Error due to empty profile application file
Applying a stereotype to a host model and then simply closing the host model results in an empty profile application file (you are not asked to save the file since no change is recognized). When opening the host model again, errors are thrown:
ERROR edu.kit.ipd.sdq.mdsd.profiles.registry.impl.ProfileApplicationFileRegistryImpl - the file '*.pa.xmi' does not contain any profile applications
ERROR edu.kit.ipd.sdq.mdsd.profiles.registry.impl.ProfileApplicationFileRegistryImpl - failed to create profile application decorator for file '*.pa.xmi'
Applying a profile should therefore actually make the contents of the host model editor "dirty", i.e., requesting users to save the file when it is closed. If changes are discarded, also the profile application needs to be removed.
This bug is no longer relevant due to the reimplemented PCM Profiles code.
Meanwhile, a simple workaround is to explicitly save the host model after profile application. For saving, the host model may be changed, saved, the change reverted, and saved again.