Right now MRApps sets the classpath to just being mrapp-generated-classpath, its content and a hardcoded list of directories.
If I understand correctly mrapp-generated-classpath is only there for testing and may change or disappear at any time
The list of hardcoded directories is defined in hadoop-mapreduce-project/hadoop-yarn/hadoop-yarn-api/src/main/java/org/apache/hadoop/yarn/api/ApplicationConstants.java at line 92.
For convenience, here is its current content:
Not all deployment scenarii fit in this layout and therefore we need a standardized way to customize this class path.