Fixup dead links

docs/administration/admin_api/README.md

@@ -7,7 +7,11 @@ server admin. (Note that a server admin is distinct from a room admin.)
 
 An existing user can be marked as a server admin by updating the database directly.
 
-Check your [database settings](config_documentation.md#database) in the configuration file, connect to the correct database using either `psql [database name]` (if using PostgreSQL) or `sqlite3 path/to/your/database.db` (if using SQLite) and elevate the user `@foo:bar.com` to administrator.
+Check your [database settings](../../usage/configuration/config_documentation.md#database)
+in the configuration file, connect to the correct database using either 
+`psql [database name]` (if using PostgreSQL) or 
+`sqlite3 path/to/your/database.db` (if using SQLite) and elevate the user 
+`@foo:bar.com` to administrator.
 ```sql
 UPDATE users SET admin = 1 WHERE name = '@foo:bar.com';
 ```
@@ -19,7 +23,7 @@ already on your `$PATH` depending on how Synapse was installed.
 Finding your user's `access_token` is client-dependent, but will usually be shown in the client's settings.
 
 ## Making an Admin API request
-For security reasons, we [recommend](reverse_proxy.md#synapse-administration-endpoints)
+For security reasons, we [recommend](../../setup/reverse_proxy.md#synapse-administration-endpoints)
 that the Admin API (`/_synapse/admin/...`) should be hidden from public view using a
 reverse proxy. This means you should typically query the Admin API from a terminal on
 the machine which runs Synapse.
@@ -35,7 +39,7 @@ For example, suppose we want to
 [query the account](user_admin_api.md#query-user-account) of the user
 `@foo:bar.com`. We need an admin access token (e.g.
 `syt_AjfVef2_L33JNpafeif_0feKJfeaf0CQpoZk`), and we need to know which port
-Synapse's [`client` listener](config_documentation.md#listeners) is listening
+Synapse's [`client` listener](../../usage/configuration/config_documentation.md#listeners) is listening
 on (e.g. `8008`). Then we can use the following command to request the account
 information from the Admin API.
 

docs/upgrade.md

@@ -797,8 +797,8 @@ Any scripts still using the above APIs should be converted to use the
 ## User-interactive authentication fallback templates can now display errors
 
 This may affect you if you make use of custom HTML templates for the
-[reCAPTCHA](../synapse/res/templates/recaptcha.html) or
-[terms](../synapse/res/templates/terms.html) fallback pages.
+[reCAPTCHA](https://github.com/matrix-org/synapse/blob/v1.42.0/synapse/res/templates/recaptcha.html) or
+[terms](https://github.com/matrix-org/synapse/blob/v1.42.0/synapse/res/templates/terms.html) fallback pages.
 
 The template is now provided an `error` variable if the authentication
 process failed. See the default templates linked above for an example.
@@ -1396,7 +1396,7 @@ New templates (`sso_auth_confirm.html`, `sso_auth_success.html`, and
 is configured to use SSO and a custom
 `sso_redirect_confirm_template_dir` configuration then these templates
 will need to be copied from
-[synapse/res/templates](synapse/res/templates) into that directory.
+[synapse/res/templates](https://github.com/matrix-org/synapse/tree/v1.13/synapse/res/templates) into that directory.
 
 ## Synapse SSO Plugins Method Deprecation
 

docs/usage/configuration/config_documentation.md

@@ -2088,7 +2088,7 @@ set.
 
 This is primarily intended for use with the `register_new_matrix_user` script
 (see [Registering a user](../../setup/installation.md#registering-a-user));
-however, the interface is [documented](../../admin_api/register_api.html).
+however, the interface is [documented](../../administration/admin_api/register_api.md).
 
 See also [`registration_shared_secret_path`](#registration_shared_secret_path).
 

docs/usage/configuration/server_notices.md

@@ -58,4 +58,4 @@ displayname and avatar of the Server Notices user.
 ## Sending notices
 
 To send server notices to users you can use the
-[admin_api](../../admin_api/server_notices.md).
+[admin_api](../../administration/admin_api/server_notices.md).

docs/usage/configuration/user_authentication/password_auth_providers.md

@@ -1,7 +1,7 @@
 <h2 style="color:red">
 This page of the Synapse documentation is now deprecated. For up to date
 documentation on setting up or writing a password auth provider module, please see
-<a href="modules/index.md">this page</a>.
+<a href="../../../modules/index.md">this page</a>.
 </h2>
 
 # Password auth provider modules

docs/usage/configuration/user_authentication/single_sign_on/sso_mapping_providers.md

@@ -120,7 +120,7 @@ specified in the config. It is located at
 ## SAML Mapping Providers
 
 The SAML mapping provider can be customized by editing the
-[`saml2_config.user_mapping_provider.module`](docs/usage/configuration/config_documentation.md#saml2_config)
+[`saml2_config.user_mapping_provider.module`](../../config_documentation.md#saml2_config)
 config option.
 
 `saml2_config.user_mapping_provider.config` allows you to provide custom

docs/usage/configuration/workers.md

@@ -111,7 +111,7 @@ redis:
     enabled: true
 ```
 
-See the [configuration manual](usage/configuration/config_documentation.html) for the full documentation of each option.
+See the [configuration manual](config_documentation.md) for the full documentation of each option.
 
 Under **no circumstances** should the replication listener be exposed to the
 public internet; replication traffic is:

docs/welcome_and_overview.md

@@ -16,7 +16,7 @@ This documentation covers topics for **installation**, **configuration** and
 * See how to [upgrade](upgrade.md) between Synapse versions.
 
 * Administer your instance using the [Admin
-  API](usage/administration/admin_api/index.html), installing [pluggable
+  API](administration/admin_api/index.html), installing [pluggable
   modules](modules/index.html), or by accessing the [manhole](administration/manhole.md).
 
 * Learn how to [read log lines](administration/request_log.md), configure