Track native and manufactured construct sequences with lossless audits - #428

Summary

• Add immutable native/final construct records with attributed sequence edits and separately attributed chemical changes/rationales.
• Preserve explicit native occurrence coordinates, target masks, source identity and missing/removed target distinctions; added/substituted residues never receive native coordinates.
• Add allowlisted native import/export and non-mutating final-context MHC audits with escaped HTML reports and explicit unassessed processing/chemistry.
• Preserve provenance in peptide/mRNA manufacturing manifests and peptide order forms; validate actual emitted sequences and CDS translation.
• Fix complete-window exact-self source loss (Complete-window safety assessment drops non-CTA exact-self source provenance #426) using the existing batched provenance-aware matcher.
• Fix pathlib mRNA output-directory handling (mRNA output directory validation rejects pathlib.Path with AttributeError #427).
• Bump to 3.15.0.

Closes #421.
Closes #426.
Closes #427.

Evidence and boundaries

The independent DYNC1H1 page documents the JLF V2/V3 terminal KK. Solubility rationale is separately attributed to the project owner's report; CSBio involvement remains tentative. No automatic tail design, rank change, clinical safety claim, or claim of historical vaccine selection agreement.

The subsequent #414, #422 and #423 PRs still own historical final-selection comparisons, complete cleavage maps and the real-data combined construct audit. See CONSTRUCT_AUDIT.md for the complete delivery plan.

Completed review and verification

• Lint and diff checks pass.
• Focused construct/safety checks pass, including tail-created boundary ligands and non-CTA shared-source preservation.
• Peptide/mRNA emitted-file regressions pass.
• Final local full suite: 1,333 passed (Python 3.12).
• CI: Python 3.10–3.13 test matrices and docs build green at bc6dce4.
• B16 smoke passed with nonempty ASCII/HTML/PDF/JSON/XLSX/CSV artifacts and 10 processing annotations.
• Reviewed native-coordinate validation, lossless class registry, new edit boundaries, unsupported-chemistry behavior, non-CTA source retention and actual mRNA sequence/translation consistency.
• Initial restricted-environment font discovery failure reported upstream as [Bug]: macOS font discovery raises KeyError('_items') for an incomplete system_profiler font record matplotlib/matplotlib#32328. A transient full-disk condition also resolved; no unrelated files were deleted. Normal-cache reruns passed.
• Ready for merge and the mandatory 3.15.0 deployment.