Pylint fixes for master

Fixes case where there is no phase encoding contrast present in the SE_EPI images (and hence they need to be combined with the DWI b=0 data for tuopup to possibly be applicable), and also the SE-EPI volumes are defined on a different image grid to the DWIs.

dwifslpreproc: Fix for rare usage

dwidenoise: limit patch size to image dimensions

dwifslpreproc: fix help for -align_seepi option

- afdconnectivity: Add reference and hyperlink to documentation page.
- tcksift2: Add reference for use of -linear option.
- mrtransform: Fix typo in -reorient_fod help text.

Minor command docs updates

Prevents unhandled Python exception from attempting to access number of volumes in a 3D image.

dwifslpreproc: On -rpe_pair, ensure -se_epi is 4D

This fixes #2245

Fixes issue when double-clicking quarantined files on macos.

Since these currently cause CI to fail

This step takes a long time, is prone to failure, and unnecessary at the
moment - we can rely on the default install being sufficiently up to
date.

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