2.1.45 update silently resets MCP configs, user ID, and project trust dialogs

Bug Report

Environment

• OS: Windows 10 (MSYS_NT-10.0-19045)
• Claude Code version: 2.1.45 (updated from 2.1.44)
• Install method: native

What happened

After updating from Claude Code 2.1.44 to 2.1.45, the following data was silently reset:

1. All MCP server configurations wiped — every project's mcpServers in .claude.json is now {}. A previously configured TickTick MCP (User-level MCP) is gone.
2. User ID changed — the userID field in .claude.json changed between sessions, indicating re-authentication was forced without notice.
3. numStartups reset to 1 — as if it were a fresh install.
4. Project trust dialogs reset — every project now re-prompts for permissions as if never seen before, despite months of accumulated approvals.

What survived

• Global settings.json permission rules (allow/deny/ask lists)
• Hooks configuration
• Plugin settings

Impact

• MCP configurations lost — user has to remember and manually re-add all MCP servers
• Permission fatigue — every tool call now triggers a permission prompt, making the tool unusable until permissions are re-approved one by one
• No backup created — no .bak or migration file was created before the reset
• No warning given — the update did not inform the user that data would be reset

Expected behavior

• Updates should migrate existing configs, not wipe them
• If migration isn't possible, create a backup file (e.g., .claude.json.pre-2.1.45.bak)
• At minimum, warn the user before destroying their configuration

Steps to reproduce

1. Have Claude Code 2.1.44 with configured MCP servers and accumulated project trust/permissions
2. Update to 2.1.45
3. Observe that MCP configs, user ID, and trust dialogs are reset

Additional context

This affected a user with months of carefully accumulated permission approvals across multiple projects. The partial nature of the reset (permissions survived but MCPs and trust didn't) suggests a migration bug rather than intentional behavior.