Move the legacy Perl toolchain to legacy_perl/ - #1098
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Pure git mv, no content edits: the 12 Perl executables, the Perl-era release packager, plotly/ (report assets), and test_data.fastq. Path fixes for every in-repo consumer follow in the next commit so renames stay cleanly detectable.
…le layout gate Follow-up to the pure move: updates all 23 in-repo path sites (8 oracle-test literals, 2 plotly drift guards, 6 golden-generation scripts, 4 scripts/ byte-identity harnesses, 44 ci_tests.yml invocations + hints), adds tests/legacy_perl_layout.rs (unconditional existence gate for the 12 scripts + 4 code-read plotly assets — cannot skip, needs no Perl), and updates .gitattributes/.dockerignore/README/CHANGELOG prose. The six tests/data golden scripts had a stale up-count resolving to rust/ (multicall-consolidation relic) — repaired to the real repo root while touching them. filter_nonconversion's hardcoded absolute default is now a computed repo root. copy_bismark_files_for_release.pl moves as a historical artifact, accepted broken (its Docs/ inputs no longer exist; PLAN Open-5). Verification (PLAN §12): oracle battery baseline 72 ok on dev; post-move pre-fix sabotage failed exactly the 20 loud gates while the 13 skip-capable summary/template oracles stayed silently green (the hazard the layout gate closes); post-fix battery 73 ok = baseline + the new gate, 0 failed; layout gate observed red under deliberate sabotage; fmt + clippy (default and rammap-inprocess) clean; Perl bismark2report proven to resolve plotly from the new location.
… name legacy_perl/plotly Dual code review (A+B, both APPROVE) + coverage audit (COMPLETE) fixes: - legacy_perl_layout.rs asserts mode +x on the 12 scripts (cfg(unix)) — ci_tests.yml runs them as ./legacy_perl/<name>, so the bit is load-bearing - drift-guard assert messages and comments now name legacy_perl/plotly/ - rust/README.md v0.25.1 sentence leads with the tag layout it instructs - .gitattributes block realigned; filter_nonconversion golden script reuses HERE; c2c matrix help text word restored - PLAN §12/§13: 7th golden script recorded (true counts 7/24), V2 ok-count marked toolchain-sensitive, published-tarball constraint noted
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The frozen Perl v0.25.x toolchain moves from the repository root into
legacy_perl/so the landing page reads Rust-first: the 12 Perl scripts, theirplotly/report assets,test_data.fastq, and the Perl-era release packager. No behaviour change to any tool — commit 1 is a pure rename, commit 2 points every in-repo consumer at the new path and adds an unskippable layout gate.Consumers updated (24 code sites): 8 oracle-test path literals, both plotly drift guards, 7 golden-generation scripts (their stale up-counts — which resolved to
rust/, a multicall-consolidation relic — repaired to the real repo root while touching them), 4scripts/byte-identity harnesses, and all 44ci_tests.ymlinvocations..gitattributes' root-anchoredplotly/**line is rewritten;legacy_perl/is excluded from the Docker build context (~20 MB); README/CHANGELOG updated.license.txtstays at root (release packaging copies it from there).New gate:
tests/legacy_perl_layout.rsasserts the 12 scripts + 4 code-read plotly assets exist — unconditional, no Perl needed, cannot skip. This closes a real hazard demonstrated during implementation: with the scripts moved and paths unfixed, the 12summary_perl_oracletests and the template-drift guard pass silently green (they are skip-capable and outside the perl-oracle job's EXPECTED list).Verification (full record in
plans/08082026_legacy-perl-move/PLAN.md§12): oracle-battery baseline 72 ok ondev; post-move/pre-fix sabotage failed exactly the 20 loud gates; post-fix battery 73 ok = baseline + the new gate, 0 failed; the layout gate was observed red under deliberate sabotage before being trusted; fmt + clippy (default andrammap-inprocess) clean; Perlbismark2reportproven to resolve$RealBin/plotlyfrom the new location.Known external cost (accepted, in CHANGELOG):
blob/master/<script>deep links 404 — the immutablev0.25.1tag is the stable Perl reference. bioconda/Homebrew/containers are unaffected (they build fromrust/or the tag).