The getAffectedFiles() method in ChangeLogSet.Entry is not being overridden in the repo ChangeLogEntry, leading to the exception that is thrown from here:
https://github.com/jenkinsci/jenkins/blob/master/core/src/main/java/hudson/scm/ChangeLogSet.java#L194

Some plugins use getAffectedFiles() in order to list the changes that triggered a build. For example, the one that is causing builds to fail for us is the HipChat Notifier plugin, which attempts to notify a HipChat room of changes that triggered the build.

The ChangeLogEntry does collect the list of modified files, but does not return it in the getAffectedFiles() method. The plugin has a getModifiedFiles() method, but does not override the parent class method ChangeLogSet.Entry#getAffectedFiles()