feat: reading settings from pnpm-workspace.yaml (#9121)

Related discussion: https://github.com/orgs/pnpm/discussions/9037

close #9033

.changeset/famous-sloths-wink.md

@@ -0,0 +1,5 @@
+---
+"@pnpm/workspace.manifest-writer": major
+---
+
+Initial release.

.changeset/few-walls-argue.md

@@ -0,0 +1,5 @@
+---
+"@pnpm/plugin-commands-installation": major
+---
+
+Read `onlyBuiltDependencies` and `ignoredBuiltDependencies` from options.

.changeset/five-birds-enjoy.md

@@ -0,0 +1,6 @@
+---
+"@pnpm/config": minor
+"pnpm": minor
+---
+
+Allow to set the "pnpm" settings from `package.json` via the `pnpm-workspace.yaml` file.

.changeset/friendly-hounds-notice.md

@@ -0,0 +1,5 @@
+---
+"@pnpm/plugin-commands-rebuild": major
+---
+
+Don't rebuild packages that are not in the approved list.

.changeset/gorgeous-eggs-appear.md

@@ -0,0 +1,5 @@
+---
+"@pnpm/exec.build-commands": major
+---
+
+Read `onlyBuiltDependencies` and `ignoredBuiltDependencies` from `options`.

.changeset/itchy-apricots-rest.md

@@ -0,0 +1,5 @@
+---
+"@pnpm/core": major
+---
+
+By default, don't allow to run scripts of dependencies.

.changeset/quick-monkeys-tie.md

@@ -0,0 +1,5 @@
+---
+"@pnpm/types": minor
+---
+
+Export PnpmSettings.

.changeset/rude-masks-train.md

@@ -0,0 +1,5 @@
+---
+"@pnpm/deps.status": major
+---
+
+Read `configDependencies` from `options`.

.changeset/silver-goats-lick.md

@@ -0,0 +1,5 @@
+---
+"@pnpm/workspace.read-manifest": minor
+---
+
+Extend WorkspaceManifest with PnpmSettings.

.changeset/slimy-hounds-sniff.md

@@ -0,0 +1,6 @@
+---
+"@pnpm/workspace.read-manifest": minor
+"pnpm": minor
+---
+
+The `packages` field in `pnpm-workspace.yaml` became optional.

.changeset/tender-swans-drive.md

@@ -0,0 +1,5 @@
+---
+"@pnpm/workspace.manifest-writer": major
+---
+
+Initial release.

__fixtures__/fixture-with-external-shrinkwrap/pnpm-workspace.yaml

@@ -0,0 +1,2 @@
+packages:
+  - pkg

__fixtures__/fixtureWithLinks/pnpm-workspace.yaml

@@ -0,0 +1,2 @@
+packages:
+  - "*"

config/config/src/Config.ts

@@ -7,6 +7,7 @@ import {
   type SslConfig,
 } from '@pnpm/types'
 import type { Hooks } from '@pnpm/pnpmfile'
+import { type OptionsFromRootManifest } from './getOptionsFromRootManifest'
 
 export type UniversalOptions = Pick<Config, 'color' | 'dir' | 'rawConfig' | 'rawLocalConfig'>
 
@@ -17,7 +18,7 @@ export interface WantedPackageManager {
 
 export type VerifyDepsBeforeRun = 'install' | 'warn' | 'error' | 'prompt' | false
 
-export interface Config {
+export interface Config extends OptionsFromRootManifest {
   allProjects?: Project[]
   selectedProjectsGraph?: ProjectsGraph
   allProjectsGraph?: ProjectsGraph

config/config/src/getOptionsFromRootManifest.ts

@@ -6,10 +6,12 @@ import {
   type PackageExtension,
   type PeerDependencyRules,
   type ProjectManifest,
+  type PnpmSettings,
 } from '@pnpm/types'
 import mapValues from 'ramda/src/map'
+import pick from 'ramda/src/pick'
 
-export interface OptionsFromRootManifest {
+export type OptionsFromRootManifest = {
   allowedDeprecatedVersions?: AllowedDeprecatedVersions
   allowNonAppliedPatches?: boolean
   overrides?: Record<string, string>
@@ -22,63 +24,50 @@ export interface OptionsFromRootManifest {
   patchedDependencies?: Record<string, string>
   peerDependencyRules?: PeerDependencyRules
   supportedArchitectures?: SupportedArchitectures
-}
+} & Pick<PnpmSettings, 'configDependencies'>
 
