Fetching files, loading metadata, and test scripts
io.py and test-files files
fix to_json import
Merge with devel
Fixing CLI parsing

Separating standard arguments from wrapper arguments with --
Some python3 fixes.
test paths fixed
Fixed command line parsing one more

Hopefully this time covered all cases of pre-parsing, help printing
and parsing of tool dependant options
Merge pull request #65 from rabix/feature/fetch-files

Feature/fetch files