Add bin directory with symlinks to src

Ideally, nothing in src should be touched directly when executing the pipeline scripts. Executing any in src causes some issues with job directories being created there and having to switch between directories to access the scripts in the first place. Instead, a bin directory was created at the top level to house symlinks to each of the shell and python scripts in src. This gives access to the scripts without needing to install them in an environment or traverse the src directory.

Minor changes:

• add bin directory with symlinks to all scripts in src

closed

No longer being done. Moving to package framework instead and setting any CLI options necessary in the pyproject.toml file