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Lady Justice Hallett confirmed there are two other cases where letters were sent in error in a scheme which was kept quiet.
The findings of a four-month inquiry into On-The-Runs letters are unlikely to appease the families of IRA victims.
Sinn Fein Stormont Assembly Member Jennifer McCann has said that those behind the killing of former Continuity IRA figure Tommy Crossan had no consideration for anyone in the community except themselves and their own criminal agenda.
She said: "They have shot a man dead and endangered anyone in the immediate vicinity. There is now a family in mourning and a community traumatised by this shooting.
Crossan, 43, was shot dead at a fuel depot in the grounds of an industrial complex in full view of surrounding houses.
Ms McCann added: "It will not go unnoticed that, with sadness, at Easter time as republicans gather to commemorate their patriot dead, that there are criminals on the streets masquerading as republicans for their own ends.
"This community does not want them. They need to listen to this community, stop these senseless actions and go away."
Detectives have launched a murder investigation and have combed the scene for forensics clues, after ex-Continuity IRA (CIRA) figure Tommy Crossan was shot dead in Belfast yesterday afternoon.
On Springfield Rd, man shot dead named locally as former CIRA leader Tommy Crossan. http://t.co/W83ZSsD7a4
Dissident republican suspects in the killing of one of their former commanders in Belfast are "dinosaurs trapped in the past", the city's Lord Mayor said.
Ex-Continuity IRA (CIRA) figure Tommy Crossan, 43, was shot dead at a fuel depot in the grounds of an industrial complex in full view of surrounding houses. Three gunmen may have carried out the killing and a red BMW car was found on fire nearby.
First citizen Mairtin O Muilleoir of Sinn Fein said the killers existed in the dark margins of society but could not slow the pace of change in Belfast. He claimed: "They are dinosaurs trapped in the past and I urge everyone to work with the police to remove them from our streets."
Mr O'Muilleoir told BBC Radio 4's The World Tonight: "There are some micro groups of criminals masquerading under an assortment of republican labels. They have no support within the community."
The man shot dead in Belfast this afternoon was a former leader of the hardline republican group the Continuity IRA.
Tommy Crossan headed the CIRA after splitting from the more mainstream Provisional IRA during the Northern Ireland peace process.
No group has yet claimed responsibility for Mr Crossan's death, although ti has been reported that he was the subject of death threats from some of his former republican allies.
A PSNI spokeswoman said: "Detectives from Serious Crime Branch have launched a murder investigation after a man was shot dead in the Springfield Road area of West Belfast."
Police have launched an investigation after a man was shot dead in west Belfast this afternoon.
The attack took place on an industrial estate in the Springfield Road area of the city.
In a speech today, Northern Ireland Secretary Theresa Villiers is expected to call for a focus on paramilitaries rather than the police as part of future measures to heal divisions over the conflict. She is expected to say:
At least with a new process, agreed by Northern Ireland's political leaders, there is scope to write in from the start the need for an objective balance and with proper weight and a proportionate focus on the wrongdoing of paramilitaries...rather than the almost exclusive concentration on the activities of the state which characterises so many of the processes currently under way.
The Northern Ireland Secretary is to call for "proportionate" focus on wrongdoing by republicans and loyalists rather than the police as part of future measures to heal divisions over the conflict.
Many processes for addressing the legacy of the past - during which thousands were killed or maimed amid 30 years of bombings and shootings - have concentrated on the activities of security forces, Theresa Villiers will argue, rather than paramilitaries who were responsible for most cases.
The devolved ministerial Executive at Stormont is spending more than £30 million a year on historical matters, with police trawling hundreds of thousands of documents, in part to investigate shootings carried out by former officers or soldiers.
A man has been arrested by police investigating the Omagh bomb. The Real IRA blast in 1998 killed 29 people and a woman pregnant with twins.
The suspect was detained in Newry, Co Down.
Martin McGuinness has described his decision to attend a banquet hosted by the Queen as "an important thing to do" that sends "a message to everybody about how things have changed".
Speaking today, the Northern Irish Deputy First Minister and former IRA commander said that "both governments, who have been rather sluggish over the course of recent times, would do well to learn the lessons of what is happening here in the course of next week".
"They have a huge responsibility to play and unfortunately they haven't been playing it in the last number of months," he added.
Mr McGuinness, who shook the Queen's hand in an historic first meeting in June 2012, said: "We're not just involved in a peace process - we're also involved in a change process.
He added that his acceptance was "an attempt by me to stretch out the hand of friendship" to the unionist and loyalist communities of Northern Ireland.