Ciftify

[ENC] updating the fmriprep layer for the Docker to 1.1.8
[FIX] fixed MSM permissions within the docker
[DOC] finally mention BIDS-app and Docker in the documentation

- [FIX] cifti_vis_pint adjusted for ivertex-pvertex name change
- [FIX] ciftify_seedcorr and related QC subfunctions do not exclude voxels where mean is 0 (only where sd is 0)
- [FIX] fixed typo in error message of ciftify_clean_img
- [FIX] ciftify clean image forces na to zero when in covariates when doing confound regression
- [FIX] fixed the fmriprep workdir bug in the run script (it now does detect the workdir as writable)
- [ENC] cifitfy_recon_all can be called with the --resample-to-T1w32k after it completes - in this case it only does the last resampling_to_t1w_32k
- [FIX] fixed major error in resample to T1w 32k space (note: previous versions where leaving resampled surfaces in MNI space)
- [ENC] The docker run script now has a `--rerun-if-incomplete` that will delete failed or incomplete ciftify outputs and rerun them.
- [ENC] ciftify_recon_all can take a freesurfer license argument (`--fs-license`). Which makes it easier to run with `singularity exec`

The first release ready for pip

moved location of BIDS apps and some tests

fixing install bug
io.py module has been renamed niio.py to remove conflicts with base python.

switching to io.py module to niio.py to fix install issues.
fixed typy in setup.py