Android Studio cant run application after a long time - android-studio

Question

After about half a year of not working on the project, I had to open it up to do some minor changes. However upon opening the project without any issues, I get the following log message when trying to run it on my emulator:
GPBI: {"kind":"error","text":"PARSE ERROR:","sources":[{}]}
AGPBI: {"kind":"error","text":"class name (yifu/theindiestation/com/yifu/BuildConfig) does not match path (Yifu/theindiestation/com/Yifu/BuildConfig.class)","sources":[{}]}
AGPBI: {"kind":"error","text":"...while parsing Yifu/theindiestation/com/Yifu/BuildConfig.class","sources":[{}]}
AGPBI: {"kind":"error","text":"PARSE ERROR:","sources":[{}]}
AGPBI: {"kind":"error","text":"class name (yifu/theindiestation/com/yifu/R) does not match path (Yifu/theindiestation/com/Yifu/R.class)","sources":[{}]}
AGPBI: {"kind":"error","text":"...while parsing Yifu/theindiestation/com/Yifu/R.class","sources":[{}]}
AGPBI: {"kind":"error","text":"PARSE ERROR:","sources":[{}]}
AGPBI: {"kind":"error","text":"class name (yifu/theindiestation/com/yifu/R$anim) does not match path (Yifu/theindiestation/com/Yifu/R$anim.class)","sources":[{}]}
AGPBI: {"kind":"error","text":"...while parsing Yifu/theindiestation/com/Yifu/R$anim.class","sources":[{}]}
AGPBI: {"kind":"error","text":"PARSE ERROR:","sources":[{}]}
AGPBI: {"kind":"error","text":"class name (yifu/theindiestation/com/yifu/R$attr) does not match path (Yifu/theindiestation/com/Yifu/R$attr.class)","sources":[{}]}
AGPBI: {"kind":"error","text":"...while parsing Yifu/theindiestation/com/Yifu/R$attr.class","sources":[{}]}
AGPBI: {"kind":"error","text":"PARSE ERROR:","sources":[{}]}
AGPBI: {"kind":"error","text":"class name (yifu/theindiestation/com/yifu/R$bool) does not match path (Yifu/theindiestation/com/Yifu/R$bool.class)","sources":[{}]}
AGPBI: {"kind":"error","text":"...while parsing Yifu/theindiestation/com/Yifu/R$bool.class","sources":[{}]}
AGPBI: {"kind":"error","text":"PARSE ERROR:","sources":[{}]}
AGPBI: {"kind":"error","text":"class name (yifu/theindiestation/com/yifu/R$color) does not match path (Yifu/theindiestation/com/Yifu/R$color.class)","sources":[{}]}
AGPBI: {"kind":"error","text":"...while parsing Yifu/theindiestation/com/Yifu/R$color.class","sources":[{}]}
AGPBI: {"kind":"error","text":"PARSE ERROR:","sources":[{}]}
AGPBI: {"kind":"error","text":"class name (yifu/theindiestation/com/yifu/R$dimen) does not match path (Yifu/theindiestation/com/Yifu/R$dimen.class)","sources":[{}]}
AGPBI: {"kind":"error","text":"...while parsing Yifu/theindiestation/com/Yifu/R$dimen.class","sources":[{}]}
AGPBI: {"kind":"error","text":"PARSE ERROR:","sources":[{}]}
AGPBI: {"kind":"error","text":"class name (yifu/theindiestation/com/yifu/R$drawable) does not match path (Yifu/theindiestation/com/Yifu/R$drawable.class)","sources":[{}]}
AGPBI: {"kind":"error","text":"...while parsing Yifu/theindiestation/com/Yifu/R$drawable.class","sources":[{}]}
AGPBI: {"kind":"error","text":"PARSE ERROR:","sources":[{}]}
AGPBI: {"kind":"error","text":"class name (yifu/theindiestation/com/yifu/R$id) does not match path (Yifu/theindiestation/com/Yifu/R$id.class)","sources":[{}]}
AGPBI: {"kind":"error","text":"...while parsing Yifu/theindiestation/com/Yifu/R$id.class","sources":[{}]}
AGPBI: {"kind":"error","text":"PARSE ERROR:","sources":[{}]}
AGPBI: {"kind":"error","text":"class name (yifu/theindiestation/com/yifu/R$integer) does not match path (Yifu/theindiestation/com/Yifu/R$integer.class)","sources":[{}]}
AGPBI: {"kind":"error","text":"...while parsing Yifu/theindiestation/com/Yifu/R$integer.class","sources":[{}]}
AGPBI: {"kind":"error","text":"PARSE ERROR:","sources":[{}]}
AGPBI: {"kind":"error","text":"class name (yifu/theindiestation/com/yifu/R$layout) does not match path (Yifu/theindiestation/com/Yifu/R$layout.class)","sources":[{}]}
AGPBI: {"kind":"error","text":"...while parsing Yifu/theindiestation/com/Yifu/R$layout.class","sources":[{}]}
AGPBI: {"kind":"error","text":"PARSE ERROR:","sources":[{}]}
AGPBI: {"kind":"error","text":"class name (yifu/theindiestation/com/yifu/R$mipmap) does not match path (Yifu/theindiestation/com/Yifu/R$mipmap.class)","sources":[{}]}
AGPBI: {"kind":"error","text":"...while parsing Yifu/theindiestation/com/Yifu/R$mipmap.class","sources":[{}]}
AGPBI: {"kind":"error","text":"PARSE ERROR:","sources":[{}]}
AGPBI: {"kind":"error","text":"class name (yifu/theindiestation/com/yifu/R$string) does not match path (Yifu/theindiestation/com/Yifu/R$string.class)","sources":[{}]}
AGPBI: {"kind":"error","text":"...while parsing Yifu/theindiestation/com/Yifu/R$string.class","sources":[{}]}
AGPBI: {"kind":"error","text":"PARSE ERROR:","sources":[{}]}
AGPBI: {"kind":"error","text":"class name (yifu/theindiestation/com/yifu/R$style) does not match path (Yifu/theindiestation/com/Yifu/R$style.class)","sources":[{}]}
AGPBI: {"kind":"error","text":"...while parsing Yifu/theindiestation/com/Yifu/R$style.class","sources":[{}]}
AGPBI: {"kind":"error","text":"PARSE ERROR:","sources":[{}]}
AGPBI: {"kind":"error","text":"class name (yifu/theindiestation/com/yifu/R$styleable) does not match path (Yifu/theindiestation/com/Yifu/R$styleable.class)","sources":[{}]}
AGPBI: {"kind":"error","text":"...while parsing Yifu/theindiestation/com/Yifu/R$styleable.class","sources":[{}]}
AGPBI: {"kind":"error","text":"15 errors; aborting","sources":[{}]}
:app:transformClassesWithDexForDebug FAILED
FAILURE: Build failed with an exception.
* What went wrong:
Execution failed for task ':app:transformClassesWithDexForDebug'.
> com.android.build.api.transform.TransformException: java.lang.RuntimeException: com.android.ide.common.process.ProcessException: java.util.concurrent.ExecutionException: com.android.ide.common.process.ProcessException: org.gradle.process.internal.ExecException: Process 'command '/Library/Java/JavaVirtualMachines/jdk1.8.0_91.jdk/Contents/Home/bin/java'' finished with non-zero exit value 1
* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.
BUILD FAILED
Total time: 8.863 secs
I completely understand what "does not match path" means, but the thing is that I never changed the folders or whatsoever. I've tried cleaning and rebuilding the project several times, updated Genymotion, but still to no avail. Where can I start looking next?
Thanks!