Yarn Optimization is removing dependencies

[ryzr]

Bug description

Installing dependencies using a lockfile skips some dependencies and results in broken builds.

Command

➜ vue create test # I created an app with PWA, but should work with default settings
➜ cd test
➜ rm -rf node_modules yarn.lock # clean slate
➜ yarn install
➜ yarn build # SUCCEEDS
➜ rm -rf node_modules
➜ yarn install --frozen-lockfile
➜ yarn build
$ vue-cli-service build
internal/modules/cjs/loader.js:1032
  throw err;
  ^

Error: Cannot find module 'normalize-package-data'
Require stack:
- /Users/ryan/Developer/web/test/node_modules/read-pkg/index.js
- /Users/ryan/Developer/web/test/node_modules/@vue/cli-shared-utils/lib/pkg.js
- /Users/ryan/Developer/web/test/node_modules/@vue/cli-shared-utils/index.js
- /Users/ryan/Developer/web/test/node_modules/@vue/cli-service/bin/vue-cli-service.js
    at Function.Module._resolveFilename (internal/modules/cjs/loader.js:1029:15)
    at Function.Module._load (internal/modules/cjs/loader.js:898:27)
    at Module.require (internal/modules/cjs/loader.js:1089:19)
    at require (internal/modules/cjs/helpers.js:73:18)
    at AsyncFunction.module.exports.sync (/Users/ryan/Developer/web/test/node_modules/read-pkg/index.js:37:3)
    at exports.resolvePkg (/Users/ryan/Developer/web/test/node_modules/@vue/cli-shared-utils/lib/pkg.js:7:20)
    at Service.resolvePkg (/Users/ryan/Developer/web/test/node_modules/@vue/cli-service/lib/Service.js:47:17)
    at new Service (/Users/ryan/Developer/web/test/node_modules/@vue/cli-service/lib/Service.js:27:21)
    at Object.<anonymous> (/Users/ryan/Developer/web/test/node_modules/@vue/cli-service/bin/vue-cli-service.js:15:17)
    at Module._compile (internal/modules/cjs/loader.js:1200:30) {
  code: 'MODULE_NOT_FOUND',
  requireStack: [
    '/Users/ryan/Developer/web/test/node_modules/read-pkg/index.js',
    '/Users/ryan/Developer/web/test/node_modules/@vue/cli-shared-utils/lib/pkg.js',
    '/Users/ryan/Developer/web/test/node_modules/@vue/cli-shared-utils/index.js',
    '/Users/ryan/Developer/web/test/node_modules/@vue/cli-service/bin/vue-cli-service.js'
  ]
}
error Command failed with exit code 1.
info Visit https://yarnpkg.com/en/docs/cli/run for documentation about this command.

What is the current behavior?
During first installation, the lockfile is created with all necessary dependencies and builds fine.

Installing later on from the lockfile (such as in CI environments), modifies the lockfile, applying some "optimizations" mentioned in #4379. Using the --pure-lockfile or --frozen-lockfile flags prevents the lockfile from being modified, but still does not install all dependencies listed in the lockfile (it skips the ones it wanted to optimize for).

What is the expected behavior?
Installs should be idempotent. If the lockfile has not changed, the install should provide the exact same dependencies on every run.

Steps to Reproduce
See above for example using Vue CLI.

Environment

• Node Version: 14.4.0
• Yarn v1 Version: 1.22.4
• OS and version: Mac OS 10.15.5