fix: packing the same file twice during publish

close #6997

cspell.json

@@ -129,6 +129,7 @@
     "noproxy",
     "nosystem",
     "nothrow",
+    "npmcli",
     "npmignore",
     "npmjs",
     "ofjergrg",

fetching/directory-fetcher/package.json

@@ -34,16 +34,18 @@
     "@pnpm/logger": "^5.0.0"
   },
   "dependencies": {
+    "@npmcli/arborist": "7.2.0",
     "@pnpm/fetcher-base": "workspace:*",
     "@pnpm/read-project-manifest": "workspace:*",
     "@pnpm/resolver-base": "workspace:*",
     "@pnpm/types": "workspace:*",
-    "npm-packlist": "^5.1.3"
+    "npm-packlist": "^8.0.0"
   },
   "devDependencies": {
     "@pnpm/directory-fetcher": "workspace:*",
     "@pnpm/test-fixtures": "workspace:*",
     "@types/npm-packlist": "^3.0.0",
+    "@types/npmcli__arborist": "5.6.4",
     "@zkochan/rimraf": "^2.1.3"
   },
   "exports": {

fetching/directory-fetcher/src/index.ts

@@ -4,6 +4,7 @@ import type { DirectoryFetcher, DirectoryFetcherOptions } from '@pnpm/fetcher-ba
 import { logger } from '@pnpm/logger'
 import { safeReadProjectManifestOnly } from '@pnpm/read-project-manifest'
 import { type DependencyManifest } from '@pnpm/types'
+import Arborist from '@npmcli/arborist'
 import packlist from 'npm-packlist'
 
 const directoryFetcherLogger = logger('directory-fetcher')
@@ -128,7 +129,9 @@ async function fetchPackageFilesFromDir (
   dir: string,
   opts: FetchFromDirOpts
 ) {
-  const files = await packlist({ path: dir })
+  const arborist = new Arborist(({ path: dir }))
+  const tree = await arborist.loadActual()
+  const files = await packlist(tree)
   const filesIndex: Record<string, string> = Object.fromEntries(files.map((file) => [file, path.join(dir, file)]))
   let manifest: DependencyManifest | undefined
   if (opts.readManifest) {

patching/plugin-commands-patching/package.json

@@ -38,11 +38,13 @@
     "@pnpm/test-fixtures": "workspace:*",
     "@types/normalize-path": "^3.0.1",
     "@types/npm-packlist": "^3.0.0",
+    "@types/npmcli__arborist": "5.6.4",
     "@types/ramda": "0.28.20",
     "@types/semver": "7.5.3",
     "write-yaml-file": "^5.0.0"
   },
   "dependencies": {
+    "@npmcli/arborist": "7.2.0",
     "@pnpm/cli-utils": "workspace:*",
     "@pnpm/config": "workspace:*",
     "@pnpm/constants": "workspace:*",
@@ -62,7 +64,7 @@
     "escape-string-regexp": "^4.0.0",
     "fast-glob": "^3.3.1",
     "normalize-path": "^3.0.0",
-    "npm-packlist": "^5.1.3",
+    "npm-packlist": "^8.0.0",
     "ramda": "npm:@pnpm/ramda@0.28.1",
     "realpath-missing": "^1.1.0",
     "render-help": "^1.0.3",

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

@@ -1,5 +1,6 @@
 import fs from 'fs'
 import path from 'path'
+import Arborist from '@npmcli/arborist'
 import { docsUrl } from '@pnpm/cli-utils'
 import { type Config, types as allTypes } from '@pnpm/config'
 import { install } from '@pnpm/plugin-commands-installation'
@@ -157,7 +158,9 @@ function removeTrailingAndLeadingSlash (p: string) {
  * 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))))
+  const arborist = new Arborist(({ path: src }))
+  const tree = await arborist.loadActual()
+  const files = Array.from(new Set((await packlist(tree)).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)) {