I would love to answer your points:
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Applying in person is NOT rare at all. It is actually common for the native portuguese speaking immigrants. They want to save money and they usually do it themselves. They often prefer applying in person than applying by mail. No one wants to take risk losing important documents by the post office. Moreover, as said, when applying in person, the officer checks all documents OK or not, then the receipt of submission is given. It feels much better and safer. Only the non-portuguese speakers need to use lawyers because of the language barriers.
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Of course I saw the contagem do tempo. I upload the photo here for everyone as well. There are lots of clips on youtube by brazilien giving instrution of how to get this document. I did not mention that an invalid card could give you a contagem do tempo. Again, when applying for contagem do tempo at Aima/sef, the officer check the validity of the card. If the card is invalid, you cannot even submit the request to get contagem do tempo. So I could call it Step -1 (minus 1).
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For entire process of citizenship, card should be valid. If it expires during the process, one must try all possible ways (including filing lawsuits) to get it renewal. In practice they check the validity of card at step 3, who guarantees that they will not look at it again at step 5 6…?
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The percentage of obtaining citizenship is very high. Almost 99%. I cannot find the article. Process is very clumsy. My recommendation is to launch nuclear weapons (lawsuits) at all and every steps. Cost more but push things moving.