Failed to start Ember after upgrade, es5-shim.js not found

I upgraded embercli, emberjs and ember data. After I run ember init. Then when I ember server, I got below stuff. I have tried to redo everything (upgrading). Same result. There is no error. Only a couple warnings when I upgrade embercli. I attached the warning at the end. I am not sure if they are relevant.

[jusfeel@localhost hillwave-ember-js]$ ember serve
version: 2.4.2
Could not start watchman; falling back to NodeWatcher for file system events.
Visit http://ift.tt/1PK1A1H for more info.
Livereload server on http://localhost:49152
Serving on http://localhost:4200/
The Broccoli Plugin: [SourceMapConcat: Concat: Vendor /assets/vendor.js] failed with:
Error: ENOENT: no such file or directory, stat '/home/jusfeel/ember/hillwave-ember-js/tmp/source_map_concat-input_base_path-http://ift.tt/1R6R89c'
    at Error (native)
    at Object.fs.statSync (fs.js:893:18)
    at ConcatWithMaps.keyForFile (/home/jusfeel/ember/hillwave-ember-js/node_modules/broccoli-caching-writer/index.js:90:20)
    at Array.map (native)
    at ConcatWithMaps.CachingWriter._conditionalBuild (/home/jusfeel/ember/hillwave-ember-js/node_modules/broccoli-caching-writer/index.js:112:65)
    at /home/jusfeel/ember/hillwave-ember-js/node_modules/broccoli-caching-writer/node_modules/broccoli-plugin/read_compat.js:61:34
    at lib$rsvp$$internal$$tryCatch (/home/jusfeel/ember/hillwave-ember-js/node_modules/rsvp/dist/rsvp.js:1036:16)
    at lib$rsvp$$internal$$invokeCallback (/home/jusfeel/ember/hillwave-ember-js/node_modules/rsvp/dist/rsvp.js:1048:17)
    at lib$rsvp$$internal$$publish (/home/jusfeel/ember/hillwave-ember-js/node_modules/rsvp/dist/rsvp.js:1019:11)
    at lib$rsvp$asap$$flush (/home/jusfeel/ember/hillwave-ember-js/node_modules/rsvp/dist/rsvp.js:1198:9)

The broccoli plugin was instantiated at:
    at ConcatWithMaps.Plugin (/home/jusfeel/ember/hillwave-ember-js/node_modules/broccoli-caching-writer/node_modules/broccoli-plugin/index.js:10:31)
    at ConcatWithMaps.CachingWriter [as constructor] (/home/jusfeel/ember/hillwave-ember-js/node_modules/broccoli-caching-writer/index.js:21:10)
    at new ConcatWithMaps (/home/jusfeel/ember/hillwave-ember-js/node_modules/broccoli-concat/concat.js:22:17)
    at module.exports (/home/jusfeel/ember/hillwave-ember-js/node_modules/broccoli-concat/index.js:26:10)
    at EmberApp.concatFiles (/home/jusfeel/ember/hillwave-ember-js/node_modules/ember-cli/lib/broccoli/ember-app.js:329:10)
    at EmberApp.javascript (/home/jusfeel/ember/hillwave-ember-js/node_modules/ember-cli/lib/broccoli/ember-app.js:1190:12)
    at EmberApp.toArray (/home/jusfeel/ember/hillwave-ember-js/node_modules/ember-cli/lib/broccoli/ember-app.js:1542:10)
    at EmberApp.toTree (/home/jusfeel/ember/hillwave-ember-js/node_modules/ember-cli/lib/broccoli/ember-app.js:1564:30)
    at module.exports (/home/jusfeel/ember/hillwave-ember-js/ember-cli-build.js:38:14)
    at Class.module.exports.Task.extend.setupBroccoliBuilder (/home/jusfeel/ember/hillwave-ember-js/node_modules/ember-cli/lib/models/builder.js:55:19)

My bower.json

{
  "name": "hillwave-ember-js",
  "dependencies": {
    "ember": "2.4.2",
    "ember-cli-shims": "0.1.0",
    "ember-cli-test-loader": "0.2.2",
    "jquery": "~2.1.0",
    "bootstrap": "~3.3.6",
    "showdown": "~1.3.0",
    "fastclick": "^1.0.6"
  },
  "resolutions": {
    "ember": "2.3.1"
  },
  "devDependencies": {
    "blanket": "~1.1.5",
    "ember-qunit-notifications": "0.1.0"
  }
}

My package.json

{
  "name": "hillwave-ember-js",
  "version": "0.0.0",
  "description": "Small description for hillwave-ember-js goes here",
  "private": true,
  "directories": {
    "doc": "doc",
    "test": "tests"
  },
  "scripts": {
    "build": "ember build",
    "start": "ember server",
    "test": "ember test"
  },
  "repository": "",
  "engines": {
    "node": ">= 0.10.0"
  },
  "author": "",
  "license": "MIT",
  "devDependencies": {
    "broccoli-asset-rev": "^2.2.0",
    "ember-ajax": "0.7.1",
    "ember-cli": "^2.4.2",
    "ember-cli-app-version": "^1.0.0",
    "ember-cli-babel": "^5.1.5",
    "ember-cli-blanket": "0.8.0",
    "ember-cli-dependency-checker": "^1.2.0",
    "ember-cli-deploy": "0.5.1",
    "ember-cli-deploy-build": "0.1.1",
    "ember-cli-deploy-display-revisions": "0.1.1",
    "ember-cli-deploy-revision-data": "0.1.1",
    "ember-cli-deploy-rsync": "0.0.4",
    "ember-cli-deploy-ssh-index": "0.2.0",
    "ember-cli-document-title": "0.3.0",
    "ember-cli-es5-shim": "^0.1.1",
    "ember-cli-fastclick": "1.1.0",
    "ember-cli-flash": "1.3.8",
    "ember-cli-htmlbars": "^1.0.1",
    "ember-cli-htmlbars-inline-precompile": "^0.3.1",
    "ember-cli-inject-live-reload": "^1.3.1",
    "ember-cli-qunit": "^1.2.1",
    "ember-cli-release": "0.2.8",
    "ember-cli-showdown": "2.5.0",
    "ember-cli-sri": "^2.1.0",
    "ember-cli-uglify": "^1.2.0",
    "ember-data": "^2.4.0",
    "ember-disable-proxy-controllers": "^1.0.1",
    "ember-export-application-global": "^1.0.4",
    "ember-i18n": "4.2.0",
    "ember-infinity": "0.2.1",
    "ember-lazy-image": "http://ift.tt/1R5RS88",
    "ember-load-initializers": "^0.5.0",
    "ember-page-object": "1.1.1",
    "ember-resolver": "^2.0.3",
    "ember-route-history": "0.1.3",
    "ember-simple-auth": "1.0.1",
    "ember-suave": "1.2.3",
    "emberx-select": "2.0.2",
    "fastclick": "1.0.6",
    "graceful-fs": "^4.1.3",
    "memory-scroll": "0.2.0"
  },
  "dependencies": {
    "fonts.css": "^1.4.0",
    "loader.js": "^4.0.0"
  }
}

Some warnings when upgrade embercli from 2.2.0 to 2.4.2.

npm WARN deprecated lodash-node@2.4.1: This package has been discontinued in favor of lodash@^4.0.0.
npm WARN deprecated graceful-fs@3.0.8: graceful-fs version 3 and before will fail on newer node releases. Please update to graceful-fs@^4.0.0 as soon as possible.
npm WARN prefer global marked@0.3.5 should be installed with -g
npm WARN prefer global npm@2.14.21 should be installed with -g