Easiest, and usually best: File Jointly, as if you were living same location as family. Military assignments are considered a 'temporary absence', you are NOT required to do a Married Filing Separately return.
Yes, file your return jointly and, in the personal information section, say you were a resident of your home state for the full year. If you have children, they will also be assumed to be living with you. All your overseas time is considered just a temporary absence and is not recognized as time away from home.
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