QMake: Fix vcxproj filter folders in shadow builds

The folder structure below the "Source Files" and "Header Files"
filters was built from the file paths relative to the build
directory. In an out-of-source build these paths start with "..",
so the project showed nested folders called ".." and the whole path
to the source directory.

Build the folder structure from the path relative to the project
directory instead. Files outside of the project directory are
grouped by their path without the leading "..".

Fixes: QTBUG-133296
Change-Id: I6761b53082eab8d6df0976e3b16f91f8b7899098
Reviewed-by: Oliver Wolff <oliver.wolff@qt.io>