Improve package reloading logic when manifest is changed

[ahoppen]

Two improvements to the logic that determines if we need to reload the package on a file change:

1. Only reload a package if the modified package manifest or Package.resolved is in the root of the package folder. This is relevant if we have a multi-root workspace, in which currently a single change to a package manifest or Package.resolved causes all packages to get reloaded.
2. While I was at it, I noticed that we didn’t properly handle version-specific package manifests. Also trigger a package reload if a version-specific package manifest is modified, created or deleted.

[ahoppen]

@swift-ci Please test