 export function getOptionsFromRootManifest (manifestDir: string, manifest: ProjectManifest): OptionsFromRootManifest {
-  // We read Yarn's resolutions field for compatibility
-  // but we really replace the version specs to any other version spec, not only to exact versions,
-  // so we cannot call it resolutions
-  const overrides = mapValues(
-    createVersionReferencesReplacer(manifest),
-    {
+  const settings: OptionsFromRootManifest = getOptionsFromPnpmSettings(manifestDir, {
+    ...manifest.pnpm,
+    // We read Yarn's resolutions field for compatibility
+    // but we really replace the version specs to any other version spec, not only to exact versions,
+    // so we cannot call it resolutions
+    overrides: {
       ...manifest.resolutions,
       ...manifest.pnpm?.overrides,
-    }
-  )
-  const neverBuiltDependencies = manifest.pnpm?.neverBuiltDependencies
-  let onlyBuiltDependencies = manifest.pnpm?.onlyBuiltDependencies
-  const onlyBuiltDependenciesFile = manifest.pnpm?.onlyBuiltDependenciesFile
-  if (onlyBuiltDependenciesFile == null && neverBuiltDependencies == null && onlyBuiltDependencies == null) {
-    onlyBuiltDependencies = []
+    },
+  }, manifest)
+  return settings
+}
+
+export function getOptionsFromPnpmSettings (manifestDir: string, pnpmSettings: PnpmSettings, manifest?: ProjectManifest): OptionsFromRootManifest {
+  const settings: OptionsFromRootManifest = pick([
+    'allowNonAppliedPatches',
+    'allowedDeprecatedVersions',
+    'configDependencies',
+    'ignoredBuiltDependencies',
+    'ignoredOptionalDependencies',
+    'neverBuiltDependencies',
+    'onlyBuiltDependencies',
+    'onlyBuiltDependenciesFile',
+    'overrides',
+    'packageExtensions',
+    'peerDependencyRules',
+    'supportedArchitectures',
+  ], pnpmSettings)
+  if (settings.overrides && manifest) {
+    settings.overrides = mapValues(createVersionReferencesReplacer(manifest), settings.overrides)
   }
-  const packageExtensions = manifest.pnpm?.packageExtensions
-  const ignoredOptionalDependencies = manifest.pnpm?.ignoredOptionalDependencies
-  const peerDependencyRules = manifest.pnpm?.peerDependencyRules
-  const allowedDeprecatedVersions = manifest.pnpm?.allowedDeprecatedVersions
-  const allowNonAppliedPatches = manifest.pnpm?.allowNonAppliedPatches
-  let patchedDependencies = manifest.pnpm?.patchedDependencies
-  if (patchedDependencies) {
-    patchedDependencies = { ...patchedDependencies }
-    for (const [dep, patchFile] of Object.entries(patchedDependencies)) {
+  if (pnpmSettings.onlyBuiltDependenciesFile) {
+    settings.onlyBuiltDependenciesFile = path.join(manifestDir, pnpmSettings.onlyBuiltDependenciesFile)
+  }
+  if (pnpmSettings.patchedDependencies) {
+    settings.patchedDependencies = { ...pnpmSettings.patchedDependencies }
+    for (const [dep, patchFile] of Object.entries(pnpmSettings.patchedDependencies)) {
       if (path.isAbsolute(patchFile)) continue
-      patchedDependencies[dep] = path.join(manifestDir, patchFile)
+      settings.patchedDependencies[dep] = path.join(manifestDir, patchFile)
     }
   }
-
-  const supportedArchitectures = {
-    os: manifest.pnpm?.supportedArchitectures?.os ?? ['current'],
-    cpu: manifest.pnpm?.supportedArchitectures?.cpu ?? ['current'],
-    libc: manifest.pnpm?.supportedArchitectures?.libc ?? ['current'],
-  }
-
-  const settings: OptionsFromRootManifest = {
-    allowedDeprecatedVersions,
-    allowNonAppliedPatches,
-    overrides,
-    neverBuiltDependencies,
-    packageExtensions,
-    ignoredOptionalDependencies,
-    peerDependencyRules,
-    patchedDependencies,
-    supportedArchitectures,
-    ignoredBuiltDependencies: manifest.pnpm?.ignoredBuiltDependencies,
-  }
-  if (onlyBuiltDependencies) {
-    settings.onlyBuiltDependencies = onlyBuiltDependencies
-  }
-  if (onlyBuiltDependenciesFile) {
-    settings.onlyBuiltDependenciesFile = path.join(manifestDir, onlyBuiltDependenciesFile)
-  }
   return settings
 }
 

config/config/src/index.ts

@@ -31,9 +31,10 @@ import { getWorkspaceConcurrency } from './concurrency'
 import { readWorkspaceManifest } from '@pnpm/workspace.read-manifest'
 
 import { types } from './types'
+import { getOptionsFromPnpmSettings, getOptionsFromRootManifest } from './getOptionsFromRootManifest'
 export { types }
 
