Make proxy settings one atomic dictionary in the PrefStores such that modifications are atomic.

chrome/common/extensions/api/extension_api.json

 [
   {
     "namespace": "extension",
     "unprivileged": true,
     "types": [
       {
         "id": "MessageSender",
         "type": "object",
         "description": "An object containing information about the script context that sent a message or request.",
         "properties": {
@@ skipping 3726 matching lines @@
         "description": "An object encapsulating a single proxy server's specification.",
         "properties": {
           "scheme": {"type": "string", "optional": true, "enum": ["http", "socks", "socks4", "socks5"], "description": "The scheme (protocol) of the proxy server itself."},
           "host": {"type": "string", "description": "The URI of the proxy server."},
           "port": {"type": "integer", "optional": true, "description": "The port of the proxy server."}
         }
       },
       {
         "id": "ProxyRules",
         "type": "object",
-        "description": "An object encapsulating the set of proxy rules for all protocols.",
+        "description": "An object encapsulating the set of proxy rules for all protocols. Use either 'singleProxy' or (a subset of) 'proxyForHttp', 'proxyForHttps', 'proxyForFtp' and 'socksProxy'.",
         "properties": {
           "singleProxy": {"$ref": "ProxyServer", "optional": true, "description": "The proxy server to be used for all per-URL requests (i.e., http, https, and ftp)."},
           "proxyForHttp": {"$ref": "ProxyServer", "optional": true, "description": "The proxy server to be used for HTTP requests."},
           "proxyForHttps": {"$ref": "ProxyServer", "optional": true, "description": "The proxy server to be used for HTTPS requests."},
           "proxyForFtp": {"$ref": "ProxyServer", "optional": true, "description": "The proxy server to be used for FTP requests."},
           "socksProxy": {"$ref": "ProxyServer", "optional": true, "description": "The proxy server to be used for SOCKS requests."}
         }
       },
       {
         "id": "PacScript",
         "type": "object",
         "description": "An object holding proxy auto-config information. Only one of the fields should be non-empty.",
         "properties": {
           "url": {"type": "string", "optional": true, "description": "URL of he PAC file to be used."}
         }
       },
       {
         "id": "ProxyConfig",
         "type": "object",
         "description": "An object encapsulating a complete proxy configuration.",
         "properties": {
-          "rules": {"$ref": "ProxyRules", "optional": true, "description": "The proxy rules describing this configuration."},
-          "pacScript": {"$ref": "PacScript", "optional": true, "description": "The proxy auto-config (PAC) script for this configuration."},
+          "rules": {"$ref": "ProxyRules", "optional": true, "description": "The proxy rules describing this configuration. Use this for 'fixed_servers' mode."},
+          "pacScript": {"$ref": "PacScript", "optional": true, "description": "The proxy auto-config (PAC) script for this configuration. Use this for 'pac_script' mode."},
           "mode": {
             "type": "string",
             "enum": ["direct", "auto_detect", "pac_script", "fixed_servers", "system"],
             "description": "'direct' = Never use a proxy<br>'auto_detect' = Auto detect proxy settings<br>'pac_script' = Use specified PAC script<br>'fixed_servers' = Manually specify proxy servers<br>'system' = Use system proxy settings"
           }
         }
       }
     ],
     "functions": [
       {
@@ skipping 744 matching lines @@
                   "token": { "type": "string", "optional": true }
                 }
               }
             ]
           }
         ]
       }
     ]
   }
 ]