diff --git a/package.json b/package.json
index ee32092..9197c18 100644
--- a/package.json
+++ b/package.json
@@ -121,6 +121,7 @@
     "atom-workspace": [
       "atom-beautify:help-debug-editor",
       "atom-beautify:beautify-editor",
+      "atom-beautify:migrate-settings",
       "core:save",
       "core:save-as"
     ],
diff --git a/spec/atom-beautify-spec.coffee b/spec/atom-beautify-spec.coffee
index bd22702..9ca2aee 100644
--- a/spec/atom-beautify-spec.coffee
+++ b/spec/atom-beautify-spec.coffee
@@ -198,6 +198,25 @@ describe "Atom-Beautify", ->
           editor = e
           expect(editor.getText()).toEqual("")
 
+    describe "Migrate Settings", ->
+
+      migrateSettings = (beforeKey, afterKey, val) ->
+        # set old options
+        atom.config.set("atom-beautify.#{beforeKey}", val)
+        atom.commands.dispatch workspaceElement, "atom-beautify:migrate-settings"
+        # Check resulting config
+        expect(_.has(atom.config.get('atom-beautify'), beforeKey)).toBe(false)
+        expect(atom.config.get("atom-beautify.#{afterKey}")).toBe(val)
+
+      it "should migrate js_indent_size to js.indent_size", ->
+        migrateSettings("js_indent_size","js.indent_size", 10)
+
+      it "should migrate analytics to general.analytics", ->
+        migrateSettings("analytics","general.analytics", true)
+
+      it "should migrate _analyticsUserId to general._analyticsUserId", ->
+        migrateSettings("_analyticsUserId","general._analyticsUserId", "userid")
+
     beautifyEditor = (callback) ->
       isComplete = false
       beforeText = null
@@ -238,9 +257,9 @@ describe "Atom-Beautify", ->
           # See https://discuss.atom.io/t/solved-settimeout-not-working-firing-in-specs-tests/11427/17
           jasmine.unspy(window, 'setTimeout')
 
-      afterEach ->
-        atom.packages.deactivatePackages()
-        atom.packages.unloadPackages()
+      # afterEach ->
+      #   atom.packages.deactivatePackages()
+      #   atom.packages.unloadPackages()
 
       describe ".jsbeautifyrc", ->
 
@@ -249,7 +268,7 @@ describe "Atom-Beautify", ->
         getOptions = (callback) ->
           options = null
           waitsForPromise ->
-            console.log('beautifier', beautifier.getOptionsForPath, beautifier)
+            # console.log('beautifier', beautifier.getOptionsForPath, beautifier)
             allOptions = beautifier.getOptionsForPath(null, null)
             # Resolve options with promises
             return Promise.all(allOptions)
@@ -308,7 +327,7 @@ describe "Languages", ->
       namespaceGroups = _.groupBy(languages.languages, "namespace")
       namespacePairs = _.toPairs(namespaceGroups)
       namespaceOverlap = _.filter(namespacePairs, ([namespace, group]) -> group.length > 1)
-      console.log('namespaces', namespaceGroups, namespacePairs, namespaceOverlap)
+      # console.log('namespaces', namespaceGroups, namespacePairs, namespaceOverlap)
       expect(namespaceOverlap.length).toBe(0, \
         "Language namespaces are overlapping.\n\
         Namespaces are unique: only one language for each namespace.\n"+
diff --git a/spec/beautify-languages-spec.coffee b/spec/beautify-languages-spec.coffee
index 097588c..e3f9f24 100644
--- a/spec/beautify-languages-spec.coffee
+++ b/spec/beautify-languages-spec.coffee
@@ -15,7 +15,7 @@ isWindows = process.platform is 'win32' or
   process.env.OSTYPE is 'cygwin' or
   process.env.OSTYPE is 'msys'
 
-xdescribe "BeautifyLanguages", ->
+describe "BeautifyLanguages", ->
 
   optionsDir = path.resolve(__dirname, "../examples")
 
diff --git a/src/beautifiers/index.coffee b/src/beautifiers/index.coffee
index 23a680e..81ee292 100644
--- a/src/beautifiers/index.coffee
+++ b/src/beautifiers/index.coffee
@@ -286,16 +286,16 @@ module.exports = class Beautifiers extends EventEmitter
 
           # Setup Analytics
           analytics = new Analytics(analyticsWriteKey)
-          unless atom.config.get("atom-beautify.general.analyticsUserId")
+          unless atom.config.get("atom-beautify.general._analyticsUserId")
             uuid = require("node-uuid")
-            atom.config.set "atom-beautify.general.analyticsUserId", uuid.v4()
+            atom.config.set "atom-beautify.general._analyticsUserId", uuid.v4()
 
