Let me try to answer your questions based on my understanding of what you are asking. If I have misunderstood please let me know.
You had asked earlier:
[quote user="Stian Soevik"]
AFAIK, new versions of CCS automatically includes all .cmd files in the project directories. Is it possible to disable this, and explicitly state which files to include?
[/quote]
When you create a new CCS project using the project wizard, in most cases a linker command file is added by default based on the device selected. If you are asking if it is possible to disable this automatic addition of a linker command file, then yes you can. In the New Project wizard, under Advanced Settings, change the Linker command file field from <automatic> to <none>. This will not add any linker command file to the project. After this you may add the files you wish, whether they be multiple .cmd files or a single master .cmd file which in turn adds other .cmd files based on a predefined symbol.
If you only have one linker .cmd file to add to the project in place of the default, you can also use the Browse button next to the Linker command file field and browse directly to it.
Does this help answer your question?