yarn check --verify-tree --node_modules checks package.json from the wrong directory

[allenwu1973]

Do you want to request a feature or report a bug?
bug

What is the current behavior?
yarn check --verify-tree should work with --modules-folder

If the current behavior is a bug, please provide the steps to reproduce.

$ yarn add webpack --modules-folder vendor/node_modules
$ yarn check --verify-tree --modules-folder vendor/node_modules
yarn check v1.17.3
warning package.json: No license field
error "webpack#micromatch#define-property" is wrong version: expected "^2.0.2", got "0.2.5"
error "webpack#micromatch#extend-shallow" is wrong version: expected "^3.0.2", got "2.0.1"
error "webpack#micromatch#kind-of" is wrong version: expected "^6.0.2", got "3.2.2"
error "webpack#mkdirp#minimist" is wrong version: expected "0.0.8", got "1.2.0"
error "webpack#ajv#uri-js#punycode" is wrong version: expected "^2.1.0", got "1.4.1"
error "webpack#memory-fs#readable-stream#safe-buffer" is wrong version: expected "~5.1.1", got "5.2.0"
error "webpack#memory-fs#readable-stream#string_decoder" is wrong version: expected "~1.1.1", got "1.3.0"
error "webpack#micromatch#extglob#define-property" is wrong version: expected "^1.0.0", got "0.2.5"
error "webpack#micromatch#snapdragon#source-map" is wrong version: expected "^0.5.6", got "0.6.1"
error "webpack#node-libs-browser#assert#util" is wrong version: expected "0.10.3", got "0.11.1"
error "webpack#node-libs-browser#url#punycode" is wrong version: expected "1.3.2", got "1.4.1"
error "webpack#node-libs-browser#util#inherits" is wrong version: expected "2.0.3", got "2.0.4"
error "webpack#micromatch#braces#split-string#extend-shallow" is wrong version: expected "^3.0.0", got "2.0.1"
error "webpack#micromatch#snapdragon#define-property#is-descriptor" is wrong version: expected "^0.1.0", got "1.0.2"
error "webpack#watchpack#chokidar#anymatch#normalize-path" is wrong version: expected "^2.1.1", got "3.0.0"
error "webpack#watchpack#chokidar#glob-parent#is-glob" is wrong version: expected "^3.1.0", got "4.0.1"
error "webpack#micromatch#snapdragon#base#mixin-deep#is-extendable" is wrong version: expected "^1.0.1", got "0.1.1"
error "webpack#terser-webpack-plugin#cacache#mississippi#pumpify#pump" is wrong version: expected "^2.0.0", got "3.0.0"
error "webpack#micromatch#snapdragon#base#cache-base#unset-value#has-value" is wrong version: expected "^0.3.1", got "1.0.0"
error "webpack#micromatch#snapdragon#base#cache-base#has-value#has-values#kind-of" is wrong version: expected "^4.0.0", got "3.2.2"
error Found 20 errors.
info Visit https://yarnpkg.com/en/docs/cli/check for documentation about this command.

What is the expected behavior?
yarn check --verify-tree should success

I found yarn was getting version of "webpack#micromatch#define-property" from the wrong file.
Yarn read the version from
vendor/node_modules/define-property/package.json

Where it should be
vendor/node_modules/micromatch/node_modules/define-property/package.json

Please mention your node.js, yarn and operating system version.
node v8.11.1
yarn master latest commit (1a57117)
ubuntu 16.04