fix setting the 'explicit' flag

So far, only the root package set had the explicit flag set, while
what we want is for all package sets listed in the manifest to have
it
fix package set sort order for explicit package sets

While the imported package sets have (among themselves) no necessary
order, the explicit package sets (the ones listed in the manifest)
should be inserted in the specified order so that the overrides
work properly.

This commit fixes package set loading to explicitly take this order
into account