Couple of errors corrected from my previous commits. 
Couple of errors corrected from my previous commits. 

1. dwi.json was modified, becasue otherwise bval and bvec is incorrect (it would contain json files) 
2. handling sbref: in earlier version it did not check if EPI is _bold.nii.gz, if not it overwrites the nii.gz with json, this version checks for it

Now it checked with bids/validator and it is good. 
jmtyszka/bidskit