fix: Address Gemini Code Assist review feedback

- Repository URL consistency: Updated all references to BeehiveInnovations/zen-mcp-server format
- Documentation clarity: Fixed misleading table headers and improved Docker configuration examples
- File conventions: Added missing final newlines to all files
- Configuration consistency: Clarified API key placeholder format in documentation

Addresses all points raised in PR #17 review by Gemini Code Assist.

🤖 Generated with Claude Code

Co-Authored-By: Claude <noreply@anthropic.com>

docs/contributing/setup.md

@@ -21,8 +21,8 @@ This guide helps you set up a development environment for contributing to the Ge
 ### 1. Clone Repository
 
 ```bash
-git clone https://github.com/BeehiveInnovations/gemini-mcp-server.git
-cd gemini-mcp-server
+git clone https://github.com/BeehiveInnovations/zen-mcp-server.git
+cd zen-mcp-server
 ```
 
 ### 2. Choose Development Method
@@ -377,4 +377,5 @@ docker system prune -f
 **Next Steps:**
 - Read [Development Workflows](workflows.md)
 - Review [Code Style Guide](code-style.md)
-- Understand [Testing Strategy](testing.md)
+- Understand [Testing Strategy](testing.md)
+