Connector per-tool permissions still reset — root cause is server identity rotation, not just app upgrades (re-raising #56954)

Re-raising #56954, which was closed as "not planned" but is still reproducing on Claude Code CLI 2.1.220.

What's wrong

Per-tool "Always Allow" permissions for connector-based MCP servers (e.g. a Linear connector added via claude.ai Connectors) silently reset to "Ask"/blocked, forcing re-approval of every tool.

New evidence on root cause

#56954 attributed this to Electron IndexedDB not surviving app upgrades. That's one trigger, but I found a second, independent one: the connector's internal server identifier itself is not stable, and changes on its own (not tied to an app version bump).

Concretely: a permissions allow-list checked into a project's .claude/settings.json months ago recorded a Linear connector's tools under the prefix mcp__claude_ai_Linear__*. Today, the same connector (same account, same Linear integration, no reinstall) exposes its tools under mcp__<opaque-uuid>__*. Since per-tool permission state is keyed to that identity, the rotation alone invalidates every previously granted permission — independent of whether an upgrade ever happened in between.

This means the fix needs to cover more than upgrade-time migration: either the server identity needs to stay stable across reconnects, or per-tool permission state needs to be keyed to something stable (e.g. the server's declared name/URL) rather than a regenerated id.

Impact

Same as #56954 — painful for anyone with multiple connectors/tools, since it forces full manual re-approval with no warning and no visible trigger (it isn't always tied to a Desktop update).

Environment

• Claude Code CLI: 2.1.220

Related

• #56954 (closed, not planned)