Merge pull request #13 from ai4curation/claude/issue-12-20250912-2059

docs: enhance just setup-ai instructions with detailed explanation

Author: cmungall

README.md

@@ -94,9 +94,23 @@ CBORG_API_KEY
 
 ### Setup
 
-After setting up env vars:
+After running copier and setting up environment variables, run the following command to complete the AI integration setup:
 
-`just -f ai.just setup-ai`
+
+```bash
+just -f ai.just setup-ai
+```
+
+This command performs two main setup tasks:
+
+1. **AI Agent Configuration** (`setup-ai-instructions`):
+   - Creates `CLAUDE.md` symlink to `AGENTS.md` for Claude Code instructions
+   - Creates `.goosehints` symlink to `AGENTS.md` for Goose agent instructions  
+   - Creates `.github/copilot-instructions.md` symlink to `AGENTS.md` for GitHub Copilot instructions
+
+2. **GitHub Repository Setup** (`setup-gh`):
+   - Adds repository topics for discoverability (`monarchinitiative,ai4curation`)
+   - Configures repository secrets from your environment variables (PAT_FOR_PR, ANTHROPIC_API_KEY, etc.)
 
 # FAQ
 
@@ -110,3 +124,4 @@ Error: Failed to setup GitHub token: Error: Workflow validation failed. The work
 If you instead wish to use this action with a custom GitHub token or custom GitHub app, provide a `github_token` in the `uses` section of the app in your workflow yml file.
 Error: Process completed with exit code 1.
 ```
+