MCP migration says an update is needed to keep working but drops registry auto-updates

## Description The Agent Customizations (Copilot) > Migrations UI presents migration of a registry-installed Atlassian MCP server as necessary to keep customizations working, but warns that migrating will stop automatic updates from the MCP registry. This leaves the user choosing between an apparently required compatibility migration and losing an existing update capability, without explaining why or how updates should be managed afterward. ## Environment - VS Code: 1.142.0 (user setup) - Commit: 6d62b1d5dace93a33b3a6d3eca1317bd5e15bcb1 - Build date: 2026-10-15T03:02:17Z - OS: Windows_NT x64 10.0.26300 - Electron: 43.7.7 - @github/copilot: 1.0.95-0.unstable.r38345923974.g3754b70 - @github/copilot-sdk: 1.0.19.38345923974.g3754b70 ## Steps to reproduce / observed setup 1. Have the registry-installed `com.atlassian/atlassian-mcp-server` configured in the VS Code user `mcp.json`. 2. Open Agent Customizations (Copilot) > Migrations. 3. Observe the proposed migration under "MCP Servers (User)" to `%USERPROFILE%\.copilot\mcp-config.json`. 4. Compare the page-level guidance with the warning on the selected server. ## Actual behavior The page says: > Some of your agent customizations need an update to keep working. Use Migrate to have VS Code update selected customizations, or Migrate with Agent for a guided migration in chat. Agent migration uses credits. The Atlassian server entry simultaneously warns: > Migrating will stop auto-updates from the MCP registry. The UI offers Ignore and Migrate, but does not explain: - Why registry update support is lost during the recommended migration. - Whether ignoring migration is safe, and for how long the existing configuration remains supported. - Exactly what stops updating: registry-managed connection/configuration metadata, a locally installed server package, or something else. In particular, users should not have to infer what this means for a remotely hosted server. - How to receive or apply future registry changes after migrating. ## Expected behavior Preferably preserve the server's registry association and automatic update capability across migration. If that is not currently supported, clearly explain the limitation, its scope, the supported update procedure afterward, and the compatibility implications of choosing Ignore before asking users to migrate. ## Scope This report concerns the observed pre-migration warning and update-management/UX trade-off. Migration has not been verified as part of this report; there is no claim that this user's Atlassian server has failed or that Atlassian's hosted service would stop receiving updates. Related but different: #340677 reports MCP servers not working after migration.