disabledMcpjsonServers does not block built-in MCP servers (claude_ai_Atlassian)

Bug Description

disabledMcpjsonServers in ~/.claude/settings.json does not prevent built-in MCP servers (e.g., claude_ai_Atlassian) from being loaded and called.

Steps to Reproduce

1. Add "disabledMcpjsonServers": ["claude_ai_Atlassian"] to ~/.claude/settings.json
2. Start a new Claude Code session
3. The Atlassian MCP tools still appear in the deferred tool list
4. Fetching the tool schema via ToolSearch succeeds
5. Calling the tool (e.g., createConfluencePage) executes — it reaches the Atlassian API and only fails due to invalid parameters, not because the server is disabled

Expected Behavior

Built-in MCP servers listed in disabledMcpjsonServers should not load their tools or allow execution.

Actual Behavior

The tools load, schemas are fetchable, and calls execute normally despite the server being in the disabled list.

Environment

• Claude Code CLI
• macOS (Darwin 25.3.0)
• Setting location: ~/.claude/settings.json (global)
• No project-level MCP config overriding the global setting

Config

{
  "disabledMcpjsonServers": ["claude_ai_Atlassian", "github"]
}