Limitations

1. npm-shrinkwrap.json and package-lock.json are ignored. Unlike pnpm, npm can install the same name@version multiple times and with different sets of dependencies. npm's shrinkwrap file is designed to reflect the node_modules layout created by npm. pnpm cannot create a similar layout, so it cannot respect npm's lockfile format. However, see pnpm import.
2. You can't publish npm modules with bundleDependencies managed by pnpm.
3. Binstubs (files in node_modules/.bin) are always shell files not symlinks to JS files. The shell files are created to help pluggable CLI apps in finding their plugins in the unusual node_modules structure. This is very rarely an issue and if you expect the file to be a js file, just reference the original file instead, as described in #736.
4. Node.js doesn't work with the --preserve-symlinks flag when executed in a project that uses pnpm.

Got an idea for workarounds for these issues? Share them.