-export { getOptionsFromRootManifest, type OptionsFromRootManifest } from './getOptionsFromRootManifest'
+export { getOptionsFromRootManifest, getOptionsFromPnpmSettings, type OptionsFromRootManifest } from './getOptionsFromRootManifest'
 export * from './readLocalConfig'
 
 export type { Config, UniversalOptions, WantedPackageManager, VerifyDepsBeforeRun }
@@ -484,13 +485,19 @@ export async function getConfig (opts: {
     if (pnpmConfig.rootProjectManifest.packageManager) {
       pnpmConfig.wantedPackageManager = parsePackageManager(pnpmConfig.rootProjectManifest.packageManager)
     }
+    if (pnpmConfig.rootProjectManifest) {
+      Object.assign(pnpmConfig, getOptionsFromRootManifest(pnpmConfig.rootProjectManifestDir, pnpmConfig.rootProjectManifest))
+    }
   }
 
   if (pnpmConfig.workspaceDir != null) {
     const workspaceManifest = await readWorkspaceManifest(pnpmConfig.workspaceDir)
 
-    pnpmConfig.workspacePackagePatterns = cliOptions['workspace-packages'] as string[] ?? workspaceManifest?.packages
+    pnpmConfig.workspacePackagePatterns = cliOptions['workspace-packages'] as string[] ?? workspaceManifest?.packages ?? ['.']
     pnpmConfig.catalogs = getCatalogsFromWorkspaceManifest(workspaceManifest)
+    if (workspaceManifest) {
+      Object.assign(pnpmConfig, getOptionsFromPnpmSettings(pnpmConfig.workspaceDir, workspaceManifest, pnpmConfig.rootProjectManifest))
+    }
   }
 
   pnpmConfig.failedToLoadBuiltInConfig = failedToLoadBuiltInConfig

config/config/test/fixtures/settings-in-workspace-yaml/pnpm-workspace.yaml

@@ -0,0 +1,4 @@
+packages: []
+onlyBuiltDependencies:
+  - foo
+

config/config/test/getOptionsFromRootManifest.test.ts

@@ -80,7 +80,7 @@ test('getOptionsFromRootManifest() throws an error if cannot resolve an override
 
 test('getOptionsFromRootManifest() should return an empty onlyBuiltDependencies list by default', () => {
   const options = getOptionsFromRootManifest(process.cwd(), {})
-  expect(options.onlyBuiltDependencies).toStrictEqual([])
+  expect(options.onlyBuiltDependencies).toStrictEqual(undefined)
 })
 
 test('getOptionsFromRootManifest() should return the list fromm onlyBuiltDependencies', () => {

config/config/test/index.ts

@@ -1009,3 +1009,18 @@ test('xxx', async () => {
 
   process.env = oldEnv
 })
+
+test('settings from pnpm-workspace.yaml are read', async () => {
+  const workspaceDir = f.find('settings-in-workspace-yaml')
+  process.chdir(workspaceDir)
+  const { config } = await getConfig({
+    cliOptions: {},
+    workspaceDir,
+    packageManager: {
+      name: 'pnpm',
+      version: '1.0.0',
+    },
+  })
+
+  expect(config.onlyBuiltDependencies).toStrictEqual(['foo'])
+})

deps/status/src/checkDepsStatus.ts

@@ -59,6 +59,7 @@ export type CheckDepsStatusOptions = Pick<Config,
 | 'workspaceDir'
 | 'patchesDir'
 | 'pnpmfile'
+| 'configDependencies'
 > & {
   ignoreFilteredInstallCache?: boolean
   ignoredWorkspaceStateSettings?: Array<keyof WorkspaceStateSettings>
@@ -136,7 +137,7 @@ async function _checkDepsStatus (opts: CheckDepsStatusOptions, workspaceState: W
       }
     }
   }
-  if ((rootProjectManifest?.pnpm?.configDependencies != null || workspaceState.configDependencies != null) && !equals(rootProjectManifest?.pnpm?.configDependencies ?? {}, workspaceState.configDependencies ?? {})) {
+  if ((opts.configDependencies != null || workspaceState.configDependencies != null) && !equals(opts.configDependencies ?? {}, workspaceState.configDependencies ?? {})) {
     return {
       upToDate: false,
       issue: 'Configuration dependencies are not up to date',

exec/build-commands/package.json

@@ -30,7 +30,6 @@
   },
   "homepage": "https://github.com/pnpm/pnpm/blob/main/exec/build-commands#readme",
   "devDependencies": {
-    "@pnpm/config": "workspace:*",
     "@pnpm/exec.build-commands": "workspace:*",
     "@pnpm/plugin-commands-installation": "workspace:*",
     "@pnpm/prepare": "workspace:*",
@@ -47,6 +46,7 @@
     "@pnpm/prepare-temp-dir": "workspace:*",
     "@pnpm/read-project-manifest": "workspace:*",
     "@pnpm/util.lex-comparator": "catalog:",
+    "@pnpm/workspace.manifest-writer": "workspace:*",
     "chalk": "catalog:",
     "enquirer": "catalog:",
     "render-help": "catalog:"

exec/build-commands/src/approveBuilds.ts

@@ -6,9 +6,10 @@ import renderHelp from 'render-help'
 import { prompt } from 'enquirer'
 import chalk from 'chalk'
 import { rebuild, type RebuildCommandOpts } from '@pnpm/plugin-commands-rebuild'
+import { updateWorkspaceManifest } from '@pnpm/workspace.manifest-writer'
 import { getAutomaticallyIgnoredBuilds } from './getAutomaticallyIgnoredBuilds'
 
