Update internal usage of `git_transfer_progress` to
`git_indexer_progreses`.

This is another option which we should not be keeping in the remote, but
is specific to each particular operation.

While this will rarely be different from the default, having it in the
remote adds yet another setting it has to keep around and can affect its
behaviour. Move it to the options.

Having the setting be different from calling its actions was not a great
idea and made for the sake of the wrong convenience.

Instead of that, accept either fetch options, push options or the
callbacks when dealing with the remote. The fetch options are currently
only the callbacks, but more options will be moved from setters and
getters on the remote to the options.

This does mean passing the same struct along the different functions but
the typical use-case will only call git_remote_fetch() or
git_remote_push() and so won't notice much difference.

This was but down to 5 when GitHub made a change to their server which
made them stop honouring the include-tag request.

This has recently been corrected, so we can bring it back up to six.

The signature for the reflog is not something which changes
dynamically. Almost all uses will be NULL, since we want for the
repository's default identity to be used, making it noise.

In order to allow for changing the identity, we instead provide
git_repository_set_ident() and git_repository_ident() which allow a user
to override the choice of signature.

When we fetch twice with the same remote object, we did not properly
clear the connection flags, so we would leak state from the last
connection.

This can cause the second fetch with the same remote object to fail if
using a HTTP URL where the server redirects to HTTPS, as the second
fetch would see `use_ssl` set and think the initial connection wanted to
downgrade the connection.

This brings it in line with the rest of the lookup functions.