Also in the file was a letter Kate had written to Paolo Rebelo, the head of the investigation, begging to be kept informed of developments. 'I am appealing to you as a fellow human being to work with us (if possible to include us) and to remember that we are Madeleine's parents . . . lack of communication is torture,' she wrote.
She appears to have received no reply. Once again the file rams home how coldly the Portuguese had treated the family.
Yesterday a friend of the McCann's said: 'There is a sense of anger, frustration and great sadness. They've waited for this [evidence of sightings] for a long time. It's work they could have started 15 months ago. But this is the time for them to keep focus and consider everything carefully before deciding what course of action to take. Then they will have their day, they will make their views clear.'
The couple's priority remains finding Madeleine, but they are angry and hurt by what the files reveal. They are now considering suing the Portuguese police.
Rogerio Alves, the couple's Portuguese lawyer, has been briefed to examine the files for evidence of incompetence, negligence and malicious intent and then to prepare to lay charges. 'I believe he can recommend charges or action be taken against the police as a whole as well as individual officers if it's felt necessary,' said a friend of the family.
Why did the Policia Judiciaria get it so wrong' Why were they obsessed with proving the McCann's guilt' From the beginning the dossier reveals how incompetence blighted the investigation. Carlos Pinto de Abreu, one of the McCann lawyers examining the police files, said: 'The early stages of the investigation, led by detectives in Portimao, really were very poor.'
When those detectives arrived at 3.30pm on May 4, more than 17 hours after Madeleine's disappearance, they discovered that dozens of local police, friends and family had traipsed through the room, heavily contaminating the scene.
One report in the voluminous files released last week records: 'A number of people had touched the window and entered Madeleine's and the twins' room prior to the arrival of the GNR [local] police . . .' There was a 'lack of preservation of the crime scene'.
The case file also reveals how four other families were allowed to stay in the holiday apartment from which Madeleine disappeared before further detailed forensic searches took place.
From the start the McCanns were keenly aware how publicising information about their daughter could help the investigation. So they have been dismayed to discover that the Portuguese police had detailed e-fits of potential suspects - but refused to make them public.
The case files reveal that the police had two near-identical PhotoFits of a man who was seen acting suspiciously near the McCann's apartment before Madeleine's disappearance. Yet the only image of a suspect circulated publicly was a vague drawing with no facial details. It was ridiculed as an 'egg with hair'.
Among the witness reports in the dossier are also three sightings of a girl matching Madeleine's description in Belgium and one in Holland. The McCanns were never told about them. A further potential link with Belgium came in April when the Portuguese police were passed intelligence from Scotland Yard suggesting that Madeleine had been abducted by a Belgian paedophile ring.
John Shord, from the Metropolitan police clubs and vice intelligence unit, wrote: 'Intelligence suggests that a paedophile ring in Belgium made an order for a young girl three days before Madeleine McCann was taken. Somebody connected to this group saw Maddie, took a photograph of her and sent it to Belgium. The purchaser agreed that the girl was suitable and Maddie was taken.'
Last week British police were playing down the strength of that report. But the McCann's view is that if they had been kept informed, they and their private investigators could have helped.
The Portuguese, however, had other ideas. What the case files make clear is just how suspicious the Policia Judiciaria became that the McCann's were responsible for Madeleine's disappearance - and yet how weak the evidence for it was.
The pivotal shift in the investigation came at the end of July, after the Portuguese police called in British experts to help review the case. The experts suggested using specialist British sniffer dogs capable of detecting the scent of dead bodies.
According to the case files, the dogs detected scent at five locations in the McCann's' apartment, including by the door of the back bedroom, behind the sofa in the living room, on the veranda outside the parents' bedroom and in the garden under the veranda. The dogs later 'marked' the boot of the McCann's car.
The case file contains documents showing that Mark Harrison, the British search expert, and Martin Grimes, the dog-handler, warned that the results should be treated with caution. They insisted that 'corroborating evidence' was needed and that no 'intelligence reliability could be placed on the results'.
