We keep nbproject/configurations.xml and nbproject/project.xml under source control.  If another developer pushes changes to the nbproject files but I pull while Netbeans is open, the IDE does not re-load the file.  This is EXTREMELY annoying because Netbeans will overwrite the more recently changed files when it saves them, undoing the other developer's changes.  

This should be transparent, since the configurations.xml file isn't meant to be read by developers and it's quite difficult to merge changes manually.  Even if I merge the changes manually, Netbeans will ignore the changes, unless I close Netbeans before doing a pull/update.

Conversely, Netbeans is very good about updating source files when they are updated through revision control, so developers assume it's safe to pull and update while the IDE is up.

We are doing C++ development with mercurial, but not sure that matters for this bug.