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docs(repo): AGENTS.md, recording the traps that are invisible until they bite - #146
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…hey bite Instructions for coding agents, loaded at startup by the agents.md convention. Two things this session measured the hard way: - renv.lock and ci.yml's two hardcoded R-package verification lists are coupled: removing a package from the lock fails CI at install verification, nowhere near the code that stopped using it (JoshuaJewell#57). Any lock change must grep .github/workflows/ci.yml for the package name and update both lists in the same commit. And tibble cannot leave the lock while dada2 is in it: dada2 -> ggplot2 -> tibble is dada2's own chain, and the lock's Requirements arrays are not evidence against it. - commit signing needs the SSH agent (the fixed socket at /tmp/lcb-ssh-agent.sock, exported by ~/.profile when it exists); a non-interactive shell cannot prompt for the passphrase, and disabling signing to work around it is how unsigned commits happen. The root-shape allowlist gains AGENTS.md: the convention only loads it from the root, so it cannot live under .github/ with the other health files. Generated by Mistral Vibe. Co-Authored-By: Mistral Vibe <vibe@mistral.ai>
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What this changes
An
AGENTS.mdat the repository root -- the agents.md convention that coding agents (Vibe, Claude Code, Codex and the rest) load automatically at startup -- recording the two traps this session measured the hard way, so the next agent does not have to:renv.lock and ci.yml's two hardcoded R-package verification lists are coupled. Removing a package from the lock fails CI at install verification, nowhere near the code that stopped using it. MEASURED on refactor(dada2): assemble the taxonomy CSVs in base R, dropping dplyr entirely JoshuaJewell/MetaManifold-WebUI#57: dplyr left the lock and both checks ("Install R packages" and "Verify R packages visible from RCall") failed until the lists were updated in the same PR. The instruction is mechanical: any lock change greps
.github/workflows/ci.ymlfor the package name and updates both lists in the same commit. Plus the corollary:tibblecannot leave the lock while dada2 is in it (dada2 -> ggplot2 -> tibbleis dada2's own chain), and the lock'sRequirementsarrays are not evidence -- only a handful of records carry one.Commit signing needs the SSH agent, not a passphrase prompt. A non-interactive shell has no askpass, so signing fails with a misleading error unless the agent's fixed socket (
/tmp/lcb-ssh-agent.sock, exported by~/.profilewhen it exists) is reachable. The instruction: check the agent withssh-add -l; never work around a signing failure withcommit.gpgsign=false.The root-shape allowlist in
test/unit/test_install_pins.jlgainsAGENTS.md: the convention only loads it from the root, so it cannot live under.github/with the other health files, and the bidirectional root check would otherwise (correctly) refuse it.How to run its tests
Documentation only otherwise: no code, workflow or config change. The commit is signed.
What this leaves out
Nothing upstreaming: this file is fork tooling (upstream has no agents.md convention in use, and its own CONTRIBUTING already governs PRs there). The same coupling exists in upstream's ci.yml and is documented in the comments of JoshuaJewell#57 itself.
Versions tested
Julia 1.13.1 locally (CI pins 1.12.5). Nothing else touched.
Generated by Mistral Vibe.
Co-Authored-By: Mistral Vibe vibe@mistral.ai