How?
Parapona has merely confirmed what no one (so far as I am aware) ever disputed, that moving and concealing a body is a criminal offence in Portugal.
Meanwhile, the culmination of an enquiry in which Mark Harrison confirms, in numerous cites in his reports, that he was tasked to investigate that Madeleine had been murdered, was that Kate and Gerry were made arguidos, accused of murdering their eldest daughter.
I have produced the cites, innumerable times on this board, and will do so again if required.
But it really ought not to be necessary.
Meanwhile, the 'plea-bargain' thing was journalist Giles Tremlett getting entirely the wrong-end of the stick on the basis of incomplete information, in an article written before the files were released.
What Parapono has revealed, at least to me, is that the information in the criminal code aligns precisely with the two years passed on to Kate, so there was no deal. It was a simple and accurate explanation of the law.
As to Mark Harrison's brief, I have not checked the wording in the Files. Some 3 or 4 months after Madeleine had disappeared, there was a good chance Madeleine was dead. Bringing in a cadaver and blood dog is hardly compatible with searching for a living person.
I'm not aware of the capabilities of Tito and Muzzy (?), but it suggestive that OG also included a dead body in their home-set agenda.
The McCanns were made arguidos for the same reason the other 5 have - that they might incriminate themselves under questioning. If it was the McCanns only, a claim of murder might pass muster. However, with 7 arguidos, murder is akin to Agatha Christie's Murder on the Orient Express.