The court also dismissed Shah's request to become a party and a witness in the case, saying he was politically affiliated.
The court has ordered fresh trial in the case that will begin on October 22. It has also summoned three witnesses.
On June 25, the Federal Investigation Agency had submitted a final chargesheet against Musharraf that declared him the “prime accused”.
The anti-terrorism court indicted Musharraf on August 20.
The 70-year-old former army chief was arrested by the FIA on April 26 and later granted bail in the case against two surety bonds of Rs 1 million each.
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