[FIX] Stop series download from failing silently

[DESm1th]

Recently we've noticed that xnat downloads of some dicom series were failing sporadically. Then, dcm2bids was exporting from the incompletely downloaded data. Our code was then seeing the bids folder for the session and skipping it for future re-extraction attempts causing the data to be missing from the archive until an RA notices and points it out to us.

This fixes this situation by:

1. Increasing the starting timeout duration for downloads
2. Fixing a bug that was making our code susceptible to 404 errors after our xnat session timed out
3. Adding error files to the nii folder when NiiLinkExporter is used, so the missing scans can be reported in the dashboard
4. Adding a mode to dm_xnat_extract to re-extract using the tmp folder for situations when the bids config changes (unrelated to the above error, but sneaking this enhancement in here since I needed it incidentally while working on CDIA's missing files).