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Makefile-Release.mk, Makefile-Debug.mk are currently located in nbproject dir It's wrong location for this files because if you share project across multiple developers and platforms those files are comitted to SVN/CVS and inside referring wrong paths/tools. For example on windows CXX=g++.exe which doesn't work if you develop on Unix The correct location is nbproject/private which is not stored in RCS and should be regenerated by Makefile-impl to allow builds without IDE on build server
We consider Makefile-Release.mk and Makefile-Debug.mk as part of the project and therefor should be under VS. Usually you would create one configuration per platform and have a Windows configuration, a Linux configuration (using GNU) , and a Solaris configuration (using Sun Studio), etc. Doing that would make the generated makefiles sharable and the project would be buildable on any platform if you pick the right configuration. What you suggest may also work but that is not how it is designed.