It seems that's impossible to get a cc.xml file that also contains the jobs from subfolders and if you one of many users of GitHub Organisation Plugin which creates folders and jobs for each repository and branch in yout GitHub organization, you are to hopeless.

Imagine that you do have over 20 repositories and with an average of 5 branches per repository. This means that you will not be able to get these inside a cc.xml file that you can reuse.

Also, even if you attempt to use each cc.xml file from each subfolder you will be really dissapointed to discover that the name of the job is the name of the branch, meaning that you will have the same "master", "develop" job names and be unable to distinguish between master of repo foo and the master of repo bar.