Fix project files absolute paths when a work copy is used #790
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To avoid unintended source code modifications, Cachi2 makes a copy of the source directory when some package managers are used (currently, it's being done just for yarn).
This creates a problem with project files, since the absolute path of files now is pointing to the temporary working copy. The solution introced by this patch reverts these paths back to the original source dir path.
This is intended to be a quick fix, and should only be kept until we solve #712.
Resolves #785.
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