Refactor planemo.shed module

The module is growing unwieldy -

```
planemo/shed/__init__.py # external interface
planemo/shed/interface.py # low-lever opts on top of bioblend
planemo/shed/config.py # shed yaml operations
planemo/shed/realization.py # Methods aim at realizing repositories.
planemo/shed/operations.py # utilities used directly by shed commands built on rest of this
...
```