I’ve found a very simple (and more comfortable) solution to get around this problem:
Create 2 symbolic links in your filesystem in smt-test/SW4STM/smt-test:
1.: link to ../../Src
2: link to ../..Inc
Next in Eclipse exclude smt-test/Application/User from build.
From now on, you can create your source and headers as usual in Src and inc, and everybody is happy (including CubeMX)