Bump!
Same problem here!
Project structure:
project.pro (main pro file)
tools.pri (in tools subfolder)
gui.pri (in gui subfolder)
project.pro ( http://paste.ubuntu.com/9279754/ )
tools.pri ( http://paste.ubuntu.com/9279756/ )
gui.pri ( http://paste.ubuntu.com/9279762/ )
All the files specified inside the .pri files are inside the respective folders. Only with the $$PWD prefix the files are shown inside QtCreator (so in the above pasted files, only the gui/about.h file is shown, screenshot: http://i.imgur.com/V6fnGwL.png ).
An interesting note: The invisible files can be accessed using the Ctrl+Click technique when viewing the .pri file from inside the QtCreator, so something is fishy.