-export type ApproveBuildsCommandOpts = Pick<Config, 'modulesDir' | 'dir' | 'rootProjectManifest' | 'rootProjectManifestDir'>
+export type ApproveBuildsCommandOpts = Pick<Config, 'modulesDir' | 'dir' | 'rootProjectManifest' | 'rootProjectManifestDir' | 'onlyBuiltDependencies' | 'ignoredBuiltDependencies'>
 
 export const commandNames = ['approve-builds']
 
@@ -87,28 +88,24 @@ export async function handler (opts: ApproveBuildsCommandOpts & RebuildCommandOp
   } as any) as any // eslint-disable-line @typescript-eslint/no-explicit-any
   const buildPackages = result.map(({ value }: { value: string }) => value)
   const ignoredPackages = automaticallyIgnoredBuilds.filter((automaticallyIgnoredBuild) => !buildPackages.includes(automaticallyIgnoredBuild))
+  let updatedIgnoredBuiltDependencies: string[] | undefined
   if (ignoredPackages.length) {
-    if (opts.rootProjectManifest.pnpm?.ignoredBuiltDependencies == null) {
-      opts.rootProjectManifest.pnpm = {
-        ...opts.rootProjectManifest.pnpm,
-        ignoredBuiltDependencies: sortUniqueStrings(ignoredPackages),
-      }
+    if (opts.ignoredBuiltDependencies == null) {
+      updatedIgnoredBuiltDependencies = sortUniqueStrings(ignoredPackages)
     } else {
-      opts.rootProjectManifest.pnpm.ignoredBuiltDependencies = sortUniqueStrings([
-        ...opts.rootProjectManifest.pnpm.ignoredBuiltDependencies,
+      updatedIgnoredBuiltDependencies = sortUniqueStrings([
+        ...opts.ignoredBuiltDependencies,
         ...ignoredPackages,
       ])
     }
   }
+  let updatedOnlyBuiltDependencies: string[] | undefined
   if (buildPackages.length) {
-    if (opts.rootProjectManifest.pnpm?.onlyBuiltDependencies == null) {
-      opts.rootProjectManifest.pnpm = {
-        ...opts.rootProjectManifest.pnpm,
-        onlyBuiltDependencies: sortUniqueStrings(buildPackages),
-      }
+    if (opts.onlyBuiltDependencies == null) {
+      updatedOnlyBuiltDependencies = sortUniqueStrings(buildPackages)
     } else {
-      opts.rootProjectManifest.pnpm.onlyBuiltDependencies = sortUniqueStrings([
-        ...opts.rootProjectManifest.pnpm.onlyBuiltDependencies,
+      updatedOnlyBuiltDependencies = sortUniqueStrings([
+        ...opts.onlyBuiltDependencies,
         ...buildPackages,
       ])
     }
@@ -126,9 +123,26 @@ Do you approve?`,
     }
   }
   const { writeProjectManifest } = await readProjectManifest(opts.rootProjectManifestDir)
-  await writeProjectManifest(opts.rootProjectManifest)
+  if (opts.rootProjectManifest.pnpm?.ignoredBuiltDependencies != null || opts.rootProjectManifest.pnpm?.onlyBuiltDependencies != null || opts.workspaceDir == null) {
+    opts.rootProjectManifest.pnpm = opts.rootProjectManifest.pnpm ?? {}
+    if (updatedOnlyBuiltDependencies) {
+      opts.rootProjectManifest.pnpm.onlyBuiltDependencies = updatedOnlyBuiltDependencies
+    }
+    if (updatedIgnoredBuiltDependencies) {
+      opts.rootProjectManifest.pnpm.ignoredBuiltDependencies = updatedIgnoredBuiltDependencies
+    }
+    await writeProjectManifest(opts.rootProjectManifest)
+  } else {
+    await updateWorkspaceManifest(opts.workspaceDir, {
+      onlyBuiltDependencies: updatedOnlyBuiltDependencies,
+      ignoredBuiltDependencies: updatedIgnoredBuiltDependencies,
+    })
+  }
   if (buildPackages.length) {
-    return rebuild.handler(opts, buildPackages)
+    return rebuild.handler({
+      ...opts,
+      onlyBuiltDependencies: updatedOnlyBuiltDependencies,
+    }, buildPackages)
   }
 }
 

exec/build-commands/tsconfig.json

@@ -30,6 +30,9 @@
     {
       "path": "../../pkg-manifest/read-project-manifest"
     },
+    {
+      "path": "../../workspace/manifest-writer"
+    },
     {
       "path": "../plugin-commands-rebuild"
     }

