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diff --git a/docs/SUMMARY.md b/docs/SUMMARY.md
index cdedf8bccc..9af7d006c0 100644
--- a/docs/SUMMARY.md
+++ b/docs/SUMMARY.md
@@ -1,42 +1,42 @@
 # Summary
 
 # Introduction
-- [Welcome and Overview](welcome_and_overview.md)
+- [Welcome and Overview](introduction/welcome_and_overview.md)
 
 # Setup
   - [Installation](setup/installation.md)
-  - [Using Postgres](postgres.md)
-  - [Configuring a Reverse Proxy](reverse_proxy.md)
+  - [Using Postgres](setup/postgres.md)
+  - [Configuring a Reverse Proxy](setup/reverse_proxy.md)
   - [Configuring a Forward/Outbound Proxy](setup/forward_proxy.md)
-  - [Configuring a Turn Server](turn-howto.md)
-  - [Delegation](delegate.md)
+  - [Configuring a Turn Server](setup/turn-howto.md)
+  - [Delegation](setup/delegation.md)
 
 # Upgrading
   - [Upgrading between Synapse Versions](upgrade.md)
-  - [Upgrading from pre-Synapse 1.0](MSC1711_certificates_FAQ.md)
+  - [Upgrading from pre-Synapse 1.0](upgrading/upgrading_from_pre_synapse_1.0.md)
 
 # Usage
-  - [Federation](federate.md)
+  - [Federation](usage/federation/README.md)
   - [Configuration](usage/configuration/README.md)
     - [Homeserver Sample Config File](usage/configuration/homeserver_sample_config.md)
     - [Logging Sample Config File](usage/configuration/logging_sample_config.md)
-    - [Structured Logging](structured_logging.md)
-    - [Templates](templates.md)
+    - [Structured Logging](usage/configuration/structured_logging.md)
+    - [Templates](usage/configuration/templates.md)
     - [User Authentication](usage/configuration/user_authentication/README.md)
       - [Single-Sign On](usage/configuration/user_authentication/single_sign_on/README.md)
-        - [OpenID Connect](openid.md)
+        - [OpenID Connect](usage/configuration/user_authentication/single_sign_on/openid.md)
         - [SAML](usage/configuration/user_authentication/single_sign_on/saml.md)
         - [CAS](usage/configuration/user_authentication/single_sign_on/cas.md)
-        - [SSO Mapping Providers](sso_mapping_providers.md)
-      - [Password Auth Providers](password_auth_providers.md)
-      - [JSON Web Tokens](jwt.md)
-    - [Registration Captcha](CAPTCHA_SETUP.md)
-    - [Application Services](application_services.md)
-    - [Server Notices](server_notices.md)
-    - [Consent Tracking](consent_tracking.md)
+        - [SSO Mapping Providers](usage/configuration/user_authentication/single_sign_on/sso_mapping_providers.md)
+      - [Password Auth Providers](usage/configuration/user_authentication/password_auth_providers.md)
+      - [JSON Web Tokens](usage/configuration/json_web_tokens.md)
+    - [Registration Captcha](usage/configuration/registration_captcha.md)
+    - [Application Services](usage/configuration/application_services.md)
+    - [Server Notices](usage/configuration/server_notices.md)
+    - [Consent Tracking](usage/configuration/consent_tracking.md)
     - [URL Previews](development/url_previews.md)
-    - [User Directory](user_directory.md)
-    - [Message Retention Policies](message_retention_policies.md)
+    - [User Directory](usage/configuration/user_directory.md)
+    - [Message Retention Policies](usage/configuration/message_retention_policies.md)
     - [Pluggable Modules](modules/index.md)
       - [Writing a module](modules/writing_a_module.md)
         - [Spam checker callbacks](modules/spam_checker_callbacks.md)
@@ -45,8 +45,8 @@
         - [Account validity callbacks](modules/account_validity_callbacks.md)
         - [Password auth provider callbacks](modules/password_auth_provider_callbacks.md)
         - [Porting a legacy module to the new interface](modules/porting_legacy_module.md)
-    - [Workers](workers.md)
-      - [Using `synctl` with Workers](synctl_workers.md)
+    - [Workers](usage/configuration/workers/README.md)
+      - [Using `synctl` with Workers](usage/configuration/workers/synctl_workers.md)
       - [Systemd](systemd-with-workers/README.md)
   - [Administration](usage/administration/README.md)
     - [Admin API](usage/administration/admin_api/README.md)
@@ -64,33 +64,33 @@
       - [Statistics](admin_api/statistics.md)
       - [Users](admin_api/user_admin_api.md)
       - [Server Version](admin_api/version_api.md)
-    - [Manhole](manhole.md)
-    - [Monitoring](metrics-howto.md)
+    - [Manhole](usage/administration/manhole.md)
+    - [Monitoring](usage/administration/monitoring.md)
     - [Request log format](usage/administration/request_log.md)
     - [Scripts]()
 
 # Development
   - [Contributing Guide](development/contributing_guide.md)
-  - [Code Style](code_style.md)
+  - [Code Style](development/code_style.md)
   - [Git Usage](development/git.md)
   - [Testing]()
-  - [OpenTracing](opentracing.md)
+  - [OpenTracing](development/opentracing.md)
   - [Database Schemas](development/database_schema.md)
   - [Experimental features](development/experimental_features.md)
   - [Synapse Architecture]()
-    - [Log Contexts](log_contexts.md)
-    - [Replication](replication.md)
-    - [TCP Replication](tcp_replication.md)
+    - [Log Contexts](development/synapse_architecture/log_contexts.md)
+    - [Replication](development/synapse_architecture/replication.md)
+    - [TCP Replication](development/synapse_architecture/tcp_replication.md)
   - [Internal Documentation](development/internal_documentation/README.md)
     - [Single Sign-On]()
       - [SAML](development/saml.md)
       - [CAS](development/cas.md)
     - [Room DAG concepts](development/room-dag-concepts.md)
     - [State Resolution]()
-      - [The Auth Chain Difference Algorithm](auth_chain_difference_algorithm.md)
-    - [Media Repository](media_repository.md)
-    - [Room and User Statistics](room_and_user_statistics.md)
+      - [The Auth Chain Difference Algorithm](development/internal_documentation/state_resolution/auth_chain_difference_algorithm.md)
+    - [Media Repository](development/internal_documentation/media_repository.md)
+    - [Room and User Statistics](development/internal_documentation/room_and_user_statistics.md)
   - [Scripts]()
 
 # Other
-  - [Dependency Deprecation Policy](deprecation_policy.md)
+  - [Dependency Deprecation Policy](other/dependency_deprecation_policy.md)