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The best way to work with MDS and PJS files is to keep common version under source control (TFS in your case). If you need to modify it, you have to check out the latest version, make changes and then commit the changes. Do not try to merge these files, most probably you'll get a broken file. Also do not simply commit your local file copy without checking out it first, because you can have a lot of changes in your local file copy and after commit it will affect all team members.
Also to add to above comments..........
you would be better-off sharing single name maping file (NameMapping.tcNM) if it's same application.
but should be done very very very carefully..!
I mean everybody should use same pattern of mapping. (no single object mapped twice in deferent hierarchy)
initially one person would be responsible for maintain name-mapping.