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I understand your problem, but looking at source code I don't see where problem resides.
Could you be more precise and provide path of unwanted commited files ?
In fact, I rely on DirectoryScanner for file-to-commit inclusion.
Regarding javadoc of this class, providing an include pattern of "jobs/*/config.xml" should only commit config.xml files located in root directory (only!) of every jobs.
If this is not the case, this is not the intended behaviour and should be considered as a bug.