We really need some more details about this. What is the filename? Where is it stored? When is it updated? These details are necessary so that the workspace can be added to a source controlled repository and thus included with the project files are checked out.
The default filename seems to be default.workspace. It does not seem to be updated when "save all files" is executed ( why not? ) - only the special "save workspace" command.
There is also a default.workspace.layout file that appears. Should this be checked in to a repository?