From 293ad331d6cb912fc92e1536deb8db592263de5e Mon Sep 17 00:00:00 2001
From: Chris Mungall <cjm@berkeleybop.org>
Date: Tue, 2 Sep 2025 18:16:40 -0700
Subject: [PATCH] Switching to AGENTS.md (this repo, not the copier template)

This follows #9, we apply the template to ourself to get the changes
that affect AI usage for this repo itself.
---
 .github/copilot-instructions.md |  1 +
 .goosehints                     |  1 +
 AGENTS.md                       | 22 ++++++++++++++++++
 CLAUDE.md                       | 23 +------------------
 ai.just                         | 40 ++++++++++++++++++++++++++-------
 5 files changed, 57 insertions(+), 30 deletions(-)
 create mode 120000 .github/copilot-instructions.md
 create mode 120000 .goosehints
 create mode 100644 AGENTS.md
 mode change 100644 => 120000 CLAUDE.md

diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
new file mode 120000
index 0000000..be77ac8
--- /dev/null
+++ b/.github/copilot-instructions.md
@@ -0,0 +1 @@
+../AGENTS.md
\ No newline at end of file
diff --git a/.goosehints b/.goosehints
new file mode 120000
index 0000000..47dc3e3
--- /dev/null
+++ b/.goosehints
@@ -0,0 +1 @@
+AGENTS.md
\ No newline at end of file
diff --git a/AGENTS.md b/AGENTS.md
new file mode 100644
index 0000000..232902c
--- /dev/null
+++ b/AGENTS.md
@@ -0,0 +1,22 @@
+# CLAUDE.md for 
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+WARNING: read this closely as it gets a bit meta.
+
+This is a repo for a copier project intended to allow people to set up their github repo with AI github actions.
+
+- template files are in `template/`
+- all other files are for this repo itself
+
+So for example
+
+- template/.github/workflows/claude.yml - A template that is copied into a users target repo to set up claude gh actions
+- .github/workflows/claude.yml - The actual github actions for this repo itself.
+
+This repo eats its own dogfood! We will occasionally run
+
+`copier copy template .`
+
+
+
diff --git a/CLAUDE.md b/CLAUDE.md
deleted file mode 100644
index 232902c..0000000
--- a/CLAUDE.md
+++ /dev/null
@@ -1,22 +0,0 @@
-# CLAUDE.md for 
-
-This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
-
-WARNING: read this closely as it gets a bit meta.
-
-This is a repo for a copier project intended to allow people to set up their github repo with AI github actions.
-
-- template files are in `template/`
-- all other files are for this repo itself
-
-So for example
-
-- template/.github/workflows/claude.yml - A template that is copied into a users target repo to set up claude gh actions
-- .github/workflows/claude.yml - The actual github actions for this repo itself.
-
-This repo eats its own dogfood! We will occasionally run
-
-`copier copy template .`
-
-
-
diff --git a/CLAUDE.md b/CLAUDE.md
new file mode 120000
index 0000000..47dc3e3
--- /dev/null
+++ b/CLAUDE.md
@@ -0,0 +1 @@
+AGENTS.md
\ No newline at end of file
diff --git a/ai.just b/ai.just
index 3d35238..dc76eac 100644
--- a/ai.just
+++ b/ai.just
@@ -1,12 +1,15 @@
+claude:
+  [ -f CLAUDE.md ] || ln -s AGENTS.md CLAUDE.md
+
 goosehints:
-  [ -f .goosehints ] || ln -s CLAUDE.md .goosehints
+  [ -f .goosehints ] || ln -s AGENTS.md .goosehints
 
 copilot-instructions:
-  [ -f .github/copilot-instructions.md ] || cd .github && ln -s ../CLAUDE.md copilot-instructions.md
+  [ -f .github/copilot-instructions.md ] || cd .github && ln -s ../AGENTS.md copilot-instructions.md
 
 setup-ai: setup-ai-instructions setup-gh
 
-setup-ai-instructions: goosehints copilot-instructions
+setup-ai-instructions: claude goosehints copilot-instructions
 
 setup-gh: gh-add-topics gh-add-secrets
 
@@ -14,9 +17,30 @@ gh-add-topics:
   gh repo edit --add-topic "monarchinitiative,ai4curation"
 
 gh-add-secrets:
-  gh secret set PAT_FOR_PR --body "$PAT_FOR_PR"
-  gh secret set ANTHROPIC_API_KEY --body "$ANTHROPIC_API_KEY"
-  gh secret set OPENAI_API_KEY --body "$OPENAI_API_KEY"
-  gh secret set CBORG_API_KEY --body "$CBORG_API_KEY"
-  gh secret set CLAUDE_CODE_OATH_TOKEN --body "$CLAUDE_CODE_OATH_TOKEN"
+  #!/usr/bin/env bash
+  set -euo pipefail
+  
+  # Function to set secret if env var exists
+  set_secret_if_exists() {
+    local secret_name="$1"
+    local gh_var="GH_$secret_name"
+    local plain_var="$secret_name"
+    
+    if [ -n "${!gh_var:-}" ]; then
+      echo "Setting $secret_name from $gh_var"
+      gh secret set "$secret_name" --body "${!gh_var}"
+    elif [ -n "${!plain_var:-}" ]; then
+      echo "Setting $secret_name from $plain_var"
+      gh secret set "$secret_name" --body "${!plain_var}"
+    else
+      echo "Skipping $secret_name (neither $gh_var nor $plain_var is set)"
+    fi
+  }
+  
+  # Set each secret if the corresponding env var exists
+  set_secret_if_exists "PAT_FOR_PR"
+  set_secret_if_exists "ANTHROPIC_API_KEY"
+  set_secret_if_exists "OPENAI_API_KEY"
+  set_secret_if_exists "CBORG_API_KEY"
+  set_secret_if_exists "CLAUDE_CODE_OAUTH_TOKEN"