remove root check and allow_root flag in all sub-programs #598
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Currently we are doing checks for running as root in many places, requiring the
--allow_rootflag to be passed everywhere.This flag however was not always passed through, e.g. see #597 causing
recon-surf.shto error and stop.The two options to fix this are i) forward
--allow_rooteverywhere or ii) avoid checking this in so many places and reduce it to the top level entry scripts (currently run_fastsurfer.sh ).I took the second approach to simplify things and avoid future such bugs.
This needs to be tested when running as root and passing the
--allow_rootflag. Maybe also test as non-root, just in case.