refactor: restructure documentation into organized docs directory (#383)

- Move FAQ.md to docs/faq.md
- Create structured documentation files:
  - setup.md: Manual setup and custom GitHub app instructions
  - usage.md: Basic usage and workflow configuration
  - custom-automations.md: Automation examples
  - configuration.md: MCP servers and advanced settings
  - experimental.md: Execution modes and network restrictions
  - cloud-providers.md: AWS Bedrock and Google Vertex setup
  - capabilities-and-limitations.md: Features and constraints
  - security.md: Security information
- Condense README.md to overview with links to detailed docs
- Keep CONTRIBUTING.md, SECURITY.md, CODE_OF_CONDUCT.md at top level

docs/security.md

@@ -0,0 +1,38 @@
+# Security
+
+## Access Control
+
+- **Repository Access**: The action can only be triggered by users with write access to the repository
+- **No Bot Triggers**: GitHub Apps and bots cannot trigger this action
+- **Token Permissions**: The GitHub app receives only a short-lived token scoped specifically to the repository it's operating in
+- **No Cross-Repository Access**: Each action invocation is limited to the repository where it was triggered
+- **Limited Scope**: The token cannot access other repositories or perform actions beyond the configured permissions
+
+## GitHub App Permissions
+
+The [Claude Code GitHub app](https://github.com/apps/claude) requires these permissions:
+
+- **Pull Requests**: Read and write to create PRs and push changes
+- **Issues**: Read and write to respond to issues
+- **Contents**: Read and write to modify repository files
+
+## Commit Signing
+
+All commits made by Claude through this action are automatically signed with commit signatures. This ensures the authenticity and integrity of commits, providing a verifiable trail of changes made by the action.
+
+## ⚠️ Authentication Protection
+
+**CRITICAL: Never hardcode your Anthropic API key or OAuth token in workflow files!**
+
+Your authentication credentials must always be stored in GitHub secrets to prevent unauthorized access:
+
+```yaml
+# CORRECT ✅
+anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
+# OR
+claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+
+# NEVER DO THIS ❌
+anthropic_api_key: "sk-ant-api03-..." # Exposed and vulnerable!
+claude_code_oauth_token: "oauth_token_..." # Exposed and vulnerable!
+```