It might be a good idea to manage the Makefile of a project manually, instead of letting the IDE do it. One way of changing the project is described below. (let me know of any errors)
Eclipse
Go to Properties for the project (alt + enter) and select C/C++ Build
Uncheck "Generate Makefiles automatically", and change the Build directory to the root of the project folder.
Create a makefile called "Makefile" in the root of the project.>/li>
The old build folders should be safe to delete now.
Netbeans
Go to Properties for the project.
In the build screen, change the Configuration type to Makefile.
Change Makefile in the project root folder, and delete old generated build files.
Subversion stuff
Guide for setting up a Subversion repo. in the IMADA system: SVN guide.
A SVN plugin exists in Netbenas in the standard installation.
Installing Subclipse in Eclipse 3.5
In Eclipse, go to Help, Install New Software
Press Add and use "Subclipse" as name and "http://subclipse.tigris.org/update_1.6.x" as location.
Press OK, and mark Subclipse in the list. Press Next a few times and accept the license aggreement.