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

Question

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://www.ember-cli.com/user-guide/#watchman 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-CxIUyeSW.tmp/0/bower_components/es5-shim/es5-shim.js'
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": "https://github.com/twokul/ember-lazy-image.git",
"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
Edit
/*jshint node:true*/
/* global require, module */
var EmberApp = require('ember-cli/lib/broccoli/ember-app');
module.exports = function(defaults) {
var app = new EmberApp(defaults, {
// Add options here
minifyCSS: {
enabled: true,
compatibility: '-properties.backgroundSizeMerging'
}
});
// Use `app.import` to add additional libraries to the generated
// output files.
//
// If you need to use different assets in different
// environments, specify an object as the first parameter. That
// object's keys should be the environment name and the values
// should be the asset to use in that environment.
//
// If the library that you are including contains AMD or ES6
// modules that you would like to import into your application
// please specify an object with the list of modules as keys
// along with the exports of each module as its value.
app.import('bower_components/bootstrap/dist/css/bootstrap.css');
app.import('bower_components/bootstrap/dist/css/bootstrap.css.map',{
destDir: 'assets'
});
app.import('vendor/royal_preloader/royal_preloader.css');
app.import('bower_components/bootstrap/dist/js/bootstrap.js');
app.import('vendor/royal_preloader/royal_preloader.min.js');
app.import('vendor/jquery.qrcode.min.js');
app.import('vendor/royal_preloader/config.js');
return app.toTree();
};

Answer 1

It's a mistake I made. When I do ember init, I didn't pay attention to remove es5-shim from package.json and left it there. That's why this issue caught me.
I guess I should be much much more careful when I do ember init like the release doc actually had warned.
The most common source of upgrade pain is missing changes in this
step.