install: fix root prefix handling

Previously, we'd execute some operations with the root prefix applied, while
others without (which was a bug). Clean this up: all paths are now prefixed
properly with the root path, and we strip it off when necessary.

(Of course, an alternative option would be to strictly pass around paths
without the prefix prepended and only prepend it right before hitting the disk,
however, I am came to the conclusion this would result in more code.)

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