Patch 1

lib/controller/service-controller.coffee

@@ -27,17 +27,16 @@ module.exports = ServiceController =
     @config.initialise obj
 
   onSave: (obj) ->
-    config = @config.load obj
-    @onSync obj, 'up' if config?.behaviour?.uploadOnSave
+    config = @config.loadReal obj
+    @onSync config.filename, 'up' if config?.behaviour?.uploadOnSave
 
   onOpen: (obj) ->
-    config = @config.load obj
-    @onSync obj, 'down' if config?.behaviour?.syncDownOnOpen
+    config = @config.loadReal obj
+    @onSync config.filename, 'down' if config?.behaviour?.syncDownOnOpen
 
   onSync: (obj, direction) ->
-    obj = path.normalize obj
-
     try
+      obj = path.normalize obj
       config = @config.assert obj
     catch err
       @console.show()

lib/helper/config-helper.coffee

@@ -18,6 +18,18 @@ module.exports = ConfigHelper =
     return if not config or not fs.isFileSync config
     cson.readFileSync config
 
+  loadReal: (f) ->
+    config = @load f
+    if config
+      config.filename = f
+    else
+      for fRealPath in atom.project.getPaths() 
+        if (f.indexOf fRealPath) is -1
+          config = cson.readFileSync fRealPath + '/' + @configFileName
+          if config and (f.indexOf config?.option?.localRoot) isnt -1
+            config.filename = fRealPath + f.substr config.option.localRoot.length
+    config
+
   assert: (f) ->
     config = @load f
     if not config then throw new Error "You must create remote config first"
@@ -52,6 +64,7 @@ module.exports = ConfigHelper =
       alwaysSyncAll: false
     option:
       deleteFiles: false
+      localRoot: false
       exclude: [
         '.sync-config.cson'
         '.git'