chore: sync PR #102/#103 tracking + Nle regression guard

docs/DISCOVERY_PREDICTION.md

@@ -803,6 +803,18 @@ No biological activity has been demonstrated. The lab is the judge.*
 
 ---
 
+**Tracking note (post-PR #103):** ASSAY_PREREGISTRATION.md: serum stability model limitations
+block extended to cover all 5 affected families — SEED-003 (pre-existing, 11 AA length edge),
+SEED-007 (added: Met/Nle substitution + 11 AA length edge), SEED-008 (pre-existing, Trp steric,
+13 AA length edge), SEED-009 (pre-existing, Pro-bond protease resistance), SEED-005 (added:
+safety gate, hemolysis at MIC/3 mandatory, exclude from Wave 2 if HC₅₀ < 10× MIC). All
+actionable limitations are now pre-registered before synthesis.
+
+**Tracking note (post-PR #102):** presynth_check.py: Met oxidation flag upgraded — now explicitly
+recommends Nle (norleucine) substitution for oxidation-resistant synthesis, inert-atmosphere
+storage, and mandatory HPLC purity check at receipt. Actionable guidance surfaces at QC report
+level for all SEED-007 pilot variants (Met×1 at position 6 in all 4 sequences).
+
 **Tracking note (post-PR #101):** EXPERT_REVIEW_PACK.md: SEED-007 and SEED-005 reviewer notes
 added (parallel to SEED-008/009 notes already present); SEED-007 Met oxidation risk row added
 to Pipeline Limitations table. All 7 families now have equal depth in both the wet-lab handoff

docs/ROADMAP.md

@@ -87,6 +87,8 @@ Implemented during the pre-wet-lab improvement loop (PRs #31–#54):
 - EXPERT_REVIEW_PACK.md: note added on new CSV columns for within-family prioritization (PR #98)
 - EXPERT_REVIEW_PACK.md: SEED-007 reviewer note (Met oxidation, bombolitin origin, SAR framing, top-10 slots) and SEED-005 reviewer note (lowest priority, safety margin) added; SEED-007 Met oxidation row in Pipeline Limitations table (PR #101)
 - WET_LAB_HANDOFF.md completed with dedicated special notes for all 7 seed families: SEED-007 (bombolitin-II, 4 pilot slots, all NOVEL, best serum stability, Met oxidation guidance, breakthrough-candidate framing), SEED-005 (cecropin-magainin hybrid, safety/serum risk note), SEED-008 (puroindoline-a, Trp aggregation handling, aromatic-mechanism CD interpretation), SEED-009 (Bac2A proline-rich, Pro coupling guidance, RPMI-parallel assay note restated as standalone); Serum Stability section header updated to "All 7 Seeds" with SEED-006 and SEED-007 table rows added; DISCOVERY_PREDICTION.md tracking updated (PR #100)
+- presynth_check.py Met oxidation flag strengthened: Nle (norleucine) substitution explicitly recommended, inert-atmosphere storage, mandatory HPLC purity at receipt — actionable guidance now surfaces at QC report level for all SEED-007 pilot variants (PR #102)
+- ASSAY_PREREGISTRATION.md serum stability model limitations block extended to cover all 5 affected families: SEED-003 (pre-existing, 11 AA length edge), SEED-007 (added: Met/Nle substitution + 11 AA length edge), SEED-008 (pre-existing, Trp steric, 13 AA length edge), SEED-009 (pre-existing, Pro-bond protease resistance), SEED-005 (added: safety gate, hemolysis at MIC/3 mandatory, exclude if HC₅₀ < 10× MIC); all limitations pre-registered before synthesis order (PR #103)
 
 ## v1.0 — Validated dry-lab-to-wet-lab loop
 

tests/test_presynth_qc.py

@@ -104,6 +104,7 @@ def test_met_flag_in_flags_list(self):
         qc = check_sequence("s", "KRLMKKIGSAIKFL")
         met_flags = [f for f in qc.flags if "MET" in f]
         assert len(met_flags) == 1
+        assert "Nle" in met_flags[0], "Met flag must recommend Nle substitution (regression guard for PR #102)"
 
 
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