This can be used by tools to show mesages about failing to communicate
with the server. The error message in this case will often contain the
server's error message, as far as it managed to send anything.

When we fail to read from stdout, it's typically because the URL was
wrong and the server process has sent some output over its stderr
output.

Read that output and set the error message to whatever we read from it.

Use a diff for iteration in index_update_all and index_add_all

We set an error if we get an error when reading, but we don't bother
setting an error message for write failing. This causes a cryptic error
to be shown to the user when the target filesystem is full.

Now that `git_path_direach` lets us specify an error message to report,
set an appropriate error message while linking.

This function deals with functions doing IO which means the amount of
errors that can happen is quit large. It does not help if it always
ovewrites the underlying error message with a less understandable
version of "something went wrong".

Instead, only use this generic message if there was no error set by the
callback.

Without this option, we would not be able to catch exec bit changes.

Instead of going through each entry we have and re-adding, which may not
even be correct for certain crlf options and has bad performance, use
the function which performs a diff against the worktree and try to add
and remove files from that list.