exec/plugin-commands-rebuild/src/implementation/extendRebuildOptions.ts

@@ -51,7 +51,7 @@ export type StrictRebuildOptions = {
   peersSuffixMaxLength: number
   strictStorePkgContentCheck: boolean
   fetchFullMetadata?: boolean
-} & Pick<Config, 'sslConfigs'>
+} & Pick<Config, 'sslConfigs' | 'onlyBuiltDependencies' | 'onlyBuiltDependenciesFile' | 'neverBuiltDependencies'>
 
 export type RebuildOptions = Partial<StrictRebuildOptions> &
 Pick<StrictRebuildOptions, 'storeDir' | 'storeController'> & Pick<Config, 'rootProjectManifest' | 'rootProjectManifestDir'>
@@ -106,5 +106,8 @@ export async function extendRebuildOptions (
     ...(opts.rootProjectManifest ? getOptionsFromRootManifest(opts.rootProjectManifestDir, opts.rootProjectManifest) : {}),
   }
   extendedOpts.registries = normalizeRegistries(extendedOpts.registries)
+  if (extendedOpts.neverBuiltDependencies == null && extendedOpts.onlyBuiltDependencies == null && extendedOpts.onlyBuiltDependenciesFile == null) {
+    extendedOpts.onlyBuiltDependencies = []
+  }
   return extendedOpts
 }

exec/plugin-commands-rebuild/test/utils/index.ts

@@ -28,6 +28,7 @@ export const DEFAULT_OPTS = {
   localAddress: undefined,
   lock: false,
   lockStaleDuration: 90,
+  neverBuiltDependencies: [],
   networkConcurrency: 16,
   offline: false,
   pending: false,

exec/plugin-commands-script-runners/test/runRecursive.ts

@@ -726,7 +726,9 @@ test('`pnpm run -r` should avoid infinite recursion', async () => {
       },
     },
   ])
-  writeYamlFile('pnpm-workspace.yaml', {})
+  writeYamlFile('pnpm-workspace.yaml', {
+    packages: ['**'],
+  })
 
   await execa(pnpmBin, [
     'install',

packages/make-dedicated-lockfile/test/fixtures/fixture/pnpm-workspace.yaml

@@ -0,0 +1,2 @@
+packages:
+  - packages/**

packages/types/src/package.ts

@@ -127,33 +127,35 @@ export interface PeerDependencyRules {
 
 export type AllowedDeprecatedVersions = Record<string, string>
 
+export interface PnpmSettings {
+  configDependencies?: Record<string, string>
+  neverBuiltDependencies?: string[]
+  onlyBuiltDependencies?: string[]
+  onlyBuiltDependenciesFile?: string
+  ignoredBuiltDependencies?: string[]
+  overrides?: Record<string, string>
+  packageExtensions?: Record<string, PackageExtension>
+  ignoredOptionalDependencies?: string[]
+  peerDependencyRules?: PeerDependencyRules
+  allowedDeprecatedVersions?: AllowedDeprecatedVersions
+  allowNonAppliedPatches?: boolean
+  patchedDependencies?: Record<string, string>
+  updateConfig?: {
+    ignoreDependencies?: string[]
+  }
+  auditConfig?: {
+    ignoreCves?: string[]
+    ignoreGhsas?: string[]
+  }
+  requiredScripts?: string[]
+  supportedArchitectures?: SupportedArchitectures
+  executionEnv?: ExecutionEnv
+}
+
 export interface ProjectManifest extends BaseManifest {
   packageManager?: string
   workspaces?: string[]
-  pnpm?: {
-    configDependencies?: Record<string, string>
-    neverBuiltDependencies?: string[]
-    onlyBuiltDependencies?: string[]
-    onlyBuiltDependenciesFile?: string
-    ignoredBuiltDependencies?: string[]
-    overrides?: Record<string, string>
-    packageExtensions?: Record<string, PackageExtension>
-    ignoredOptionalDependencies?: string[]
-    peerDependencyRules?: PeerDependencyRules
-    allowedDeprecatedVersions?: AllowedDeprecatedVersions
-    allowNonAppliedPatches?: boolean
-    patchedDependencies?: Record<string, string>
-    updateConfig?: {
-      ignoreDependencies?: string[]
-    }
-    auditConfig?: {
-      ignoreCves?: string[]
-      ignoreGhsas?: string[]
-    }
-    requiredScripts?: string[]
-    supportedArchitectures?: SupportedArchitectures
-    executionEnv?: ExecutionEnv
-  }
+  pnpm?: PnpmSettings
   private?: boolean
   resolutions?: Record<string, string>
 }

pkg-manager/core/src/install/extendInstallOptions.ts

@@ -268,6 +268,9 @@ export function extendOptions (
       }
     }
   }
+  if (opts.neverBuiltDependencies == null && opts.onlyBuiltDependencies == null && opts.onlyBuiltDependenciesFile == null) {
+    opts.onlyBuiltDependencies = []
+  }
   if (opts.onlyBuiltDependencies && opts.neverBuiltDependencies) {
     throw new PnpmError('CONFIG_CONFLICT_BUILT_DEPENDENCIES', 'Cannot have both neverBuiltDependencies and onlyBuiltDependencies')
   }

