Index: synapse/contrib/example_log_config.yaml
===================================================================
--- synapse.orig/contrib/example_log_config.yaml
+++ synapse/contrib/example_log_config.yaml
@@ -26,7 +26,7 @@ handlers:
   file:
     class: logging.handlers.RotatingFileHandler
     formatter: fmt
-    filename: /var/log/synapse/homeserver.log
+    filename: /var/log/matrix-synapse/homeserver.log
     maxBytes: 100000000
     backupCount: 3
     filters: [context]
Index: synapse/synapse/config/key.py
===================================================================
--- synapse.orig/synapse/config/key.py
+++ synapse/synapse/config/key.py
@@ -102,7 +102,7 @@ class KeyConfig(Config):
             signing_key_path = config.get("signing_key_path")
             if signing_key_path is None:
                 signing_key_path = os.path.join(
-                    config_dir_path, config["server_name"] + ".signing.key"
+                    '/etc/matrix-synapse/keys.d', config["server_name"] + ".signing.key"
                 )
 
             self.signing_key = self.read_signing_keys(signing_key_path, "signing_key")
@@ -169,7 +169,7 @@ class KeyConfig(Config):
     def generate_config_section(
         self, config_dir_path, server_name, generate_secrets=False, **kwargs
     ):
-        base_key_name = os.path.join(config_dir_path, server_name)
+        base_key_name = os.path.join('/etc/matrix-synapse/keys.d', server_name)
 
         if generate_secrets:
             macaroon_secret_key = 'macaroon_secret_key: "%s"' % (
Index: synapse/synapse/config/logger.py
===================================================================
--- synapse.orig/synapse/config/logger.py
+++ synapse/synapse/config/logger.py
@@ -150,7 +150,7 @@ class LoggingConfig(Config):
         self.no_redirect_stdio = config.get("no_redirect_stdio", False)
 
     def generate_config_section(self, config_dir_path, server_name, **kwargs) -> str:
-        log_config = os.path.join(config_dir_path, server_name + ".log.config")
+        log_config = os.path.join('/etc/matrix-synapse/', server_name + ".log.config")
         return (
             """\
         ## Logging ##
Index: synapse/synapse/config/server.py
===================================================================
--- synapse.orig/synapse/config/server.py
+++ synapse/synapse/config/server.py
@@ -696,7 +696,7 @@ class ServerConfig(Config):
             bind_port = 8448
             unsecure_port = 8008
 
-        pid_file = os.path.join(data_dir_path, "homeserver.pid")
+        pid_file = os.path.join("/run/matrix-synapse", "homeserver.pid")
 
         # Bring DEFAULT_ROOM_VERSION into the local-scope for use in the
         # default config string
Index: synapse/synapse/config/tls.py
===================================================================
--- synapse.orig/synapse/config/tls.py
+++ synapse/synapse/config/tls.py
@@ -151,7 +151,7 @@ class TlsConfig(Config):
         """If the TLS paths are not specified the default will be certs in the
         config directory"""
 
-        base_key_name = os.path.join(config_dir_path, server_name)
+        base_key_name = os.path.join('/etc/matrix-synapse/keys.d', server_name)
 
         if bool(tls_certificate_path) != bool(tls_private_key_path):
             raise ConfigError(