Prevent git package clones being picked up as git root

When adding a git reference into `manifest.json` and refreshing Unity in the background, Unity will temporarily clone the git package to `Library/PackageCache/.tmp*`, then check out the appropriate version and finally copy into the correctly named `PackageCache` folder. However, if Rider is active while this is happening, it is possible to pick up the temporary clone as a VCS root. When it's disabled, IntelliJ then complains that the root no longer exists.

Can this detection be suppressed for certain folders, or when we know that `manifest.json` has been modified?

Start by tracing VCS-root detection during Unity's background refresh, focusing on manifest.json changes and temporary clones under Library/PackageCache/.tmp*. Reproduce a git package refresh with Rider active, then verify that temporary clones are not retained as roots and that disabling detection does not leave an invalid root.

Written by the indexing model from the issue text.