pkg-manager/core/test/install/lifecycleScripts.ts

@@ -473,9 +473,10 @@ test('selectively allow scripts in some dependencies by onlyBuiltDependencies',
   prepareEmpty()
   const reporter = sinon.spy()
   const onlyBuiltDependencies = ['@pnpm.e2e/install-script-example']
+  const neverBuiltDependencies: string[] | undefined = undefined
   const { updatedManifest: manifest } = await addDependenciesToPackage({},
     ['@pnpm.e2e/pre-and-postinstall-scripts-example@1.0.0', '@pnpm.e2e/install-script-example'],
-    testDefaults({ fastUnpack: false, onlyBuiltDependencies, reporter })
+    testDefaults({ fastUnpack: false, onlyBuiltDependencies, neverBuiltDependencies, reporter })
   )
 
   expect(fs.existsSync('node_modules/@pnpm.e2e/pre-and-postinstall-scripts-example/generated-by-preinstall.js')).toBeFalsy()
@@ -494,6 +495,7 @@ test('selectively allow scripts in some dependencies by onlyBuiltDependencies',
     fastUnpack: false,
     frozenLockfile: true,
     ignoredBuiltDependencies: ['@pnpm.e2e/pre-and-postinstall-scripts-example'],
+    neverBuiltDependencies,
     onlyBuiltDependencies,
     reporter,
   }))

pkg-manager/core/test/install/patch.ts

@@ -23,6 +23,7 @@ test('patch package', async () => {
     'is-positive@1.0.0': patchPath,
   }
   const opts = testDefaults({
+    neverBuiltDependencies: undefined,
     onlyBuiltDependencies: [],
     fastUnpack: false,
     sideEffectsCacheRead: true,
@@ -288,6 +289,7 @@ test('patch package when the package is not in onlyBuiltDependencies list', asyn
     sideEffectsCacheRead: true,
     sideEffectsCacheWrite: true,
     patchedDependencies,
+    neverBuiltDependencies: undefined,
     onlyBuiltDependencies: [],
   }, {}, {}, { packageImportMethod: 'hardlink' })
   await install({
@@ -355,6 +357,7 @@ test('patch package when the package is not in onlyBuiltDependencies list', asyn
     fastUnpack: false,
     sideEffectsCacheRead: true,
     sideEffectsCacheWrite: true,
+    neverBuiltDependencies: undefined,
     onlyBuiltDependencies: [],
     offline: true,
   }, {}, {}, { packageImportMethod: 'hardlink' }))

pkg-manager/core/test/utils/testDefaults.ts

@@ -56,6 +56,7 @@ export function testDefaults<T> (
   )
   const result = {
     cacheDir,
+    neverBuiltDependencies: [] as string[],
     registries: {
       default: registry,
     },

pkg-manager/headless/test/fixtures/workspace/pnpm-workspace.yaml

@@ -0,0 +1,2 @@
+packages:
+  - "*"

pkg-manager/headless/test/fixtures/workspace2/pnpm-workspace.yaml

@@ -0,0 +1,2 @@
+packages:
+  - "*"

pkg-manager/plugin-commands-installation/src/add.ts

@@ -191,7 +191,9 @@ export async function handler (
     !opts.recursive &&
     opts.workspaceDir === opts.dir &&
     !opts.ignoreWorkspaceRootCheck &&
-    !opts.workspaceRoot
+    !opts.workspaceRoot &&
+    opts.workspacePackagePatterns &&
+    opts.workspacePackagePatterns.length > 1
   ) {
     throw new PnpmError('ADDING_TO_ROOT',
       'Running this command will add the dependency to the workspace root, ' +

pkg-manager/plugin-commands-installation/src/install.ts

@@ -259,6 +259,7 @@ export type InstallCommandOptions = Pick<Config,
 | 'bin'
 | 'catalogs'
 | 'cliOptions'
+| 'configDependencies'
 | 'dedupeInjectedDeps'
 | 'dedupeDirectDeps'
 | 'dedupePeerDependents'

