Bugfixes runscript

[edickie]

many upgrades and bug fixes to ciftify_recon_all and run …

• fixed the fmriprep work dir bug in the run script
• changed ciftify_recon_all function so that resampling to T1w32k can be done as a post step
• adding clobber functionality to run script ('--rerun-if-incomplete') will delete failed/incomplete ciftify outputs and rerun ciftify steps
• ciftify_recon_all can take a freesurfer license argument, which allows it to be called more simply with singularity exec