What versions & operating system are you using?

System:
  OS: Linux 6.8 Ubuntu 24.04.4 LTS (Noble Numbat)
  CPU: (12) x64 AMD Ryzen 5 5600X 6-Core Processor
  Shell: 5.2.21 - /bin/bash
Binaries:
  Node: 25.9.0
  Yarn: 4.14.1
  npm: 11.12.1
Packages (yarn info --name-only):
  miniflare@npm:4.20260426.0
  wrangler@npm:4.86.0
  @cloudflare/workerd-linux-64@npm:1.20260429.1
  @cloudflare/puppeteer@npm:1.1.0

Please provide a link to a minimal reproduction

https://github.com/NormalGaussian/wrangler-pnp-local-explorer-repro

Describe the Bug

When running wrangler dev in a project that uses Yarn with Plug'n'Play (nodeLinker: pnp, the Yarn 4 default), miniflare crashes at startup with:

Directory named "core:local-explorer-disk" not found: <path>/miniflare-npm-<ver>.zip/node_modules/miniflare/dist/local-explorer-ui

Root cause: miniflare's local explorer registers a workerd disk service pointing at dist/local-explorer-ui inside the miniflare package (packages/miniflare/src/plugins/core/explorer.ts:129, called from packages/miniflare/src/plugins/core/index.ts:1149-1180). Under Yarn PnP, packages live as zip archives in .yarn/cache/. PnP patches Node's fs so existsSync reads into those zips transparently, so miniflare's pre-flight check passes — but workerd is a separate native process with no PnP awareness and cannot read the zip as a directory, so it fails late with the cryptic error above.

This regressed for PnP users when the local explorer was switched on by default in #12848 — X_LOCAL_EXPLORER defaults to true in getLocalExplorerEnabledFromEnv (packages/workers-utils/src/environment-variables/misc-variables.ts:343-347), and that flows into unsafeLocalExplorer in packages/wrangler/src/dev/miniflare/index.ts:1059 and the Vite plugin (packages/vite-plugin-cloudflare/src/miniflare-options.ts:469,674).

Workarounds:

• X_LOCAL_EXPLORER=false wrangler dev
• yarn unplug miniflare (extracts miniflare to .yarn/unplugged/ so workerd can read it)

Suggested fixes (in order of effort):

1. Detect Yarn PnP at startup (e.g. process.versions.pnp is set) and either skip the local-explorer disk service with a warning, or transparently copy local-explorer-ui to a temp dir and point workerd there.
2. Always copy the UI assets to a temp directory at startup so miniflare doesn't depend on its own __dirname being a real filesystem path. This also helps with bundlers that flatten __dirname.

Please provide any relevant error logs

In the original (non-containerised) project, the visible error is:

Directory named "core:local-explorer-disk" not found: <path>/dist/local-explorer-ui

In the Docker repro, the same root cause surfaces as a cascading TypeError in getFreshSourceMapSupport because miniflare/wrangler tries to source-map workerd's structured stderr by reading into another PnP zip (@cspotcode/source-map-support) and throws — eating the original log line. Both manifestations go away with X_LOCAL_EXPLORER=false. Stack:

TypeError: Cannot read properties of undefined (reading '/root/.yarn/berry/cache/@cspotcode-source-map-support-npm-0.8.1-964f2de99d-10c0.zip/node_modules/@cspotcode/source-map-support/source-map-support.js')
    at Object.getFreshSourceMapSupport (file:///.../miniflare/dist/src/index.js:76883:40)
    at getSourceMappingPrepareStackTrace (file:///.../wrangler/wrangler-dist/cli.js:62528:29)
    at getSourceMappedString (file:///.../wrangler/wrangler-dist/cli.js:62576:24)
    at handleStructuredLogs (file:///.../wrangler/wrangler-dist/cli.js:65316:25)
    ...
MiniflareCoreError [ERR_RUNTIME_FAILURE]: The Workers runtime failed to start.