[BUG] .mcp.json is loaded even --mcp-config is used

Environment

• Platform (select one):
• [X] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [ ] Other: <!-- specify -->
• Claude CLI version: 1.0.17 (Claude Code)
• Operating System: OSX
• Terminal: Ghostty

Bug Description

When launching claude with the --mcp-config file paramter, it still loads .mcp.json as well. This is undesirable because it certain situations we want to launch claude from the root of our repository but with a very specific MCP config.

Steps to Reproduce

1. Add a .mcp.json
2. Run claude --mcp-config some.other.mcp.json
3. Run /mcp to see that the combination of MCPs is loaded

Expected Behavior

I would assume when passing in the config flag that it would only load the config passed in

Actual Behavior

Both files are run

Additional Context

Doesn't have to be the default behavior if not desired but some way to skip .mcp.json when passing the flag is needed