I have a really annoying problem since several days, after I tried to restore a previously working Android Studio project from a backup, after getting a new computer.
I had this very same problem with two libraries in our project, com.koushikdutta.ion and uk.co.senab.photoview which are used thoughout our multi-app project but are declared as dependencies deep down a library project. The symptoms were like this:
My solution is as follows: first of all, close Android Studio. Then :
cd
mv .idea/ .idea-old/
mv .iml .iml-old
re-open Android Studio but select the option "Open an existing Android Studio project". Wait for the project to be reparsed and enjoy perfect cleanness.