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.

Author: cmungall

.github/copilot-instructions.md

@@ -0,0 +1 @@
+../AGENTS.md

.goosehints

@@ -0,0 +1 @@
+AGENTS.md

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 .`
+
+
+

CLAUDE.md

@@ -0,0 +1 @@
+AGENTS.md

CLAUDE.md

@@ -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_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"