prisma: fix dangling symlinks

Make sure we don't leave dangling symlinks in `$out` when building
`prisma`.

1. We remove the original `node_modules` after buliding the packages to
   re-install the runtime dependencies without the dev dependencies. The
   way it was done was incorrect: only the root `node_modules` directory
   was removed but not the nested ones inside the packages. The
   follow-up `pnpm install` command didn't re-create or empty them and
   only created new files within, so we were left with tons of dangling
   symlinks from the first, full, `pnpm install` invocation.

2. `.pnpm/node_modules` inside the root `node_modules` contains symlinks
   to each workspace member package. However, we don't copy every
   package to `$out`, so we need to clean up this directory to remove
   the references to the missing packages.

Fixes: https://github.com/NixOS/nixpkgs/issues/380427

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