I am trying to build Qt 5.9 in C:\Qt which is actually a symlink to D:\Qt (no free space on C). Unfortunately it doesn't work well as at some point qmake discovers that c:\qt is actually d:\qt and starts mixing paths to both folders while performing initial configuration in configure.bat

It finally comes to qtbase\configure.pri where the following two lines are at the top:

QT_SOURCE_TREE = $$PWD
QT_BUILD_TREE = $$shadowed($$PWD)

Although I run configure.bat from disk C: and terminal shows path on disk C:, the first $$PWD returns the target path on disk D:. That's not a big deal, but at the second line $$shadowed() returned empty string as that path lies outside of the build tree.

This consequently affects the generation of proper qt.conf file, as it is saved to 

$$QT_BUILD_TREE/bin/qt.conf

which in my case means c:\bin\qt.conf instead of the actual path like

c:\qt\version\qtbase\bin\qt.conf

To reproduce the issue simply create a symlink to another drive in Windows and try a simple pro-file like:

message($$PWD)

there. You'll get the target path instead of the current one. I believe we should get the current path instead.

According to qmake sources, it finally comes to

QFileInfo::canonicalFilePath()

and I am not sure where it needs to be fixed - at qmake or Qt level.

Also, it seems that we had something similar in the past: QTBUG-20431