I have an electron app that is part of an Nx Monorepo. Since updating electron-builder on this project that has been working great for years I started seeing the following error when attempting to build:

• packaging       platform=darwin arch=universal electron=39.2.7 appOutDir=release/mac-universal
⨯ Detected file "Contents/Resources/app.asar.unpacked/node_modules/@nx/nx-darwin-arm64/nx.darwin-arm64.node" that's the same in both x64 and arm64 builds and not covered by the x64ArchFiles rule: "undefined"  failedTask=build stackTrace=Error: Detected file "Contents/Resources/app.asar.unpacked/node_modules/@nx/nx-darwin-arm64/nx.darwin-arm64.node" that's the same in both x64 and arm64 builds and not covered by the x64ArchFiles rule: "undefined"
    at makeUniversalApp (/Users/johnwoodruff/test/node_modules/@electron/universal/src/index.ts:181:17)
    at processTicksAndRejections (node:internal/process/task_queues:105:5)
    at MacPackager.doPack (/Users/johnwoodruff/test/node_modules/app-builder-lib/src/macPackager.ts:188:9)
    at MacPackager.pack (/Users/johnwoodruff/test/node_modules/app-builder-lib/src/macPackager.ts:252:9)
    at Packager.doBuild (/Users/johnwoodruff/test/node_modules/app-builder-lib/src/packager.ts:519:11)
    at executeFinally (/Users/johnwoodruff/test/node_modules/builder-util/src/promise.ts:12:14)
    at Packager.build (/Users/johnwoodruff/test/node_modules/app-builder-lib/src/packager.ts:439:31)
    at executeFinally (/Users/johnwoodruff/test/node_modules/builder-util/src/promise.ts:12:14)

Updating electron-builder was the only change I had made, there was no code or configuration changes made. I originally found #9399 and thought it was the same issue, but after chatting with @mmaietta on a couple attempts, the resolution for that issue did not help me. As a result I dug in deeper to see if my error had a different root cause. After walking through all the app-builder-lib code that handles this, I finally discovered this change: https://github.com/electron-userland/electron-builder/pull/9401/changes#diff-2acfffb0f522ae856a790f8c948ffa38d0f86f846bbd931495fa9643ab2b9c78R185 Specifically the appFileCopier.ts change. It changes the order of node_module search to look at projectDir first instead of appDir which it had been previously. While I am sure this was to fix something else, it ended up breaking for me in my usecase.

The reason why I need to search appDir first is due to how my Nx monorepo works. In this monorepo I have not only my electron app, but also other "apps" such as backend services, mobile apps, etc. So my root package.json and node_modules (the projectDir) include dependencies from all the various apps. So I do a two package.json structure as I need to define only my subset of dependencies that are important to the electron app. So once I've built my app into dist/apps/myapp and then move into the actual electron-builder portion that specifies that as the app directory. Prior to updating, it would use the correct node_modules in the appDir, and now it's pulling from the root directory which contains all those dependencies that should not be packaged.

Hopefully this provides enough info around my issue. I understand there's likely a reason for the change of the ordering of directories, so maybe a configuration that could allow specifying the preferred order as an override from the default behavior?