Switch to AGENTS.md as standard in copier template

justfile

@@ -6,3 +6,4 @@ test target:
     rm -rf tmp/{{target}} || echo fresh
     cp -pr test/{{target}} tmp
     copier copy template tmp/{{target}}
+    cd tmp/{{target}} && just -f ai.just setup-ai-instructions

template/.github/workflows/claude.yml

@@ -1,3 +1,8 @@
+# Claude Code GitHub action
+# ---
+# This github action is from the copier template in https://github.com/ai4curation/github-ai-integrations, donated by the Monarch Initiative
+# For more documentation, see https://ai4curation.github.io/aidocs/how-tos/set-up-github-actions/
+# Author: Chris Mungall (@cmungall)
 name: Claude Code
 
 on:

template/.github/workflows/dragon-ai.yml

@@ -1,3 +1,8 @@
+# DRAGON-AI GitHub action
+# ---
+# This github action is from the copier template in https://github.com/ai4curation/github-ai-integrations, donated by the Monarch Initiative
+# For more documentation, see https://ai4curation.github.io/aidocs/how-tos/set-up-github-actions/
+# Author: Chris Mungall (@cmungall)
 name: Dragon AI Agent GitHub Mentions
 
 env:

template/CLAUDE.md.jinja → template/AGENTS.md.jinja

@@ -1,4 +1,4 @@
-# CLAUDE.md for {{project_name}}
+# AGENTS.md for {{project_name}}
 
 {{ project_description }}
 

template/ai.just

@@ -1,22 +1,46 @@
+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
 
 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_OAUTH_TOKEN --body "$CLAUDE_CODE_OAUTH_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"