[rwjblue]

Implements the follow-ups from the repo review: install-task fixes, removal of duplicated agent skills, a new CI workflow, and doc updates. Each change is its own commit.

Script and install fixes

• scripts/commit_changed_file.sh is now bash, to match its extension. It detects new files with git status --porcelain and commits only the named path, so unrelated staged changes are left alone.
• dot:install: with FORCE=true, existing symlinks are replaced and real files or directories are moved into one per-run backup directory, ${XDG_STATE_HOME:-~/.local/state}/dotfiles/backups/<timestamp>/, instead of being deleted with rm -rf. Each backup keeps its path relative to $HOME. The run prints where backups went and how to clear them. The duplicate Linux-only jj link is gone.
• system:install no longer runs tools:update, so ./install installs the locked tool versions instead of upgrading everything.
• SHARED_BINUTILS_PATH is defined once in mise/config.toml instead of in four tasks. It can't be overridden, because the Cargo path dependencies in packages/binutils/Cargo.toml hard-code the same sibling checkout.
• ./install now runs with set -euo pipefail and downloads mise with curl -fsSL.
• agent-review.nvim: repo_root now falls back to git when jj isn't installed. Before, Neovim raised an error for the missing executable, so the git fallback never ran.

Skills

• Removed the nine skills under packages/codex/skills/ that were byte-identical copies of packages/agents/skills/. Codex already reads ~/.agents/skills. fastmail-email stays Codex-only because it reads ~/.codex/config.toml.
• .claude/skills/{dotfiles,dotfiles-tasks,nvim} are now symlinks to the .agents/skills copies, which had started to drift. .gitignore now allows those symlinks.
• New mise run skills:check task that fails on either kind of duplication.

CI

.github/workflows/ci.yml runs:

• shellcheck at --severity=warning
• skills:check
• cargo fmt --check, cargo clippy -D warnings and cargo test in packages/binutils, against a cloned shared_binutils
• agent-review:test

shfmt is left out because it would collapse the hand-aligned link_dotfile columns in dot:install.

Docs

README.md, AGENTS.md, the dotfiles skill, and the installation and symlink specs now describe the new FORCE behavior, where shared_binutils must live, the skills layout, CI, and the bash convention for tasks and scripts.

Checks run locally

• Exercised commit_changed_file.sh in a scratch repo with a new file, an unchanged file, and a modified file alongside other staged changes.
• Exercised link_dotfile with FORCE=true in a scratch $HOME against a real directory, a real file, and a symlink pointing elsewhere. The file and directory landed under one backup directory, and nothing was left next to the originals.
• mise env: SHARED_BINUTILS_PATH resolves to the sibling checkout and ignores an existing value in the environment.
• mise run skills:check: passes on the repo, and fails for an injected Codex duplicate and for a non-symlinked .claude copy.
• mise run agent-review:test: 34 of 34 pass. Six of them failed before the jj fallback fix.
• cargo fmt --check, cargo clippy and cargo test in packages/binutils. The crates have no tests yet.
• shellcheck at warning severity, and actionlint on the workflow.

  

[chatgpt-codex-connector]

Codex Review Summary

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Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-11-05T00:42:59.574852Z	702ea10	PR opened

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[chatgpt-codex-connector]

💡 Codex Review

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Reviewed commit: 702ea10de1

ℹ️ About Codex in GitHub

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• Open a pull request for review
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• Comment "@codex review".

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[chatgpt-codex-connector]

Make the binutils build honor the shared checkout override

When SHARED_BINUTILS_PATH points to a checkout outside the default location, binutils:install now clones and builds that checkout, but the subsequent local build still resolves latest_bin, test_utils, and fixturify through the hard-coded paths in packages/binutils/Cargo.toml:25–27. On a machine without a checkout at the default location, installation therefore fails while loading those dependencies; if both locations exist, it builds against a different checkout than the one selected. Make dependency resolution use the selected checkout as well so the newly documented override works throughout installation.

AGENTS.md reference: AGENTS.md:L13-L13

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