I am running macOS Sierra 10.12.5 on the 4th partition of my HDD. The partitions in order:
Partition 1, 280 MB: EFI
Partition 2, 22 GB: Storage 1
Partition 3, 186 GB: Storage 2
Partition 4, 110 GB: Macintosh HD
Partition 5, 600 MB: Recovery HD
Storage 2 has 102 GB available, and Macintosh HD only has 66 GB used, so space is not a problem. I need to copy my macOS installation from Macintosh HD to Storage 2, so that I can delete Macintosh HD, and expand Storage 2 to include the now free 110 GB. The catch is that I need to preserve all the data on both partitions while copying the installation. User data, system preferences, my command line package managers, everything. Plus in doing so I need Storage 2 to become a bootable volume. Neither reinstalling macOS, wiping Storage 2 for a restore from Macintosh HD, or wiping and repartitioning the whole disk are options here (I don't have a spare drive large enough to store all that data on.).
I have tried a simple
sudo cp -R / /Volumes/Storage\ 2/ (from in-OS that is), but some files have read/copy permissions denied even to the root user, and that's with SIP off. So... anyone have any ideas? I'm not partial to either the GUI or command line, so long as it gets the job done. Thanks in advance!