Initialize ProtocolHandlerInstaller after initializing Config

This allows it to correctly read `core.uriHandlerRegistration` and
avoids popping the notification even if set to 'never'.

Fixes atom#16201

src/atom-environment.js

@@ -206,12 +206,13 @@ class AtomEnvironment {
     this.themes.initialize({configDirPath: this.configDirPath, resourcePath, safeMode, devMode})
 
     this.commandInstaller.initialize(this.getVersion())
-    this.protocolHandlerInstaller.initialize(this.config, this.notifications)
     this.uriHandlerRegistry.registerHostHandler('core', CoreURIHandlers.create(this))
     this.autoUpdater.initialize()
 
     this.config.load()
 
+    this.protocolHandlerInstaller.initialize(this.config, this.notifications)
+
     this.themes.loadBaseStylesheets()
     this.initialStyleElements = this.styles.getSnapshot()
     if (params.onlyLoadBaseStyleSheets) this.themes.initialLoadComplete = true