fix: pnpm patch should ignore files that are not included in the patched package (#6596)

close #6565

---------

Co-authored-by: Zoltan Kochan <z@kochan.io>

patching/plugin-commands-patching/src/patchCommit.ts

@@ -5,14 +5,17 @@ import { type Config, types as allTypes } from '@pnpm/config'
 import { install } from '@pnpm/plugin-commands-installation'
 import { readPackageJsonFromDir } from '@pnpm/read-package-json'
 import { tryReadProjectManifest } from '@pnpm/read-project-manifest'
+import glob from 'fast-glob'
 import normalizePath from 'normalize-path'
 import pick from 'ramda/src/pick'
+import equals from 'ramda/src/equals'
 import execa from 'safe-execa'
 import escapeStringRegexp from 'escape-string-regexp'
 import renderHelp from 'render-help'
 import tempy from 'tempy'
 import { writePackage } from './writePackage'
 import { parseWantedDependency } from '@pnpm/parse-wanted-dependency'
+import packlist from 'npm-packlist'
 
 export const rcOptionsTypes = cliOptionsTypes
 
@@ -49,7 +52,10 @@ export async function handler (opts: install.InstallCommandOptions & Pick<Config
   const pkgNameAndVersion = `${patchedPkgManifest.name}@${patchedPkgManifest.version}`
   const srcDir = tempy.directory()
   await writePackage(parseWantedDependency(pkgNameAndVersion), srcDir, opts)
-  const patchContent = await diffFolders(srcDir, userDir)
+
+  const patchedPkgDir = await preparePkgFilesForDiff(userDir)
+  const patchContent = await diffFolders(srcDir, patchedPkgDir)
+
   const patchFileName = pkgNameAndVersion.replace('/', '__')
   await fs.promises.writeFile(path.join(patchesDir, `${patchFileName}.patch`), patchContent, 'utf8')
   const { writeProjectManifest, manifest } = await tryReadProjectManifest(lockfileDir)
@@ -129,3 +135,36 @@ function removeTrailingAndLeadingSlash (p: string) {
   }
   return p
 }
+
+/**
+ * Link files from the source directory to a new temporary directory,
+ * but only if not all files in the source directory should be included in the package.
+ * If all files should be included, return the original source directory without creating any links.
+ * This is required in order for the diff to not include files that are not part of the package.
+ */
+async function preparePkgFilesForDiff (src: string): Promise<string> {
+  const files = Array.from(new Set((await packlist({ path: src })).map((f) => path.join(f))))
+  // If there are no extra files in the source directories, then there is no reason
+  // to copy.
+  if (await areAllFilesInPkg(files, src)) {
+    return src
+  }
+  const dest = tempy.directory()
+  await Promise.all(
+    files.map(async (file) => {
+      const srcFile = path.join(src, file)
+      const destFile = path.join(dest, file)
+      const destDir = path.dirname(destFile)
+      await fs.promises.mkdir(destDir, { recursive: true })
+      await fs.promises.link(srcFile, destFile)
+    })
+  )
+  return dest
+}
+
+async function areAllFilesInPkg (files: string[], basePath: string) {
+  const allFiles = await glob('**', {
+    cwd: basePath,
+  })
+  return equals(allFiles.sort(), files.sort())
+}