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.

Synapse no longer describes the stats as anonymized since the `server_name` is included.
https://github.com/matrix-org/synapse/pull/13321

Change anonymized to more proper term as server vice this is not anonymized. Server name is the first parameter that is collected. And if server happens to be for individual use these statistics would be at personal level without any anonymising.

We've had some people get confused into installing
Matrix Corporal and having pain with that.

With this documentation change, we try to make it clearer
that it's an advanced feature not to be touched unless
you know what you're doing.

On a similar note, we also make sure other things are properly
labeled as "(optional)" and/or "(advanced)".