feature/Review-fix-first · L-260924-736ae2

[lchoquel]

Fixes the defects the 2026-09-24 plugins review ranked first. The changes are one shared MTHDS language reference, the lab stopping inputs at run-ready, run keeping saved runs out of git, the catalog saving by path, and qualified pipe codes. They also cover quoted hook commands with a Codex Bash arm, a stricter build (deep-merged tables, pruned outputs, whole-file-set orphan and marker checks), and a scaffold that plants no repository inside another. Three review rounds tightened the shared ignore procedure, the catalog's reading of a conflict with its own inline save, and the scaffold's reading of the enclosing repository, where a directory that repository ignores now gets a repository of its own, per the 2026-09-25 ruling.

Closes L-260924-736ae2
Closes L-260912-d23005
Closes L-260923-019e50
Closes L-260924-62c8f7
Leaves L-260924-9fd751
Leaves L-260924-deb436
Leaves L-260924-f00719
Leaves L-260924-afcd06
Leaves L-260924-677dd4
Leaves L-260925-5037c1
Leaves L-260925-d6d5d8

🤖 Generated with Claude Code

https://claude.ai/code/session_01NoxU85gAGjneWj89vQ2Y2u

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Summary by cubic

Fixes the defects the 2026-09-24 plugins review ranked first and carries three review rounds that tightened the save, scaffold, and build paths. Merges dev, bringing the README's open Codex install fold.

Skills

• One shared MTHDS language reference replaces design's own and the shared one, corrected against the spec; native content types document YesNo, Date, Time, and Composite.
• pipelex-inputs stops at run-ready without offering the run when the lab hands it a case.
• pipelex-run checks saved runs with git check-ignore, adds an anchored /runs/ entry, and holds the save while git still sees it; prepared inputs get the same guard.
• pipelex-catalog saves by path so every save stays linked; inline saves are offered only when the workshop refuses a path, and a conflict that is the session's own save is carried on.
• pipelex-integrate sets PIPE_CODE to the verdict's pipe_ref verbatim, domain included, and pipelex-run passes a non-main pipe's pipe_ref.

Build and scaffold

• Hook commands quote the plugin root so paths with spaces work; the Codex hook matches shell patches and checks absolute paths only.
• gen_skill_docs.py deep-merges target tables so overrides keep credential wiring, prunes stale files, and check compares whole file sets; root targets no longer overlap other targets' directories.
• commit-pristine.sh prints inside:/nested:/unversioned: verdicts and never commits in the enclosing repository; a directory that repository ignores now gets a repository of its own.
• pdm init gets -p <dir> and --no-git, and the reference warns when a pyproject.toml above would add the project to its workspace.

^{Written for commit 1718b55. Summary will update on new commits.}