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Review 2026-10-22: pool claims, forward intermediates, mutual specialization pairs, provenance, tests - #123
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…cepted recycle pools claim their nodes; forms between the starting complex and the modified form are listed; no-copies skips counted apart; mutual specialization pairs not bridged; recycle/release/ub flags fingerprinted; PIPELINE_SETTINGS lists the specialization defaults; tests (rule A precedence, claims, intermediates, mutual pairs) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Fixes from the 2026-10-22 adversarial review (deltasignal
docs/reviews/2026-10-22-review.md, findings 17, 20, 22, 23, 25, 26, 27, 29).find_recycle_pools: an accepted pool claims its nodes, so two candidates through one modified form no longer give two pools over the same nodes (started into creating pi files. Looks setup correctly #17); forms between the starting complex and the modified form are listed as intermediates and claimed (using uids instead of rids for logic network, create uid_reaction_con… #29); "no reaction copies" skips are counted apart from "claimed" (added all reactions to reaction_connections. Add a count of reactions… #22).linked_pairs: a mutual pair (each complex preceding the other) is not bridged, as the docstring promised (Added functionality #27)._FINGERPRINTED_ENVgains LNG_RECYCLE_POOLS, LNG_RELEASE_POOLS, LNG_UB_LIGASE_UNIT (changed root_input amnd terminal_output logic to be in separate funct… #26)._ub_ligase_leaves(add percentage stat for percentage of reactions that are loose in a p… #23), the claim and intermediate cases, mutual pairs. The new tests fail on the old code (the rule-B precedence test guards the mutant the review described).No network changes on canonical: variant build
20261022-2110_fcdfea4_revagainst canonical20261022-2011_233665c: 0 of 92 pathway tables differ. Local: 1258 passed; the one failure is the stale-outputtest_main_edges_proportional_to_best_matches[...983169], which fails on main too. mypy and ruff clean.Needs your review to merge.
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