Creating .patch-file not working with NPM overrides having (shared) nested dependency

[FibreFoX]

Not sure if bug or (not yet implemented) feature.

NPM supports changing and even replacing (transitive) dependencies via the "overrides" node in the package.json, this is a NPM feature since v8 (not sure since when exactly):

• v8 documentation https://docs.npmjs.com/cli/v8/configuring-npm/package-json?v=true#overrides
• v9 documentation https://docs.npmjs.com/cli/v9/configuring-npm/package-json?v=true#overrides

I now have this interesting example where I want to replace a (transitive) dependency with a different dependency (not only a different version) in order to get rid of bugs/in order to increase build-speed/because the lib got reworked under different package coordinates:

{
  "name": "some-patch-package-thing",
  "version": "0.0.0",
  "private": true,
  "scripts": {
    "postinstall": "patch-package"
  },
  "dependencies": {
    "react-use": "^17.4.0"
  },
  "devDependencies": {
    "patch-package": "^6.5.1",
    "postinstall-postinstall": "^2.1.0",
    "react-scripts": "5.0.1"
  },
  "engines": {
    "node": ">= 18.14.0"
  },
  "overrides": {
    "magic-string": {
      "sourcemap-codec": "@jridgewell/sourcemap-codec@^1.4.14"
    },
    "nano-css": {
      "sourcemap-codec": "@jridgewell/sourcemap-codec@^1.4.14"
    },
    "svgo": {
      "nth-check": "2.1.1"
    }
  }
}

After npm install all dependencies are getting downloaded, but as magic-string and nano-css are now sharing the same version, the node_modules-folder contain a symlink to the real package. Having two dependencies sharing the same version of a transitive dependency is KEY to this bug. Having only magic-string does not recreate the problem.

Here a tree-output of the magic-string in node_modules:

|   index.d.ts
|   LICENSE
|   package.json
|   README.md
|
+---dist
|       magic-string.cjs.js
|       magic-string.cjs.js.map
|       magic-string.es.js
|       magic-string.es.js.map
|       magic-string.umd.js
|       magic-string.umd.js.map
|
\---node_modules
    \---sourcemap-codec

After download is finished I need to adjust the magic-string-package to reflect the new @jridgewell/sourcemap-codec coordinates, so I edit the files node_modules/magic-string/dist/magic-string.cjs.js and node_modules/magic-string/dist/magic-string.es.js.

Now here comes the problem: when I run npx patch-package magic-string after my edits, to create a patch-file (as normal), I will get greeted with a weird warning:

(Text version of the screenshot, to improve searchability)

patch-package 6.5.1
• Creating temporary folder
• Installing magic-string@0.25.9 with npm
• Diffing your files with clean files
Error: ENOENT: no such file or directory, stat 'C:\develop\tmp\some-patch-package-thing\node_modules\magic-string\node_modules\sourcemap-codec'
    at Object.statSync (node:fs:1596:3)
    at Object.statSync (C:\develop\tmp\some-patch-package-thing\node_modules\graceful-fs\polyfills.js:318:34)
    at statSync (C:\develop\tmp\some-patch-package-thing\node_modules\fs-extra\lib\util\stat.js:10:52)
    at getStatsSync (C:\develop\tmp\some-patch-package-thing\node_modules\fs-extra\lib\util\stat.js:24:19)
    at Object.checkPathsSync (C:\develop\tmp\some-patch-package-thing\node_modules\fs-extra\lib\util\stat.js:49:33)
    at copyDirItem (C:\develop\tmp\some-patch-package-thing\node_modules\fs-extra\lib\copy-sync\copy-sync.js:121:29)
    at C:\develop\tmp\some-patch-package-thing\node_modules\fs-extra\lib\copy-sync\copy-sync.js:115:39
    at Array.forEach (<anonymous>)
    at copyDir (C:\develop\tmp\some-patch-package-thing\node_modules\fs-extra\lib\copy-sync\copy-sync.js:115:23)
    at mkDirAndCopy (C:\develop\tmp\some-patch-package-thing\node_modules\fs-extra\lib\copy-sync\copy-sync.js:110:3) {
  errno: -4058,
  syscall: 'stat',
  code: 'ENOENT',
  path: 'C:\\develop\\tmp\\some-patch-package-thing\\node_modules\\magic-string\\node_modules\\sourcemap-codec'
}
C:\develop\tmp\some-patch-package-thing\node_modules\patch-package\dist\makePatch.js:218
        throw e;
        ^

This probably is due to the node_modules folder not existing in the one which gets downloaded on the • Installing magic-string@0.25.9 with npm step. I have not tested this on MacOS or Linux systems.

OS: Windows 10 Pro
Node: v18.14.0
NPM: 9.4.2