[BUG] Claude Project MCP config should be accessible in the .claude folder

Environment

• Platform (select one):
• [x] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [ ] Other: <!-- specify -->
• Claude CLI version: 1.0.51 (Claude Code)
• Operating System: macOS 15.5
• Terminal: iTerm2

Bug Description

Claude project MCP configs are currently only available from {projectRoot}/.mcp.json

However, it is very annoying polluting the project root with more configuration files because we already have cursor files, CLAUDE.md (which also should be loadable from .claude folder IMO), typescript config files, lint config files... etc.

why can't we load project mcp configurations from the project {projectRoot}/.claude/settings.json OR at least from .claude/.mcp.json

Steps to Reproduce

1. Make a new folder
2. Add a .claude/settings.json inside it
3. Paste this into the settings.json

{
  "permissions": {
    "allow": [
      "mcp__context7__resolve-library-id",
      "mcp__context7__get-library-docs"
    ],
    "deny": []
  },
  "mcpServers": {
    "context7": {
      "type": "sse",
      "url": "https://mcp.context7.com/sse"
    }
  },
  "enabledMcpjsonServers": ["context7"]
}

1. run claude on the folder
2. observe that the MCP server is not available

Expected Behavior

the MCP server is available to claude

Actual Behavior

the MCP server is not available to claude

Additional Context

We are trying to be "considerate citizens" within the company and not polluting the repo files with things between all the different AI Agents and coding assistants used at the company.

the root CLAUDE.md was a "okay fine", if we have to add other files people will get frustrated