Duplicating a CC2650DK project so that I don't link and modify original files

I want to create fresh, local projects (without linked files) in my working directory for the CC2650DK using CCS6.1. For example, the SimpleBLEPeripheral uses files in C:\ti\simplelink and C:\ti\tirtos_simplelink_2_13_00_06. If I copy these two directories to another location such as d:\myfirmware, some files still link to C:\ti\tirtos_simplelink_2_13_00_06 instead of d:\myfirmware\tirtos_simplelink_2_13_00_06 and I may destroy the original files for other projects. How can I ensure that nothing is linked to c:\ti? Also, how can I strip down the SimpleBLEPeripheral to just the required minimum files&folders, since these two folders are ~500MB and cumbersome to duplicate.