[Sad Catapella B4][Scientific identity] Lenient experiment-design reader silently selects last duplicate column #83

Baseline and classification

Sad Catapella Batch 4, commit d7a538e56d41ac1093ba79adcad397c21b3dfd32. Confirmed behavior, deliberately covered by an existing test, but it conflicts with the requested no-silent-fallback/no-ambiguous-identity standard; this requires a backward-compatibility decision rather than being labeled an accidental regression.

Evidence

• read_experiment_design() lines 516–548 constructs a csv.DictReader and checks that required columns are merely present, not unique; duplicate columns are collapsed into the dictionary, and the last value wins.
• Existing test explicitly accepts a duplicated repeat_group column with rep1 in one column and other in the other, and asserts that the lenient reader silently selects other. The strict read_confirmed_design correctly refuses it, but the preprocessing notebook/CLI use the lenient reader to edit and re-publish design state.
• Contract §12 allows spreadsheet-friendly boolean spellings/whitespace, but it does not establish a safe scientific policy for two conflicting repeat_group columns.

Impact

A spreadsheet export carrying duplicate identity/pairing columns can silently switch biological-repeat grouping and control interpretation before the user confirms, even though the file remains parseable and a subsequent saved strict design looks valid. No pixel corruption is asserted; this is scientific experimental-design identity corruption.

Fix/acceptance

Keep deliberately lenient whitespace/boolean/CRLF/BOM handling, but reject duplicate identity-bearing and control columns at header parsing with DesignFormatError naming each duplicate; preferably reject any duplicate header. Add conflicting and equal duplicate-column fixtures and ensure no output is rewritten on refusal. Update the existing test that currently codifies the unsafe last-value-wins behavior. A compatibility migration must be explicit, never silently choose a column.

No Numba role.