Move the git_index_entry to the very top, since it provides the
main structure that needs to be understood by the reader, then
move the bitmasks for the flags and the flags_extended under that
since they are details for looking at particular fields of the
structure.

This removes the functions to duplicate and free copies of a
git_index_entry and updates the comments to explain that you
should just use the public definition of the struct as needed.

This adds git_index_entry_dup to make a copy of an existing entry
and git_index_entry_free to release the memory of the copy.  It
also updates the documentation for git_index_get_bypath and
git_index_get_byindex to make it clear that the returned structure
should *not* be modified.

The constants for extracting data from git_index_entry flags and
flags_extended are not named in a way that makes it easy to know
where to use each one.  This improves the docs for the flags (and
slightly reorganizes them), so it should be more obvious.

It is possible for there to be a submodule in a repository with
no .gitmodules file (for example, if the user forgot to commit
the .gitmodules file).  In this case, core Git will just create
an empty directory as a placeholder for the submodule but
otherwise ignore it.  We were generating an error and stopping
the checkout.  This makes our behavior match that of core git.