[Bug] MCP Server Not Persisting After Restart with Skip Permissions Flag

Bug Description
After adding a new MCP server, exiting claude code and then restarting claude code again with --dangerously-skip-permissions, does not add the MCP server.

Environment Info

• Platform: darwin
• Terminal: vscode
• Version: 2.0.14
• Feedback ID: b7ab0e7c-4b58-41ba-aa69-d34db3b22d3a

Errors

[{"error":"Error: Tool mcp__puppeteer__puppeteer_navigate not found\n    at LlB (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:2123:7930)\n    at G$ (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:73:19415)\n    at ka (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:42814)\n    at S9 (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:38355)\n    at Wm (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:38283)\n    at z$ (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:38137)\n    at WC (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:35216)\n    at H4 (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:73:4841)\n    at h5 (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:32461)\n    at Q.updateContainer (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:79:1827)","timestamp":"2025-10-10T23:33:49.126Z"},{"error":"Error: Tool mcp__puppeteer__puppeteer_navigate not found\n    at LlB (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:2123:7930)\n    at G$ (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:73:19415)\n    at ka (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:42814)\n    at S9 (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:38355)\n    at Wm (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:38283)\n    at z$ (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:38137)\n    at WC (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:35216)\n    at H4 (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:73:4841)\n    at h5 (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:75:32461)\n    at Q.updateContainer (file:///Users/jayakin/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:79:1827)","timestamp":"2025-10-10T23:33:50.313Z"}]