Minimum set of files should be changes when Solution Packager unpacks the solution


There are CRM and version control system which is used for developing. Sometimes we are using approach like this. We edit unmanaged solution in CRM and then export it and the run Solution Packager unpack command. But the problem is that after unpack there are many changes in source files. And a lot of unneceassary changes are also created along with it. These changes are not part of the solution and each developer needs to remove the changed files from his working directory.

Does anybody know the way to manage the list of files, that should be changed during Solution Packager does unpack the solution?
Thank you!