ember-cli: 2.13 ember init wipes bower.json (filesToRemove doesn't prompt before deleting)

When upgrading to 2.13, running ember init removes the bower.json file without prompting despite it containing dependencies.

Steps to reproduce:

cat bower.json:

{
  "name": "orange-whisky",
  "dependencies": {
    "remodal": "1.1"
  }
}

---

ember init

installing app
? Overwrite .travis.yml? Yes, overwrite
? Overwrite app/templates/application.hbs? Yes, overwrite
? Overwrite config/environment.js? Yes, overwrite
? Overwrite ember-cli-build.js? Yes, overwrite
? Overwrite package.json? Yes, overwrite
? Overwrite testem.js? Yes, overwrite
? Overwrite tests/helpers/start-app.js? Yes, overwrite
  identical .bowerrc
  identical .editorconfig
  identical .ember-cli
  overwrite .travis.yml
  identical .watchmanconfig
  identical README.md
  identical app/app.js
  identical app/index.html
  identical app/resolver.js
  identical app/router.js
  overwrite app/templates/application.hbs
  overwrite config/environment.js
  create config/targets.js
  overwrite ember-cli-build.js
  identical .gitignore
  overwrite package.json
  identical public/crossdomain.xml
  identical public/robots.txt
  overwrite testem.js
  identical tests/helpers/destroy-app.js
  identical tests/helpers/module-for-acceptance.js
  identical tests/helpers/resolver.js
  overwrite tests/helpers/start-app.js
  identical tests/index.html
  identical tests/test-helper.js
  remove bower.json
NPM: Installed dependencies
installing ember-cli-eslint
  create .eslintrc.js
  create tests/.eslintrc.js

The following JSHint config files were found:
  .jshintrc
  tests/.jshintrc
? What would you like to do? Remove them all

---

git status -s bower.json

 D bower.json

---

Output from ember version --verbose && npm --version:

ember-cli: 2.13.0-beta.1
http_parser: 2.7.0
node: 7.4.0
v8: 5.4.500.45
uv: 1.10.1
zlib: 1.2.8
ares: 1.10.1-DEV
modules: 51
openssl: 1.0.2j
icu: 58.2
unicode: 9.0
cldr: 30.0.3
tz: 2016j
os: darwin x64
4.0.5