Fixes #1854

This adds some missing modules in the API Reference. It adds the modules covered under "case 1" (top-level git, but only refresh and, as before, __version__) and "case 3" (the three leaf modules whose documentation wasn't previously emitted), as I classified them in #1854. It does not add "case 2".

Even if this is what should be done, there is some question about the specifics:

• I don't know what top-level entries should be grouped under in the existing naming convention. Its relationship to the actual module names is usually predictable but not precise. The general pattern doesn't allow me to predict a useful name for the section at the top that now contains git.__version__ and git.refresh; it was previously called "Version", which is no longer suitable. I picked "Top-Level", but this feels not altogether in keeping with the rest of the style.
• I don't know what order the sections for git.compat, git.db, and git.types should come in, relative to the existing sections and each other. The existing sections are ordered in a largely but not entirely alphabetical fashion, and that seems like it may be intentional. I placed them at the end with the section for git.util and I kept those modules at the end sorted alphabetically relative to each other (so they are actually before git.util). That seems to make sense, since their documentation may be less often consulted than than of other modules. But I don't know if that's really true.

Each commit is self-contained, addressing one small part of these changes or other small changes that support or relate to them. While doing this, I noticed opportunities to improve some of the especially affected docstrings or those of closely related functions; those improvements are the first four commits.