Update build.gradle for Janeway

-Jars copied to Janeway/modules now
-TODO: Add manifest.txt to .jar files
Update build.gradle to copy manifest.txt

Modules now build correctly for Janeway
Move code to follow Gradle conventions

`/src/` to `/src/main/java`
`/test/` to `/src/test/java`
Move manifest.txt files to resources folder
Fix errors from moving images to resources

-Some formatting changes and import organization
Merge changes from dev