Issues and Pull Requests were not migrated to the new
organization/repository, so `matrix-org/synapse/pull` and
`matrix-org/synapse/issues` references were kept as-is.

`matrix-org/synapse-s3-storage-provider` references were also kept,
as that module still continues living under the `matrix-org` organization.

This patch mainly aims to change documentation-related things, not actual
usage in full yet. For polish that, another more comprehensive patch is coming later.

It's been pointed out that DEBUG logs could contain sensitive
information (access tokens, etc.), which makes them unsuitable
for sharing with others. INFO should be enough.

Also discussed previously in #213 (Github Pull Request).

shared-secret-auth and rest-auth logging is still at `INFO`
intentionally, as user login events seem more important to keep.
Those modules typically don't spam as much.