pkg-manager/plugin-commands-installation/src/installDeps.ts

@@ -102,6 +102,7 @@ export type InstallDepsOptions = Pick<Config,
 | 'extraEnv'
 | 'ignoreWorkspaceCycles'
 | 'disallowWorkspaceCycles'
+| 'configDependencies'
 > & CreateStoreControllerOptions & {
   argv: {
     original: string[]
@@ -171,8 +172,8 @@ when running add/update with the --workspace option')
     opts['preserveWorkspaceProtocol'] = !opts.linkWorkspacePackages
   }
   let store = await createOrConnectStoreController(opts)
-  if (opts.rootProjectManifest?.pnpm?.configDependencies) {
-    await installConfigDeps(opts.rootProjectManifest.pnpm.configDependencies, {
+  if (opts.configDependencies) {
+    await installConfigDeps(opts.configDependencies, {
       registries: opts.registries,
       rootDir: opts.lockfileDir ?? opts.rootProjectManifestDir,
       store: store.ctrl,
@@ -346,7 +347,7 @@ when running add/update with the --workspace option')
         workspaceDir: opts.workspaceDir ?? opts.lockfileDir ?? opts.dir,
         pnpmfileExists: opts.hooks?.calculatePnpmfileChecksum != null,
         filteredInstall: allProjects.length !== Object.keys(opts.selectedProjectsGraph ?? {}).length,
-        configDependencies: opts.rootProjectManifest?.pnpm?.configDependencies,
+        configDependencies: opts.configDependencies,
       })
     }
     if (opts.strictDepBuilds && ignoredBuilds?.length) {
@@ -406,7 +407,7 @@ when running add/update with the --workspace option')
         workspaceDir: opts.workspaceDir ?? opts.lockfileDir ?? opts.dir,
         pnpmfileExists: opts.hooks?.calculatePnpmfileChecksum != null,
         filteredInstall: allProjects.length !== Object.keys(opts.selectedProjectsGraph ?? {}).length,
-        configDependencies: opts.rootProjectManifest?.pnpm?.configDependencies,
+        configDependencies: opts.configDependencies,
       })
     }
   }
@@ -432,7 +433,7 @@ async function recursiveInstallThenUpdateWorkspaceState (
       workspaceDir: opts.workspaceDir,
       pnpmfileExists: opts.hooks?.calculatePnpmfileChecksum != null,
       filteredInstall: allProjects.length !== Object.keys(opts.selectedProjectsGraph ?? {}).length,
-      configDependencies: opts.rootProjectManifest?.pnpm?.configDependencies,
+      configDependencies: opts.configDependencies,
     })
   }
   return recursiveResult

pkg-manager/plugin-commands-installation/src/recursive.ts

@@ -46,6 +46,7 @@ import { IgnoredBuildsError } from './errors'
 
 export type RecursiveOptions = CreateStoreControllerOptions & Pick<Config,
 | 'bail'
+| 'configDependencies'
 | 'dedupePeerDependents'
 | 'depth'
 | 'globalPnpmfile'

pkg-manager/plugin-commands-installation/src/remove.ts

@@ -131,6 +131,7 @@ export async function handler (
   | 'allProjectsGraph'
   | 'bail'
   | 'bin'
+  | 'configDependencies'
   | 'dev'
   | 'engineStrict'
   | 'globalPnpmfile'
@@ -164,8 +165,8 @@ export async function handler (
     optionalDependencies: opts.optional !== false,
   }
   let store = await createOrConnectStoreController(opts)
-  if (opts.rootProjectManifest?.pnpm?.configDependencies) {
-    await installConfigDeps(opts.rootProjectManifest.pnpm.configDependencies, {
+  if (opts.configDependencies) {
+    await installConfigDeps(opts.configDependencies, {
       registries: opts.registries,
       rootDir: opts.lockfileDir ?? opts.rootProjectManifestDir,
       store: store.ctrl,

pkg-manager/plugin-commands-installation/test/installConfigDeps.ts

@@ -19,6 +19,7 @@ test('configuration dependency is installed', async () => {
 
   await install.handler({
     ...DEFAULT_OPTS,
+    configDependencies: rootProjectManifest.pnpm!.configDependencies,
     dir: process.cwd(),
     rootProjectManifest,
     rootProjectManifestDir: process.cwd(),
@@ -35,6 +36,7 @@ test('configuration dependency is installed', async () => {
 
   await install.handler({
     ...DEFAULT_OPTS,
+    configDependencies: rootProjectManifest.pnpm!.configDependencies,
     dir: process.cwd(),
     rootProjectManifest,
     rootProjectManifestDir: process.cwd(),
@@ -51,6 +53,7 @@ test('configuration dependency is installed', async () => {
 
   await install.handler({
     ...DEFAULT_OPTS,
+    configDependencies: rootProjectManifest.pnpm!.configDependencies,
     dir: process.cwd(),
     rootProjectManifest,
     rootProjectManifestDir: process.cwd(),
@@ -74,6 +77,7 @@ test('patch from configuration dependency is applied', async () => {
 
   await add.handler({
     ...DEFAULT_OPTS,
+    configDependencies: rootProjectManifest.pnpm!.configDependencies,
     dir: process.cwd(),
     rootProjectManifest,
     rootProjectManifestDir: process.cwd(),
@@ -94,6 +98,7 @@ test('installation fails if the checksum of the config dependency is invalid', a
 
   await expect(install.handler({
     ...DEFAULT_OPTS,
+    configDependencies: rootProjectManifest.pnpm!.configDependencies,
     dir: process.cwd(),
     rootProjectManifest,
     rootProjectManifestDir: process.cwd(),
@@ -112,6 +117,7 @@ test('installation fails if the config dependency does not have a checksum', asy
 
