For this situation, California want you to file a nonresident return as Married Filing Joint. The military member is a statutory nonresident to California because his military income while stationed outside of California is not taxed there and can be excluded from California tax. However, the Spouse's income is included for California taxation, but taxed as Married Filing Joint instead of Married Filing Separately.
If you file this way, community property laws will not affect their return.
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