You will be able to allocate the state wages if you are filing Part Year resident tax returns. (If, however, you maintained California domicile and only resided in Mississippi for work, you would allocate the Mississippi income on the Nonresident return.) The state filing requirements for the W2 often require reporting the income differently.
For your HSA contributions, California does not allow the deduction from income so you will be able to allocate it as non-California, but it will still be on the Schedule CA. For the cap gains, if you can divide by the state you were in when it was received, you would include on that Part-Year return.
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