How to prevent nested node_modules inside node_modules

You can use npm dedupe command to accomplish this.

You can put the command in postinstall script in package.json, and every time NPM installs package, the npm dedupe command will flatten all the duplicated packages in same version for you.

For more information, see https://docs.npmjs.com/cli/dedupe

npm postinstall script

There are upside of having less nested folders and downside having more folders in node_modules folder directly and version control problems.

Use correct npm version

Correct yarn and npm (ie: npm v3) should not have such structure issue. It should always flatten the whole structure where possible and only have nested node_modules if the versions are incompatible with the one at top.

Check versions

So if you have it working properly on one project and not on another, its probably due to version. Check out if the @material-ui is same version on both. Maybe two different packages are conflicting with each other at some point.

Check how you are installing them

From your question, it says it's same version. However, you did not mention how you installed your package on both project. If you install with yarn link or npm link it should install dependencies properly as expected.

Check if you are using different packages

If you check the package, recently material-ui has been deprecated, and the notice says to upgrade to @material-ui/core instead. It might be some packages inside that folder is not same. Either way, it's like this whenever there is some dependency conflict. Check inside the @material-ui folder.

Flatten them manually (dangerous)

There are several packages to forcefully resolve this issue. They will go thru the nested node_modules folders and flatten them into single folder.

flatten-packages

• Install with, npm install -g flatten-packages.
• Run executable flatten-packages to rearrange all packages in node_modules folder in the project directory.
• Flatten will delete older version of a package. You should take care of version breaking changes related errors.