diff --git a/docs/internals/configuration.md b/docs/internals/configuration.md
index d1df1d358..ab9dbedf7 100644
--- a/docs/internals/configuration.md
+++ b/docs/internals/configuration.md
@@ -48,11 +48,6 @@ the following way:
 ```coffeescript
 # basic key update
 config.set("core.autosave", true)
-
-# if you mutate a config key, you'll need to call `config.update` to inform
-# observers of the change
-config.get("fuzzyFinder.ignoredPaths").push "vendor"
-config.update()
 ```
 
 You can also use `setDefaults`, which will assign default values for keys that
diff --git a/spec/app/config-spec.coffee b/spec/app/config-spec.coffee
index a1aa37884..41933f2db 100644
--- a/spec/app/config-spec.coffee
+++ b/spec/app/config-spec.coffee
@@ -8,6 +8,13 @@ describe "Config", ->
       expect(config.get("foo.bar.baz")).toBe 42
       expect(config.get("bogus.key.path")).toBeUndefined()
 
+    it "returns a deep clone of the key path's value", ->
+      config.set('value', array: [1, b: 2, 3])
+      retrievedValue = config.get('value')
+      retrievedValue.array[0] = 4
+      retrievedValue.array[1].b = 2.1
+      expect(config.get('value')).toEqual(array: [1, b: 2, 3])
+
   describe ".set(keyPath, value)", ->
     it "allows a key path's value to be written", ->
       expect(config.set("foo.bar.baz", 42)).toBe 42
@@ -93,21 +100,6 @@ describe "Config", ->
       expect(config.get("foo.quux.x")).toBe 0
       expect(config.get("foo.quux.y")).toBe 1
 
-  describe ".update()", ->
-    it "updates observers if a value is mutated without the use of .set", ->
-      config.set("foo.bar.baz", ["a"])
-      observeHandler = jasmine.createSpy "observeHandler"
-      config.observe "foo.bar.baz", observeHandler
-      observeHandler.reset()
-
-      config.get("foo.bar.baz").push("b")
-      config.update()
-      expect(observeHandler).toHaveBeenCalledWith config.get("foo.bar.baz")
-      observeHandler.reset()
-
-      config.update()
-      expect(observeHandler).not.toHaveBeenCalled()
-
   describe ".observe(keyPath)", ->
     observeHandler = null
 
diff --git a/spec/app/project-spec.coffee b/spec/app/project-spec.coffee
index 6367e20c4..6180ceb23 100644
--- a/spec/app/project-spec.coffee
+++ b/spec/app/project-spec.coffee
@@ -180,8 +180,9 @@ describe "Project", ->
 
       it "ignores ignored.txt file", ->
         paths = null
-        config.get("core.ignoredNames").push("ignored.txt")
-        config.update()
+        ignoredNames = config.get("core.ignoredNames")
+        ignoredNames.push("ignored.txt")
+        config.set("core.ignoredNames", ignoredNames)
         waitsForPromise ->
           project.getFilePaths().done (foundPaths) -> paths = foundPaths
 
diff --git a/src/app/config.coffee b/src/app/config.coffee
index 767959330..5fbb5e08e 100644
--- a/src/app/config.coffee
+++ b/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.
   #
diff --git a/src/app/package-config-panel.coffee b/src/app/package-config-panel.coffee
index 43a95faed..137ca6851 100644
--- a/src/app/package-config-panel.coffee
+++ b/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)
diff --git a/src/stdlib/underscore-extensions.coffee b/src/stdlib/underscore-extensions.coffee
index 6f71705d5..8251cbcd1 100644
--- a/src/stdlib/underscore-extensions.coffee
+++ b/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