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Product Version: NetBeans IDE 6.5 (Build 200811100001) Java: 1.6.0_10; Java HotSpot(TM) Client VM 11.0-b15 System: Linux version 2.6.27-9-generic running on i386; UTF-8; cs_CZ (nb) Observed: I have EAR project with EJB and WEB modules. Now I delete some empty packages in files view in EJB and WEB modules, but the EAR project can't be commited. I must commit EJB and WEB modules separately. I expect, that I could commit only EAR.