[Bug?]: directories referenced in `directories.bin` in `package.json` gets included in `bin`

[yorch]

Self-service

• I'd be willing to implement a fix

Describe the bug

When a package has a directories.bin declaration, and the referenced directory has subdirectories, those get included in bin. Yarn then fails with an error when trying to run any commands.

Internal Error: EISDIR: illegal operation on a directory, read
    at Object.readSync (node:fs:738:18)

To reproduce

Install a dependency that declares directories.bin (like: https://github.com/brenapp/robotevents/blob/master/package.json#L27). Installation of deps will run file.

Lock file will contain something like:

"robotevents@npm:6.0.4":
  version: 6.0.4
  resolution: "robotevents@npm:6.0.4"
  dependencies:
    openapi-fetch: "npm:^0.11.1"
  bin:
    events.js: out/endpoints/events.js
    generated: out/generated
    robotevents.d.ts: out/generated/robotevents.d.ts
    robotevents.js: out/generated/robotevents.js
    ...

generated: out/generated is a directory, not a file, so when running any commands with yarn in that repo, for instance, yarn lint, it will trigger the error:

Internal Error: EISDIR: illegal operation on a directory, read
    at Object.readSync (node:fs:738:18)

Environment

System:
    OS: macOS 26.1
    CPU: (14) arm64 Apple M4 Pro
  Binaries:
    Node: 24.13.0 - /private/var/folders/8k/4fndfdfj4_5g3wtn81flknf784320jn/T/xfs-e22348840/node
    Yarn: 4.12.0 - /private/var/folders/8k/4fndfdfj4_5g3wtn81flknf784320jn/T/xfs-e22348840/yarn
    npm: 11.6.2 - /Users/user/.local/state/fnm_multishells/18077_123477714321/bin/npm

Additional context

No response