Return a cloned object from config.get()

This prevents mutations to the values of the default settings.

src/app/config.coffee

@@ -106,8 +106,8 @@ class Config
   # Returns the value from Atom's default settings, the user's configuration file,
   # or `null` if the key doesn't exist in either.
   get: (keyPath) ->
-    _.valueForKeyPath(@settings, keyPath) ?
-      _.valueForKeyPath(@defaultSettings, keyPath)
+    value = _.valueForKeyPath(@settings, keyPath) ? _.valueForKeyPath(@defaultSettings, keyPath)
+    _.deepClone(value)
 
   # Retrieves the setting for the given key as an integer.
   #

src/app/package-config-panel.coffee

@@ -29,11 +29,12 @@ class PackageConfigPanel extends ConfigPanel
     @on 'change', '#packages input[type=checkbox]', (e) ->
       checkbox = $(e.target)
       name = checkbox.closest('tr').attr('name')
+      disabledPackages = config.get('core.disabledPackages')
       if checkbox.attr('checked')
-        _.remove(config.get('core.disabledPackages'), name)
+        _.remove(disabledPackages, name)
       else
-        config.get('core.disabledPackages').push(name)
-      config.update()
+        disabledPackages.push(name)
+      config.set('core.disabledPackages', disabledPackages)
 
     @observeConfig 'core.disabledPackages', (disabledPackages) =>
       @packageTableBody.find("input[type='checkbox']").attr('checked', true)

src/stdlib/underscore-extensions.coffee

@@ -126,6 +126,35 @@ _.mixin
   endsWith: (string, suffix) ->
     string.indexOf(suffix, string.length - suffix.length) isnt -1
 
+  # Transform the given object into another object.
+  #
+  # `object` - The object to transform.
+  # `iterator` -
+  #   A function that takes `(key, value)` arguments and returns a
+  #   `[key, value]` tuple.
+  #
+  # Returns a new object based with the key/values returned by the iterator.
+  mapObject: (object, iterator) ->
+    newObject = {}
+    for key, value of object
+      [key, value] = iterator(key, value)
+      newObject[key] = value
+
+    newObject
+
+  # Deep clones the given JSON object.
+  #
+  # `object` - The JSON object to clone.
+  #
+  # Returns a deep clone of the JSON object.
+  deepClone: (object) ->
+    if _.isArray(object)
+      object.map (value) -> _.deepClone(value)
+    else if _.isObject(object)
+      @mapObject object, (key, value) => [key, @deepClone(value)]
+    else
+      object
+
   valueForKeyPath: (object, keyPath) ->
     keys = keyPath.split('.')
     for key in keys