In addition to filing a joint federal return you need to file a Maryland return and your wife needs to file a Virginia return. The Military Spouse Residency Relief Act (MSRRA) allows your wife to choose your state of residency, even if you did not share the residency prior to the move to California. So, you can file separately or jointly for Maryland, and your wife needs to file a separate return for Virginia as either a full year resident or part year resident. If you file MFS for Maryland she would file a Virginia return as a full year resident. If you file a joint Maryland return she would need to file a part-year resident return for Virginia.
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