Refactor simulation architecture

[joshwlambert]

This PR addresses #42 by replacing .sim_bp_linelist(), .sim_clinical_linelist() and .sim_contacts_tbl() with .sim_internal(). sim_linelist(), sim_contacts(), and sim_outbreak() now all call .sim_internal().

The sim_utils.R file has been renamed to utils.R as the internal simulation functions have been removed.

The function documentation has been updated, the design principles vignette now refers to .sim_internal() rather than .sim_bp_linelist(), and snapshots for the regression tests have been updated.

A diagram of the {simulist} package architecture and call stack from exported functions is added to the design principles vignette.

[joshwlambert]

Will merge tomorrow, as these changes are needed to produce a reprex for an issue in another package.

[Bisaloo]

Interface is not changed so I've reviewed this summarily.

Do we need to question the fact that snapshot tests have changed? Even if you confirm this change is expected and valid, please document it in the changelog.

[joshwlambert]

During the review of this PR a diagram of the package architecture has been added to the design principles vignette. I've edited the original comment of this PR to include these changes.