1. The first thing you should be aware of, is that it is perfectly acceptable for you wife to hold both Portuguese and British citizenship, that is dual citizenship.
2. However, if your wife has set her face against ever becoming a British citizen, then she can apply for Indefinite Leave to Remain based on five years living in the UK. This will give her the right to live and work in the UK indefinitely. She should get herself a Permanent Residence card and, she should apply on the basis of being resident in the UK for five years. This gives her the right to acquire ILR. However, she will also need to show she has had private health insurance or else paid National Insurance contributions for these five years, as this is a condition of getting ILR.
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