The Portuguese police, however, treated it very differently. On August 1, the day after the searches, Inspector Joao Carlos, one of the senior investigators, wrote to his superiors stating: 'One must suppose that the child Madeleine McCann could have died inside the apartment.'
On the same day Carlos applied for court orders to plant two bugs in the McCann's rented apartment and one in their holiday home. The requests were rejected, but by this stage the police's intentions were clear. The McCann's noticed a distinct coldness in the police response to them, which culminated in them being made suspects just over a month later.
The Portuguese police's approach was also clear in their treatment of forensic evidence. On September 3, John Lowe, a scientist from the Birmingham-based Forensic Science Service, informed detectives that a sample taken from the McCann's' Renault Scenic hire car had 15 out of 19 of Madeleine's DNA components.
However, he also urged caution, warning that the result was 'too complex for meaningful interpretation or inclusion'. That qualification was ignored. The case files show that days later the Portuguese police attempted to extract a confession from Gerry by insisting Madeleine's DNA had been found in the boot of the car.
One chief inspector of the Portuguese police recorded how he found Gerry 'cold', attributing it to his work as a doctor. He noted: 'During many moments of his professional career he had to make decisions in a fraction of a second, which gives him a coldness.' Yesterday a friend of the McCann's said: 'The whole attitude throughout was one of 'we think they're involved, there are some vague indications, let's throw caution to the wind and see if we can get a conviction'.' For the McCann's, being cut off from the details of the police investigation has been even worse than being made suspects (they have now been exonerated). After Kate's letter in December, the family's lawyers made two further requests for information. Both were refused.
Disappointed but undeterred, the McCann's remain steadfast in their belief that Madeleine will be found. Two months ago the couple decided to relegate the role of M3, the gaffe-prone team of Spanish private investigators whose director boasted last year that Madeleine would be 'home by Christmas'. They are now paying an international team of private investigators '166,000 a month (partly funded from a libel settlement with a newspaper) to follow fresh leads. The release of the case files has demonstrated just how much they have to do. 'They're starting from scratch,' said the friend. 'They have to rebuild the entire police investigation.'
They hope that, better late than never, the information from police files will reinvigorate the search for their daughter. On Monday a girl resembling Madeleine was sighted at a bank in Brussels: a security guard became suspicious after spotting a woman of north African appearance struggling to speak French with a blue-eyed, blonde girl. Detectives are also investigating other leads in Belgium.
Yesterday Clarence Mitchell, the McCann's' spokesman, said: 'The documents are a field of potential leads and any one of them could unlock the case. They will never give up the search for Madeleine.'
International reach of paedophile rings
Are paedophile gangs at work, especially in Belgium' The existence of paedophile rings in Europe is well documented, writes Nicola Smith.
Last year the UK's Child Exploitation and Online Protection Centre (CEOP) brought down a ring of 700, run by a Briton, which disseminated images of horrific child abuse. Many paedophile rings stretch across borders, partly through easy internet communication. Belgian police, however, deny that such gangs operate in their country.
For a nation of just 10m, Belgium has been rocked by shocking paedophile scandals. In the 1990s the notorious Marc Dutroux kidnapped and sexually abused six young girls, killing two of them. Dutroux told a Flemish television station: 'A network with all kinds of criminal activities really does exist. But the authorities don't want to look into it.'
Are there any links with Portugal, where Madeleine McCann disappeared' In 2002 Portugal was shaken by allegations of a paedophile ring targeting a state orphanage. Press reports at the time referred to Dutch and Belgian paedophile gangs operating on Portuguese soil. Belgium is well known as a transit point for people trafficking and Belgian nationals have been caught up recently in police stings on international child abuse gangs.
Late last year police in 28 countries busted a global paedophile ring. The operation began when Australian police intercepted a video of two young girls being abused by a Belgian man.
Is there any evidence of children being snatched to order' Child crime experts say the kidnapping of specific children to order is extremely rare. 'In general, paedophiles ask for a particular type of abuse rather than a particular child,' said CEOP. 'The majority of sexual abuse occurs in the home or by people the child knows.'
The Belgian police said: 'We have never had a paedophile network like that to our knowledge, and we have not come across any cases of children being ordered by paedophiles.'
