I can't talk much about Netbeans, but I think I can say something about Eclipse. Version control, such as CVS, works great for Eclipse, but I believe that support is slightly behind in other types of version control.
Regarding the changes, Eclipse also highlights what new changes you have in the source code, and this is about providing a local history of the files you are editing. There are project-level overlays in Ecipse, but for this you need to use some kind of version control system (CVS, Subversion, etc.)
Fadzlan
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