[BUG] MCP tools from commented-out server entries still appear in context

Description

In .mcp.json, an MCP server entry is commented out using // (JSONC-style comments). Despite this, the server's tools still appear in the deferred tools list in Claude's system context, making them appear available when they are not.

This caused Claude to incorrectly assume the Atlassian-Rovo-MCP server was active and suggest using its tools.

Steps to Reproduce

1. Add an MCP server to ~/.claude/.mcp.json
2. Comment it out using // line comments
3. Start a new Claude Code session
4. Observe that the commented-out server's tools still appear as deferred tools in context

Expected Behaviour

Commented-out servers should not surface any tools in the deferred tools list.

Actual Behaviour

mcp__Atlassian-Rovo-MCP__* tools appeared as deferred tools, leading Claude to incorrectly assume the server was active.

Environment

• OS: Windows 11 Enterprise 10.0.26200
• Model: claude-sonnet-4-6
• Config file: ~/.claude/.mcp.json