           # Setup Analytics User Id
-          userId = atom.config.get("atom-beautify.general.analyticsUserId")
+          userId = atom.config.get("atom-beautify.general._analyticsUserId")
           analytics.identify userId : userId
           version = pkg.version
           analytics.track
-            userId : atom.config.get("atom-beautify.general.analyticsUserId")
+            userId : atom.config.get("atom-beautify.general._analyticsUserId")
             event : "Beautify"
             properties :
               language : language?.name
diff --git a/src/beautify.coffee b/src/beautify.coffee
index 276ed5a..572979e 100644
--- a/src/beautify.coffee
+++ b/src/beautify.coffee
@@ -67,6 +67,8 @@ showError = (error) ->
 
 beautify = ({onSave}) ->
 
+  plugin.checkUnsupportedOptions()
+
   # Continue beautifying
   path ?= require("path")
   forceEntireFile = onSave and atom.config.get("atom-beautify.general.beautifyEntireFileOnSave")
@@ -259,6 +261,8 @@ beautifyDirectory = ({target}) ->
 
 debug = () ->
 
+  plugin.checkUnsupportedOptions()
+
   # Get current editor
   editor = atom.workspace.getActiveTextEditor()
 
@@ -497,6 +501,53 @@ handleSaveEvent = ->
         )
       )
     plugin.subscriptions.add disposable
+
+getUnsupportedOptions = ->
+  settings = atom.config.get('atom-beautify')
+  schema = atom.config.getSchema('atom-beautify')
+  unsupportedOptions = _.filter(_.keys(settings), (key) ->
+    # return atom.config.getSchema("atom-beautify.${key}").type
+    # return typeof settings[key]
+    schema.properties[key] is undefined
+  )
+  return unsupportedOptions
+
+plugin.checkUnsupportedOptions = ->
+  unsupportedOptions = getUnsupportedOptions()
+  if unsupportedOptions.length isnt 0
+    atom.notifications.addWarning("You have unsupported options: #{unsupportedOptions.join(', ')} <br> Please run Atom command 'Atom-Beautify: Migrate Settings'.")
+
+plugin.migrateSettings = ->
+  unsupportedOptions = getUnsupportedOptions()
+  namespaces = beautifier.languages.namespaces
+  # console.log('migrate-settings', schema, namespaces, unsupportedOptions)
+  if unsupportedOptions.length is 0
+    atom.notifications.addSuccess("No options to migrate.")
+  else
+    rex = new RegExp("(#{namespaces.join('|')})_(.*)")
+    rename = _.toPairs(_.zipObject(unsupportedOptions, _.map(unsupportedOptions, (key) ->
+      m = key.match(rex)
+      if m is null
+        # Did not match
+        # Put into general
+        return "general.#{key}"
+      else
+        return "#{m[1]}.#{m[2]}"
+    )))
+    # console.log('rename', rename)
+    # logger.verbose('rename', rename)
+
+    # Move all option values to renamed key
+    _.each(rename, ([key, newKey]) ->
+      # console.log('rename', key, newKey)
+      # Copy to new key
+      val = atom.config.get("atom-beautify.#{key}")
+      atom.config.set("atom-beautify.#{newKey}", val)
+      # Delete old key
+      atom.config.set("atom-beautify.#{key}", undefined)
+    )
+    atom.notifications.addSuccess("Successfully migrated options: #{unsupportedOptions.join(', ')}")
+
 plugin.config = _.merge(require('./config.coffee'), defaultLanguageOptions)
 plugin.activate = ->
   @subscriptions = new CompositeDisposable
@@ -505,6 +556,7 @@ plugin.activate = ->
   @subscriptions.add atom.commands.add "atom-workspace", "atom-beautify:help-debug-editor", debug
   @subscriptions.add atom.commands.add ".tree-view .file .name", "atom-beautify:beautify-file", beautifyFile
   @subscriptions.add atom.commands.add ".tree-view .directory .name", "atom-beautify:beautify-directory", beautifyDirectory
+  @subscriptions.add atom.commands.add "atom-workspace", "atom-beautify:migrate-settings", plugin.migrateSettings
 
 plugin.deactivate = ->
   @subscriptions.dispose()
diff --git a/src/config.coffee b/src/config.coffee
index fea5262..0f33f20 100644
--- a/src/config.coffee
+++ b/src/config.coffee
@@ -15,7 +15,7 @@ module.exports = {
                 used the most, as well as other stats. Everything is anonymized and no personal
                 information, such as source code, is sent.
                 See https://github.com/Glavin001/atom-beautify/issues/47 for more details."
-      analyticsUserId :
+      _analyticsUserId :
         title: 'Analytics User Id'
         type : 'string'
         default : ""