Configuration snapshotting

Diff and status do not want core.safecrlf to actually raise an
error regardless of the setting, so this extends the filter API
with an additional options flags parameter and adds a flag so that
filters can be applied with GIT_FILTER_OPT_ALLOW_UNSAFE, indicating
that unsafe filter application should be downgraded from a failure
to a warning.

There were a couple of "init_opts()" functions a few more cases
of structure initialization that I somehow missed.

With the isolation of complex reads, we can now try to refresh the
on-disk file before reading a value from it.

This changes the semantics a bit, as before we could be sure that a
string we got from the configuration was valid until we wrote or
refreshed. This is no longer the case, as a read can also invalidate the
pointer.

In order to have consistent views of the config files for remotes,
submodules et al. and a configuration that represents what is currently
stored on-disk, we need a way to provide a view of the configuration
that does not change.

The goal here is to provide the snapshotting part by creating a
read-only copy of the state of the configuration at a particular point
in time, which does not change when a repository's main config changes.

The usefulness of these helpers came up for me while debugging
some of the iterator changes that I was making, so since they
have also been requested (albeit indirectly) I thought I'd include
them.