Bash-workbench

Added features:

- Datasets can be run with tools alone, without the need for a launcher
- All logs are being captured, instead of overwriting the menu interface
- Indexed folders are being bookmarked with a simpler reference scheme, removing the bugprone symlink system
- Support `bool` parameter types
- Show help text while browsing parameters

New features:

- After starting a dataset, any BASH files written to `._wb/bin/` can be executed directly from the `wb` menu
- Logs are printed to the screen by default after launching a dataset in the menu
- Added more checks for trusted download of repositories
- Organized tools and launchers by repository in the menu

Added:
- Show the user parameter-level help text in the menu
- Show the git repository versions in the menu

Fixed breaking issues with package distribution.

Minor update to the filesystem navigation functionality:

- move to immediately adjacent directories
- format file list with consistent indentation of description fields
- reorganize navigation menu to raise `cd` and `mkdir` to the top level
- fix bug in "jump to dataset" menu option which inappropriately handled relative paths

The BASH Workbench is a command line utility to provide convenient templating functionality for shell scripting.

The primary use-case motivating the BASH Workbench is bioinformatics analysis, in which datasets consist of collections of files contained in directories which are created and transformed by commands launched from shell scripts.

In the initial release, the BASH Workbench:
- Tracks user-driven annotations of directories with an on-disk indexing system
- Creates BASH scripts with a system of configurable `tool` and `launcher` templates
- Provides convenient user interaction via an interactive menu interface
- Can be installed with `pip3 install bash-workbench`

Example projects which currently use the templating system supported by the BASH Workbench are:
- https://www.github.com/FredHutch/bash-workbench-tools
- https://www.github.com/FredHutch/gig-map