Document deprecations

### New feature, improvement proposal

A number of methods in this project are deprecated without any docs explaining why they're deprecated or how to replace them. e.g. getWorkItem and setWorkItem in ScmProviderRepository

Document or undeprecate these.

Start by inspecting the deprecated getWorkItem and setWorkItem methods in ScmProviderRepository, then identify the other deprecated methods covered by the issue. For each, determine whether its rationale and replacement can be documented or whether it should be undeprecated; done means the identified deprecations are addressed.

Written by the indexing model from the issue text.