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She can stay indefinitely, subject to minimal conditions, if it is a registered partnership, if you are married, or if your country of residence recognizes her as your family member under the freedom of movement directive.
She can certainly stay for a total up to 90 days from the date of her entry into the Schengen area. The time spent in Malta with a Maltese residence permit does not count in the 90/180 calculation. The Schengen Borders Code, article 6(2) says in part
Periods of stay authorised under a residence permit or a long-stay visa shall not be taken into account in the calculation of the duration of stay on the territory of the Member States.
The previous sentence of Article 6(2) establishes that the days must be counted inclusively, so the date of entry and the date of exit both count. Therefore, if she entered on December 31st 2018 (and if she does not qualify for free movement), she must leave before the end of March 30th 2019.