[BUG] MCP servers, plugins, and credentials not persisting between sessions (Windows)

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Claude Code does not persist MCP servers, plugins, or authentication between sessions. On every launch:

• /mcp returns "No MCP servers configured" despite valid entries in ~/.claude/settings.json
• Enabled plugins (e.g. rust-analyzer-lsp) are not loaded
• Prompts for re-authentication despite valid, non-expired credentials in ~/.claude/.credentials.json

What Should Happen?

MCP servers, plugins, and authentication should persist between sessions. /mcp should list configured servers, plugins should remain enabled, and login should not be required when valid credentials exist on disk.

Error Messages/Logs

No error messages. /mcp simply returns: "No MCP servers configured. Please run /doctor if this is unexpected."

Steps to Reproduce

1. Install Claude Code 2.1.59 on Windows 11
2. Run claude and authenticate
3. Configure MCP servers via /mcp add or by editing ~/.claude/settings.json
4. Enable plugins
5. Exit Claude Code
6. Relaunch Claude Code
7. Run /mcp — shows no servers configured
8. Check plugins — none enabled
9. Prompted to log in again despite credentials file existing

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

2.1.53

Claude Code Version

2.1.59 (Claude Code)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

• Claude Desktop was previously installed alongside Claude Code. Config existed at both ~/.claude/settings.json

(Claude Code) and %APPDATA%/claude/ (Claude Desktop). This may cause conflicts.

• ~/.claude/settings.json contains valid config:

{
"enabledPlugins": {
"rust-analyzer-lsp@claude-plugins-official": true
},
"mcpServers": {
"dbhub": { "command": "npx", "args": ["-y", "@bytebase/dbhub", "--dsn", "..."] },
"context7": { "command": "npx", "args": ["-y", "@upstash/context7-mcp@latest"] }
}
}

• ~/.claude/.credentials.json exists with a valid non-expired OAuth token
• No OneDrive redirection of home directory