[build-system] Fix potential clash between user remappings and npm roots #5863
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This PR fixes a bug that could happen if a user remapped an npm package to one of its internal folders and, at the same time, used one of its files as a root.
For example, if you had a remapping
foo/=foo/src/and also treatedfoo/src/A.solas a project root, that needs to be compiled.