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Hi,
it can be an issue in apache DirectoryScanner or and issue in Jenkins core whicih deletes the directories. My tip is, that it's and Jenkins core issue as it deletes directories recursively so if you have a capacious sub-directory structure, I can imagine it takes quite a long time to delete it. Could you please run a test job without any filter and check how long it takes to delete this structure without nay filter to be sure that the issue is in way how Jenkins deletes the directories? Thanks and sorry for the delay to response this issue.