When a later-loaded MCP config (e.g., .claude/.mcp.json) marks a server
as disabled, it now properly removes that server from both the servers
object and loadedServers array.
Previously, disabled servers were only skipped during loading, which
meant they wouldn't override servers loaded from earlier configs. This
made it impossible to disable project-level MCPs using local overrides.
Now the disabled flag works as expected: local configs can disable
servers defined in project or user configs.
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