You will file a CA part-year joint return and a part-year separate RI return with only your spouse's income/deductions for her time in RI. Yes, CA does use the total federal AGI to arrive at a total CA AGI. However, the CA part-year return will allow you to allocate the RI income out of CA. The allocated CA only income (RI not included) is then divided by the total CA AGI to arrive at a proportion of income that is CA sourced. That proportion is multiplied by the CA tax as if resident all year to arrive at the portion of tax that is CA only. You can use your federal joint return to complete the CA joint return for e-filing as normal.
Your spouse will need to sign up for a separate TurboTax account. She will create a "Mock" federal married filing separate return indicating she lived in CA on 31 Dec but also lived in another state, RI, during the tax year. This will generate a part-year RI return and a part-year CA return which will not be completed/filed (filing CA jointly). Enter all her income and deductions as normal in the federal interview. Next, work the RI interview and allocate only the RI source income to RI. She will need to print/mail the RI return since the "Mock" federal separate return will not be filed; you already filed jointly.
Here is a RI reference indicating the separate return is allowed.
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