates. Clean upstream has the same failure (300 passed, one failed): its expected changelog underline is fixed at 26 characters, while the October heading requires 24. The untouched previous PR head also reproduces it (309 passed, one failed).
• Ruff lint/format, mypy with the CI Python 3.10 target, strict Sphinx build, changelog formatting/lint, and git diff --check pass.
• Remote Test and Lint workflows for this head are action_required, awaiting maintainer approval, with zero jobs executed. Remote CI has not passed.

Prepared and checked with OpenAI Codex assistance.

[Imkkey]

Source review found one reload failure-preservation gap. This case has not been runtime-tested.