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But analysts say security agents still have links with some Kashmiri militants.
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The dead men had been passed off as Pakistani or Kashmiri militants.
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Militants from Afghanistan, Pakistan and Pakistani Kashmir have been fighting alongside Kashmiri militants across the region.
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The attack came days after Farooq and his colleagues travelled to Pakistan for meetings with officials and top Kashmiri militants based there.
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Pakistan promised a positive response, but pro-Pakistan Kashmiri militants dismissed New Delhi's move as "another deception" and vowed to continue their fight.
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Pakistan has for years backed Kashmiri militants and India has accused Pakistan of backing militants who have attacked Indian cities, including Mumbai in November.
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The trial was switched to a special venue at the request of Mr Rao, who feared for his safety from Sikh and Kashmiri militants.