Name change and tool/DB updates

In this release, the tool name was updated to the release name, rotary. Aside from this, several minor enhancements were made, including improvements to the README, updates to tool/DB versions, and addition of more options to the config file. The main workflow remains more or less unchanged.

A few targets are left before this is released as a non-beta:

• Add summary reports of QC, assembly, and so on
• Ideally release a wrapper for the setup/run commands, for ease of use
• Add end-to-end test (at least a description of how to run locally, if not an automated test)

Summary of major changes (since 0.1.0-beta2)

• Rename tool by @jmtsuji in #6
• Basic working version (merged from develop) by @jmtsuji in #7
• End repair and GTDB enhancements/fixes by @jmtsuji in #12