In a software-project written in java you often have resources, that are part of the project and should be included on the classpath. For instance some templates or images, that should be accessible through the classpath (getResource). These files should be included into a produced JAR-file.
It’s clear that these resources should be added to the revision-control-system. But in which directory you put these files? Parallel to the java-source-files or in another directory that also reproduces the needed package-structure?
I prefer your latter solution: a separate directory that mimicks the source code’s package structure. This way they won’t clobber your source code but will be right next to the compiled class files in the packaged JAR file.