WIP: implement upgrade_all_documents

[tom-tan]

Note: it is not ready to merge!

This request will fixes the issue mentioned in #78.
It contains the following changes:

• Remove output_dir and imports parameter from upgrade_document not to write any files.
  • It break the functionality of cwl-upgrader command. It is the reason why this request also adds upgrade_all_documents.
• Add upgrade_all_documents that upgrades all CWL documents in base_dir recursively and writes upgraded CWL documents to output_dir while keeping the directory structure (e.g., basedir/path/to/tool.cwl is upgraded and written into output_dir/path/to/tool.cwl).

Here is a list to make this request ready to merge:

• implement upgrading imports
• Add tests
  • process docs in nested directories
  • process imports
• fix main and run not to break the functionality of cwl-upgrader command