Replace (almost) all matrix-org/synapse references with element-hq/synapse

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.

roles/custom/matrix-synapse/templates/synapse/homeserver.yaml.j2

@@ -342,7 +342,7 @@ listeners:
 {% if matrix_synapse_workers_enabled %}
 
 {% if matrix_synapse_replication_listener_enabled %}
-  # c.f. https://github.com/matrix-org/synapse/tree/master/docs/workers.md
+  # c.f. https://github.com/element-hq/synapse/tree/master/docs/workers.md
   # HTTP replication: for the workers to send data to the main synapse process
   - port: {{ matrix_synapse_replication_http_port }}
     bind_addresses: ['0.0.0.0']
@@ -351,7 +351,7 @@ listeners:
       - names: [replication]
 {% endif %}
 
-# c.f. https://github.com/matrix-org/synapse/tree/master/contrib/systemd-with-workers/README.md
+# c.f. https://github.com/element-hq/synapse/tree/master/contrib/systemd-with-workers/README.md
 worker_app: synapse.app.homeserver
 daemonize: false
 {% endif %}
@@ -2484,7 +2484,7 @@ email:
 # ex. LDAP, external tokens, etc.
 #
 # For more information and known implementations, please see
-# https://github.com/matrix-org/synapse/blob/master/docs/password_auth_providers.md
+# https://github.com/element-hq/synapse/blob/master/docs/password_auth_providers.md
 #
 # Note: instances wishing to use SAML or CAS authentication should
 # instead use the `saml2_config` or `cas_config` options,