Update two stale test allowlists so the suite can be read again

[adamjohnwright]

Seven tests were failing locally, and had been for long enough that the failures were background noise. Five were a stale allowlist; two needed the generator fixes that just landed.

test_and_logic_consistency — stale allowlist

It allowed AND only on input / catalyst / positive regulator, so it failed on 149k edges across all 92 pathways. It would fail on every pathway in the catalog; only the first five are sampled.

Each addition was checked against what the solver actually does with and_or, not added to make the test green:

edge type	count	reaches the solver?
assembly	61,652	No — DS_ASSEMBLY_LIMITING routes assembly inputs to a limiting-reactant (min) rule before the AND/OR branch. AND is also correct: a Complex is the AND of its subunits.
depletion	5,064	No — create_reaction_from_edges never records is_and for depletion.
dissociation	82,394	Yes, and genuinely inconsistent — all 116k output edges are or, these are and.

I tested the third rather than assuming

Dissociation edges feed terminal readout sinks with exactly one producer, so the only question is whether a lone parent gets the hill_log tanh or passes through:

 fold_in   AND(hill_log)   OR(identity)
 0.85      0.85            0.85
 1.15      1.15            1.15
 2.0       1.9977          2.0
 100.0     74.07           100.0

Identity to four decimals at both classification cutoffs, within 0.1% out to fold 2, compressing only large folds. Flipping all dissociation edges to or and re-benchmarking moved nothing real — 11 changed predictions, all in one pathway, none with both arms converged: the same uuid-relabelling noise documented in specs/003.

Inconsistent but immaterial, so it's documented in the test rather than changed without evidence.

test_negative_regulators_marked_neg — stale allowlist

Asserted every negative edge is a regulator. depletion is negative by construction and postdates the test; the solver routes it separately and applies divide-form inhibition.

The last failure is real, and #64 + #65 already fixed it

test_main_edges_proportional_to_best_matches is an O(n²) detector doing its job. Regenerating on current main:

pathway	v96	v97 pre-fix	current main
Class I MHC	54.4 FAIL	174.5 FAIL	11.2 pass
NER	4.7	62.1 FAIL	7.8 pass

Total edges fall 178,198 → 14,627 and 136,603 → 1,739.

It still fails against the local output/ tree because that tree predates both fixes. output/ is gitignored and untracked, so refreshing it is a local-artifact operation with no repository effect — and CI, which has no output/, skips these tests entirely.

930 passing, 1 failing (that one), no new lint errors.

🤖 Generated with Claude Code