Disambiguate error values: return `GIT_ENOTFOUND` when the item cannot
exist in the repository (perhaps because the repository is inmemory or
otherwise not backed by a filesystem), return `-1` when there is a hard
failure.

Initially, the setting has been solely used to enable the use of
`fsync()` when creating objects. Since then, the use has been extended
to also cover references and index files. As the option is not yet part
of any release, we can still correct this by renaming the option to
something more sensible, indicating not only correlation to objects.

This commit renames the option to `GIT_OPT_ENABLE_FSYNC_GITDIR`. We also
move the variable from the object to repository source code.

The current signature of `git_worktree_prune` accepts a flags field to
alter its behavior. This is not as flexible as we'd like it to be when
we want to enable passing additional options in the future. As the
function has not been part of any release yet, we are still free to
alter its current signature. This commit does so by using our usual
pattern of an options structure, which is easily extendable without
breaking the API.