Update docs, other changes for cookiecutter usage

[glass-ships]

Closes #132 and #134

This is a fairly large one. Several updates and changes, some needed in general, some to make it play more nicely with cookiecutter for ingests

• Updated documentation
• Remove TODO comments after converting them into issues in github
• Remove some vestigial code sections
• Add dynamic versioning
• Add min_node_count and min_edge_count to primary source config
• Add a check after transform that output contains at least the minimum specified number of rows, if included in config.yaml
• Update biolink model imports
• Update dependencies
• Rename cli_runner.py to cli_utils.py to be less confusingly named
• Plus some formatting noise