fix(config): Rewrite contents, not just filename

src/browser/application.coffee

@@ -75,6 +75,17 @@ class Application
     @sharedFileManager = new SharedFileManager()
     @nylasProtocolHandler = new NylasProtocolHandler(@resourcePath, @safeMode)
 
+
+    # Temporary as we move away from cson
+    CSON = require 'season'
+    oldConfigFilePath = fs.resolve(@configDirPath, 'config.cson')
+    newConfigFilePath = path.join(@configDirPath, 'config.json')
+    if oldConfigFilePath
+      userConfig = CSON.readFileSync(oldConfigFilePath)
+      fs.writeFileSync(newConfigFilePath, JSON.stringify(userConfig, null, 2))
+      fs.unlinkSync(oldConfigFilePath)
+    # End temporary
+
     Config = require '../config'
     @config = new Config({@configDirPath, @resourcePath})
     @config.load()

src/config.coffee

@@ -331,12 +331,7 @@ class Config
     @defaultSettings = {}
     @configFileHasErrors = false
 
-    # Temporary as we move away from cson
-    oldConfigFilePath = fs.resolve(@configDirPath, 'config.cson')
-    newConfigFilePath = path.join(@configDirPath, 'config.json')
-    if oldConfigFilePath
-      fs.renameSync(oldConfigFilePath, newConfigFilePath)
-    @configFilePath = newConfigFilePath
+    @configFilePath = path.join(@configDirPath, 'config.json')
 
     @transactDepth = 0
     @savePending = false