Return Color object when in cloned objects

This adds a custom deepClone that clones any Color objects
correctly.

spec/config-spec.coffee

@@ -1393,6 +1393,14 @@ describe "Config", ->
           atom.config.set('foo.bar.aColor', false)
           expect(atom.config.get('foo.bar.aColor')).toEqual {red: 255, green: 255, blue: 255, alpha: 1}
 
+        it "returns a clone of the Color when returned in a parent object", ->
+          color1 = atom.config.get('foo.bar').aColor
+          color2 = atom.config.get('foo.bar').aColor
+          expect(color1.toRGBAString()).toBe 'rgba(255, 255, 255, 1)'
+          expect(color2.toRGBAString()).toBe 'rgba(255, 255, 255, 1)'
+          expect(color1).not.toBe color2
+          expect(color1).toEqual color2
+
       describe 'when the `enum` key is used', ->
         beforeEach ->
           schema =

src/config.coffee

@@ -903,13 +903,13 @@ class Config
       if value instanceof Color
         value = value.clone()
       else
-        value = _.deepClone(value)
+        value = @deepClone(value)
         _.defaults(value, defaultValue) if isPlainObject(value) and isPlainObject(defaultValue)
     else
       if defaultValue instanceof Color
         value = defaultValue.clone()
       else
-        value = _.deepClone(defaultValue)
+        value = @deepClone(defaultValue)
 
     value
 
@@ -959,6 +959,16 @@ class Config
       catch e
         console.warn("'#{keyPath}' could not set the default. Attempted default: #{JSON.stringify(defaults)}; Schema: #{JSON.stringify(@getSchema(keyPath))}")
 
+  deepClone: (object) ->
+    if object instanceof Color
+      object.clone()
+    else if _.isArray(object)
+      object.map (value) => @deepClone(value)
+    else if isPlainObject(object)
+      _.mapObject object, (key, value) => [key, @deepClone(value)]
+    else
+      object
+
   # `schema` will look something like this
   #
   # ```coffee