Previous behaviour was redirecting to a file in the current directory
called `2`. Made debugging multiple jobs running on a cluster harder!

Update as per Michael Harms/SS request ( Supporting filtering of CIFTI data in FIX in the absence of applying motion regressors )

(1) Move 'mode' choice to start
(2) Disable (and restore) errexit shopt to ensure 'which' can't abort
(3) Improve documentation of variables
(4) Don't parse sections not relevant to your mode

Add mirror chooser in R so that first install_version doesn't fail.

Use this to ensure that .git files/folders don't make it into the tar

export and use the FSL_FIX_MLOPTS env var