chore(benchmarks): drop orphaned pre-loader-refactor results/forcefields (~14 MB)

[ericchansen]

Summary

Two parts:

1. Removes ~14 MB of orphaned data — 5 systems' results/ and forcefields/ directories that were generated speculatively by the old "full matrix" benchmark CLI but never wired into any documentation or test.

2. Prevents recurrence — without these changes the same mistake would just happen again. README rewrite + automated audit script.

What gets deleted (100 files)

• benchmarks/rh-enamide/{results,forcefields}/
• benchmarks/pd-allyl-amination/{results,forcefields}/
• benchmarks/rh-1,4-conjugate-addition/{results,forcefields}/
• benchmarks/heck-relay/{results,forcefields}/
• benchmarks/pd-1,4-conjugate-addition/{results,forcefields}/

Prevention

README rewrite

The old README codified the orphan layout — it documented every system as having results/forcefields/ directories, making them look canonical. New version:

• Reflects actual current layout (only ch3f has the matrix output; everything else uses convergence/, plus heck-relay has diagnostic/)
• Documents the two standard directory shapes (convergence/ vs the legacy matrix layout) and explicitly notes the legacy layout should not be added for new systems without a paired doc PR in q2mm
• Adds a "Stewardship rule" section citing q2mm AGENTS.md §2 and three committer-facing rules:
  1. Trace every commit to a doc/test reference
  2. Paired PRs when deleting a producing code path in q2mm
  3. No speculative or exploratory output here

scripts/audit-orphans.sh

Catches the issue mechanically rather than relying on humans reading the README:

scripts/audit-orphans.sh ../q2mm

Walks every benchmarks/<system>/<subdir>/, greps a sibling q2mm checkout (docs/ test/ q2mm/ scripts/ examples/) for the path, and reports any subdirectory with zero references. Exits 1 on orphans found, 0 otherwise — suitable for periodic manual runs or future CI wire-up.

Verified post-deletion:

$ scripts/audit-orphans.sh ../q2mm
Auditing benchmarks/
against q2mm checkout at /home/eric/repos/q2mm/

✅ No orphaned directories — every benchmarks/*/subdir is referenced in q2mm.

What stays

Path	Why
benchmarks/*/convergence/	Current pipeline output, actively referenced by every per-system doc page
benchmarks/ch3f/{results,forcefields}/	Populates docs/systems/small-molecules.md matrix table
benchmarks/heck-relay/diagnostic/	Three-baseline diagnostic, referenced by docs/systems/heck-relay.md
qfuerza-zenodo/	Referenced by docs/benchmarks/qfuerza-validation.md

Risk

Zero — no code references the deleted files; they're not in any test fixture; the regen script writes to fresh paths anyway. Git history preserves them at 5d210c2 if ever needed.