[Bug?]: EISDIR when reading from a directory that has the same path as a previously existing zip file

[Seinzu]

Self-service

• I'd be willing to implement a fix

Describe the bug

In a long-running process using the pnp linker an error like EISDIR: illegal operation on a directory, read can be emitted when a zip file is removed and replaced by a directory with the same name. For example some.zip is a zip file and is removed. It is then replaced with a directory called some.zip (with some contents) and a read is attempted on a subpath (e.g. some.zip/file). This appears to be due to a caching issue in the pnp FS code as it does not happen when there was never a file called some.zip (or some.zip was never accessed from the process).

To reproduce

Package.json:

{
  "name": "yarn-pnp-zip-mount-cache-demo",
  "version": "1.0.0",
  "private": true,
  "type": "module",
  "packageManager": "yarn@4.18.0"
}

.yarnrc.yml:

enableGlobalCache: false
nodeLinker: pnp
npmMinimalAgeGate: 0

repro.mjs

// Run with
//   node --require ./.pnp.cjs repro.mjs

import fs from 'node:fs'
import Path from 'node:path'

const dir = Path.join(import.meta.dirname, 'work')
fs.rmSync(dir, { recursive: true, force: true })
fs.mkdirSync(dir, { recursive: true })

const zipPath = Path.join(dir, 'demo.zip')
const nestedPath = Path.join(zipPath, 'nested.txt')

console.log('--- Step 1: create demo.zip as a plain (non-archive) file ---')
fs.writeFileSync(zipPath, 'just some ordinary file content, not a real zip')
console.log('created:', zipPath)

console.log('\n--- Step 2: touch it with a plain fs call while it is a file ---')
fs.statSync(zipPath)
console.log('stat succeeded, isFile:', fs.statSync(zipPath).isFile())

console.log('\n--- Step 3: delete the file, replace it with a real directory ---')
fs.unlinkSync(zipPath)
fs.mkdirSync(zipPath)
console.log(
  'demo.zip is now a directory:',
  fs.statSync(zipPath).isDirectory()
)

console.log('\n--- Step 4: write a file nested under the new directory ---')
try {
  fs.writeFileSync(nestedPath, 'hello from inside the real directory')
  console.log('SUCCEEDED - wrote', nestedPath)
  console.log('contents:', fs.readFileSync(nestedPath, 'utf8'))
} catch (err) {
  console.log('FAILED:', err.message)
  console.log('code:', err.code)
  console.log(err.stack)
}

console.log('\n--- Control: same thing, but demo2.zip was not a file first ---')
const zipPath2 = Path.join(dir, 'demo2.zip')
fs.mkdirSync(zipPath2)
try {
  fs.writeFileSync(Path.join(zipPath2, 'nested.txt'), 'hello')
  console.log('SUCCEEDED (as expected - a directory that was always a directory works fine)')
} catch (err) {
  console.log('FAILED (unexpected):', err.message)
}

Error appears in step 4 when run with node --require ./.pnp.cjs repro.mjs. No error when called with node repro.mjs

Environment

System:
    OS: macOS 26.5.1
    CPU: (11) arm64 Apple M3 Pro
  Binaries:
    Node: 24.14.1 - /private/var/folders/3f/5p9h4mx96q3gj7k8cc_l5qp80000gn/T/xfs-7194d65c/node
    Yarn: 4.18.0 - /private/var/folders/3f/5p9h4mx96q3gj7k8cc_l5qp80000gn/T/xfs-7194d65c/yarn
    npm: 11.11.0 - <my home>/.nvm/versions/node/v24.14.1/bin/npm
    bun: 1.3.1 - <my home>/.bun/bin/bun
    Deno: 2.1.6 - <my home>/.deno/bin/deno

Additional context

No response