Audit the research and make documentation Markdown-only

[GoGoKo699]

The repository's previous submission-ready language exceeded its verification evidence. Its validator checked a hardcoded peak table, several checks disappeared under optimized Python, and default figure commands could overwrite released evidence. The public preprint citation also used an unpublished working title.

This cleanup adds self-contained Markdown research notes with proofs, a scoped sanity check, provenance, reproducibility instructions, and verified primary references. It removes obsolete manuscript/build reports and 14 PDF duplicates, adopts PNG plot defaults without external TeX, fixes malformed-support handling and coefficient basis ordering, and makes all seven figure redraws write under generated/.

The exact mean-state, purity, entropy-bound, and residue results survive independent review. Missing original high-n global-search records, an unproved asymptotic entropy-peak law, and the revised contribution's novelty remain explicit limitations. All 50 released CSV/PNG files and the original MIT license are preserved byte-for-byte, with checksums.

Validation:

• 39 unit and regression tests passed, including corrupted-data rejection under -O and -OO.
• Exhaustive checks of 65,550 nonempty supports across n=2 and n=4 passed against production routines.
• All 12,000 residue observations were checked for summary consistency, with 36 seeded support replays.
• All seven CSV redraws and all seven reduced computation outputs completed successfully.
• Repository documentation/link checks and 51 evidence/license checksums passed.
• Original-size simulations and missing global peak searches were not rerun.

The uploaded Git tree is exactly the locally tested tree: 28fca8b1784495743c9965d2ce3a511848dd7f4a.

This is a draft for review. Main is unchanged; automatic approval review required explicit authorization before publishing this cleanup to the default branch.