Sir,
The existing procedure under Customs Act is not affected by introduction of GST. Prior to 1.7.2017 When imported goods are warehoused without payment of duty have you CVD or SAD. The answer is no since whatever duty payable will be paid only when the imported goods are finally cleared on payment of duties. Therefore while warehousing the imported goods you need not pay IGST.
Moreover as per Section 7 (2) of IGST Act, 2017 "Supply of goods imported into the territory of India, till they cross the customs frontiers of India, shall be treated to be a supply of goods in the course of inter-State trade or commerce. Therefore it can be said that the imported goods have crossed the customs frontiers of India only when they are cleared from the warehouse on payment of duty.