[MC-463] Preserve manual overrides on enrichment recompute

[TarahAssistant]

MC Task: MC-463 — Fix enrichments recompute wiping manual_overrides / Lane MC-463-A

Summary

• Made cognates/similarity recompute read-modify-write parse-enrichments.json so recompute-owned fields update only computed_at, config, auto cognate_sets, and similarity.
• Made POST /api/enrichments merge stale client snapshots into the on-disk payload so omitted or empty manual_overrides cannot erase human cognate decisions.
• Added regression coverage for cognates and similarity job dispatch, no-existing-file default behavior, and POST bodies that omit/send empty manual_overrides.

Fail on origin/main before fix

$ PYTHONPATH=python python3 -m pytest python/test_compare_enrichments_manual_overrides.py -q
FF.FF                                                                    [100%]
FAILED python/test_compare_enrichments_manual_overrides.py::test_compute_job_preserves_manual_overrides_and_unrelated_enrichment_keys[cognates]
E       AssertionError: assert {} == {'borrowing_flags': ..., 'cognate_sets': ...}
FAILED python/test_compare_enrichments_manual_overrides.py::test_compute_job_preserves_manual_overrides_and_unrelated_enrichment_keys[similarity]
E       AssertionError: assert {} == {'borrowing_flags': ..., 'cognate_sets': ...}
FAILED python/test_compare_enrichments_manual_overrides.py::test_post_enrichments_preserves_non_empty_disk_manual_overrides_when_client_omits_them[incoming_enrichments0]
E       KeyError: 'manual_overrides'
FAILED python/test_compare_enrichments_manual_overrides.py::test_post_enrichments_preserves_non_empty_disk_manual_overrides_when_client_omits_them[incoming_enrichments1]
E       AssertionError: assert {} == {'borrowing_flags': ..., 'cognate_sets': ...}
4 failed, 1 passed, 1 warning in 0.24s

Pass on branch after fix

$ PYTHONPATH=python python3 -m pytest python/test_compare_enrichments_manual_overrides.py -q
.....                                                                    [100%]
5 passed, 1 warning in 0.07s

Local validation

$ PYTHONPATH=python python3 -m pytest python/ -q -k 'not test_ortho_section_defaults_cascade_guard and not test_ortho_explicit_override_beats_defaults'
1920 passed, 6 skipped, 2 deselected, 1 warning, 3 subtests passed in 31.54s

$ PYTHONPATH=python python3 -m pytest python/ -q
1922 passed, 6 skipped, 1 warning, 3 subtests passed in 29.98s

$ uvx ruff check python/ --select E9,F63,F7,F82
All checks passed!

Root-level handoff command note: the literal root-scoped PYTHONPATH=python python3 -m pytest -q -k ... still hits pre-existing collection import errors under tests/migration/* (No module named 'migration.test_*'). Per backend-root-vs-python-scope guidance, I ran the backend-scoped equivalent above.

Follow-up out of scope

• Frontend CLEF Save & populate auto-chain to similarity recompute can remain unchanged for this data-loss fix because backend recompute is now non-destructive.
• enrichmentStore.ts optimistic-only canonical lexeme concern remains separate.