I added
version.target = version.h
version.commands = bash generate-version.sh
QMAKE_EXTRA_TARGETS += version
PRE_TARGETDEPS += version.h
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I found a better and cleaner solution
version.target = version.h
version.commands = bash ${QMAKE_VAR__PRO_FILE_PWD_}/generate-version.sh
QMAKE_EXTRA_TARGETS += version
The variable _PRO_FILE_PWD_ is documented since qt 4.5 and contains the path to the directory containing the project file in use (Contains the .pro file)
But to access this variable for QMAKE_EXTRA_TARGETS, QMAKE_VAR_ must be appended.