Related to https://etke.cc/news/d3uw4utq4t3_rpxicrrfqqou_ynmptqjgk95pt-3n2s/

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.