GHQ shifting to Islamabad is not confidential information. There were several reports about it in Pakistan's media, including the location of the new HQ (in sector E-10, as far as I remember). According to media reports, the delays in implementing the plan (President Musharraf decided on this plan back in 2004 or 2005) are due to financial problems.
Along with the GHQ, PAF HQ (AHQ) in Chaklala air base and the Navy HQ (NAQ) in Karachi will be relocated to the same district of the GHQ. I am not sure, but I believe that the Jonit Staff HQ (JSHQ) and the Ministry of Defence will be relocated too from Chaklala air base and the city of Rawalpindi (respectively) to the new complex.
However, nothing was reported about the possibility to shift the ISI HQ to the new complex, maybe in the light of its current location in another area of Islamabad.