[RaghavChamadiya]

What

The coverage and dead-code writers loaded every row they were about to replace and deleted it one ORM object at a time. They issue a single DELETE instead, the same shape the health findings and metrics writers use.

How

• save_coverage_files: one DELETE on the repo's coverage_files rows, still before the inserts, so uq_coverage_files sees the same order.
• save_dead_code_findings: one DELETE on the repo's open rows.
• replace_dead_code_findings: reads only the (file, kind, symbol) keys of acted-on rows, then deletes the open rows. With a scope, the delete goes through the existing chunked _batch_delete_in, so a scope wider than SQLite's variable limit still works. Rows outside the scope and dismissed rows are left exactly as before.
• coverage_map.save_test_coverage already used a single DELETE; nothing to change there.

Neither table has a foreign key, relationship cascade or ORM hook that the per-row delete was triggering, and no caller reads the loaded rows. The read-snapshot staleness hook fires for the bulk statement as it did for the flushed deletes.

Verification

Each copy re-saved its own stored rows with the old code and with this branch: coverage save, dead-code save, repo-wide replace, then a replace scoped to every other file with 10% of findings dismissed first. Row counts and a SHA-256 over every column except the id and the save-time stamp match between old and new on all three. Medians of 3 alternating runs:

Index	Rows	Step	Before	After
This repo	2,223 coverage files	save_coverage_files	399 ms	275 ms
Superset	2,486 dead-code findings	save_dead_code_findings	496 ms	276 ms
Superset		scoped replace_dead_code_findings	159 ms	100 ms
MLflow	2,148 dead-code findings	save_dead_code_findings	503 ms	208 ms
MLflow		scoped replace_dead_code_findings	166 ms	90 ms

Repo-wide replace_dead_code_findings is within noise (Superset 326 vs 339 ms, MLflow 353 vs 283 ms); its time goes to the inserts.

New test test_scoped_replace_past_one_delete_chunk_keeps_exactly_the_right_rows locks the rows left after a scoped replace that spans more than one delete chunk. It passes on main and on this branch. Coverage, dead-code and persist-order suites: 128 passed.