For Cryptomator 1.3, see Build with eclipse or netbeans. Use the latest JDK 8 version and you shouldn’t have to bother with JCE.
For Cryptomator 1.4, we switched from Eclipse to IntelliJ IDEA because the JDK 9 compatible versions of Eclipse contain changes to the compiler that didn’t get along with code generated by Dagger. Could be fixed in the meantime though but I haven’t tried it. I think you can’t download JDK 9 anymore but JDK 10 works fine, too.
Cryptomator for Android is not fully open-source, so you can’t build it from source.