docs(repo): AGENTS.md, recording the traps that are invisible until they bite

AGENTS.md

@@ -0,0 +1,35 @@
+# AGENTS.md
+
+Instructions for coding agents working in this repository. Read the contribution
+rules in `.github/CONTRIBUTING.md` first; this file records only the traps that
+are invisible until they bite.
+
+## renv.lock and CI's hardcoded R-package lists are coupled
+
+CI installs R from `renv.lock` (`renv::restore()`), but `.github/workflows/ci.yml`
+names the expected packages in TWO hardcoded verification lists:
+
+- the `Install R packages` step's `require()` check ("failed to install"), and
+- the `Verify R packages visible from RCall` step.
+
+Removing a package from `renv.lock` therefore fails the run at install
+verification, nowhere near the code that stopped using it. MEASURED on
+JoshuaJewell/MetaManifold-WebUI#57 (2026-10-15): dplyr left the lock and both
+checks failed until the lists were updated in the same PR. Whenever a change
+touches `renv.lock`, grep `.github/workflows/ci.yml` for every added or removed
+package name and update both lists in the same commit.
+
+Corollary, measured the same way: `tibble` cannot leave the lock while dada2 is
+in it. `dada2 -> ggplot2 -> tibble` is dada2's own dependency chain, independent
+of anything this project's code does; the lock's `Requirements` arrays are not
+evidence (only a handful of records carry one).
+
+## Commit signing needs the SSH agent, not a passphrase prompt
+
+`commit.gpgsign` is on, with a passphrase-protected SSH key. A non-interactive
+shell has no askpass and no terminal for a prompt, so signing fails with a
+misleading "failed to write commit object" unless the agent is reachable:
+`SSH_AUTH_SOCK=/tmp/lcb-ssh-agent.sock` (the fixed socket; `~/.profile` exports
+it when the socket exists). Never work around this with
+`commit.gpgsign=false` — check the agent first with
+`SSH_AUTH_SOCK=/tmp/lcb-ssh-agent.sock ssh-add -l`.

test/unit/test_install_pins.jl

@@ -333,6 +333,11 @@ end
         # configs (codecov.yml) live under .github/.
         ".github", "bench", "config", "data", "docs", "frontend",
         "proofs", "scripts", "src", "test",
+        # Agent instructions (the agents.md convention): coding agents load
+        # this at startup, and it only works from the root, which is why it
+        # is listed here rather than living under .github/ with the other
+        # health files.
+        "AGENTS.md",
         # VCS housekeeping.
         ".gitignore",
     ]