Formatting fixes for the docs

These are some issues I found while playing around with the new parser
for docurium.
index: split GIT_IDXENTRY into two flag enums

The documentation has shown this as a single enum for a long time. These
should in fact be two enums. One with the bits for the flags and another
with the bits for the extended flags.
Merge pull request #2396 from libgit2/cmn/docstuff

Documentation formatting fixes