Eeeeh....
bash Code: 
  1. mkdir src
  2. cd src
  3. svn co ... .
  4. ln -s myproject.pro myproject_lin.pro # -s is optional
  5. cp myproject.pro.user myproject_lin.pro.user
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Now open myproject.pro from Windows and myproject_lin.pro from Linux. And I don't care that FAT/NTFS doesn't support links - use another filesystem.

Or of course:
bash Code: 
  1. cd build-lin
  2. qmake ../src/myproject.pro
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Or:
qmake Code: 
  1. DEPENDPATH += src
  2. INCLUDEPATH += src
  3. win32 {
  4.   DESTDIR = build-win
  5.   UI_DIR = build-win/ui
  6.   OBJECTS_DIR = build-win/obj
  7.   MOC_DIR = build-win/moc
  8. }
  9. unix {
  10.   DESTDIR = build-lin
  11.   UI_DIR = build-lin/.ui
  12.   OBJECTS_DIR = build-lin/.obj
  13.   MOC_DIR = build-lin/.moc
  14. }
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But what do I know...