Gradle Runner v1.5.3 was just released and it changed how the include and exclude filters works; instead of a file name filter it uses a path filter now.
If you used a wildcard prefixed pattern before, like *.apk, this should not affect you at all, but if you previously used a full file name like app1.apk you should change the pattern to */app1.apk, or specify the full path (can be relative, e.g. ./app/build/outputs/apk/app1.apk or */app/build/outputs/apk/app1.apk) or part of the path with a wildcard prefix (e.g. */outputs/apk/app1.apk).
Basically you now specify a pattern for the path, instead of for the file name.