Ruffus pipeline

See merge request !16

Deleted example_config.yaml, medium_term.yaml, medium_term_prediction.py, poetry.lock, simulate.py, within_between_config.yaml, tier_info.py files

CHANGES:

1. Committed missing `case_data.py` file
2. Moved pipeline specification into `covid.ruffus_pipeline`
3. Moved pipeline initialisation into `covid.pipeline`

CHANGES:

1. Replaced `read_phe_cases` with `CasesData`
2. Column-name fix in `case_exceedance`
3. Fix column heading in `summarize.infec_incidence`
4. Add Rt_exceed to `summarize.rt`
5. Add layer option to `summary_geopackage`
6. Update `ruffus_pipeline.py` to reflect above changes
7. Update `template_config.yaml` to reflect above changes

CHANGE:

1. Reverse experimental selection of last but one xi.
2. Updated template for most recent flow data

Note: in the actual analysis, the effect of December Tiers was
removed.

CHANGES:

1. New data adapter `read_challen_tier_restriction`
2. Modified `model_spec.py` to use new data adapter

CHANGES:

1. Re-introduced Tier lockdown covariates.  National lockdown covariate is set to 0 because
   we cannot identify this from the time-varying baseline force of infection.

2. Added inference on variance parameter for the temporal Gaussian process on beta.

CHANGES:

1. update date and data name in enqueue_pipeline.sh
2. update infection time initialisation in model_spec.py