   await expect(install.handler({
     ...DEFAULT_OPTS,
+    configDependencies: rootProjectManifest.pnpm!.configDependencies,
     dir: process.cwd(),
     rootProjectManifest,
     rootProjectManifestDir: process.cwd(),
@@ -131,6 +137,7 @@ test('selectively allow scripts in some dependencies by onlyBuiltDependenciesFil
 
   await add.handler({
     ...DEFAULT_OPTS,
+    configDependencies: rootProjectManifest.pnpm!.configDependencies,
     dir: process.cwd(),
     rootProjectManifest,
     rootProjectManifestDir: process.cwd(),
@@ -144,6 +151,7 @@ test('selectively allow scripts in some dependencies by onlyBuiltDependenciesFil
 
   await install.handler({
     ...DEFAULT_OPTS,
+    configDependencies: rootProjectManifest.pnpm!.configDependencies,
     dir: process.cwd(),
     frozenLockfile: true,
     rootProjectManifest,
@@ -169,6 +177,7 @@ test('selectively allow scripts in some dependencies by onlyBuiltDependenciesFil
 
   await add.handler({
     ...DEFAULT_OPTS,
+    configDependencies: rootProjectManifest.pnpm!.configDependencies,
     dir: process.cwd(),
     rootProjectManifest,
     rootProjectManifestDir: process.cwd(),
@@ -182,6 +191,7 @@ test('selectively allow scripts in some dependencies by onlyBuiltDependenciesFil
 
   await install.handler({
     ...DEFAULT_OPTS,
+    configDependencies: rootProjectManifest.pnpm!.configDependencies,
     dir: process.cwd(),
     frozenLockfile: true,
     rootProjectManifest,

pnpm-lock.yaml

@@ -2099,6 +2099,9 @@ importers:
       '@pnpm/util.lex-comparator':
         specifier: 'catalog:'
         version: 3.0.0
+      '@pnpm/workspace.manifest-writer':
+        specifier: workspace:*
+        version: link:../../workspace/manifest-writer
       chalk:
         specifier: 'catalog:'
         version: 4.1.2
@@ -8006,6 +8009,19 @@ importers:
         specifier: workspace:*
         version: 'link:'
 
+  workspace/manifest-writer:
+    dependencies:
+      '@pnpm/workspace.read-manifest':
+        specifier: workspace:*
+        version: link:../read-manifest
+      write-yaml-file:
+        specifier: 'catalog:'
+        version: 5.0.0
+    devDependencies:
+      '@pnpm/workspace.manifest-writer':
+        specifier: workspace:*
+        version: 'link:'
+
   workspace/pkgs-graph:
     dependencies:
       '@pnpm/npm-package-arg':
@@ -8042,6 +8058,9 @@ importers:
       '@pnpm/error':
         specifier: workspace:*
         version: link:../../packages/error
+      '@pnpm/types':
+        specifier: workspace:*
+        version: link:../../packages/types
       read-yaml-file:
         specifier: 'catalog:'
         version: 2.1.0

pnpm/test/__fixtures__/workspace-with-circular-peers/pnpm-workspace.yaml

@@ -0,0 +1,2 @@
+packages:
+  - "**"

pnpm/test/install/misc.ts

@@ -240,7 +240,8 @@ test('`pnpm -r add` should fail if no package name was provided', () => {
     },
   ])
 
-  fs.writeFileSync('pnpm-workspace.yaml', '', 'utf8')
+  fs.writeFileSync('pnpm-workspace.yaml', `packages:
+  - project`, 'utf8')
 
   const { status, stdout } = execPnpmSync(['-r', 'add'])
 
@@ -303,7 +304,8 @@ test('recursive install should fail if the used pnpm version does not satisfy th
     },
   ])
 
-  fs.writeFileSync('pnpm-workspace.yaml', '', 'utf8')
+  fs.writeFileSync('pnpm-workspace.yaml', `packages:
+  - "*"`, 'utf8')
 
   process.chdir('project-1')
 
@@ -336,7 +338,8 @@ test('engine-strict=true: recursive install should fail if the used Node version
     },
   ])
 
-  fs.writeFileSync('pnpm-workspace.yaml', '', 'utf8')
+  fs.writeFileSync('pnpm-workspace.yaml', `packages:
+  - "*"`, 'utf8')
 
   process.chdir('project-1')
 
@@ -369,7 +372,8 @@ test('engine-strict=false: recursive install should not fail if the used Node ve
     },
   ])
 
-  fs.writeFileSync('pnpm-workspace.yaml', '', 'utf8')
+  fs.writeFileSync('pnpm-workspace.yaml', `packages:
+  - "*"`, 'utf8')
 
   process.chdir('project-1')
 

pnpm/test/recursive/misc.ts

@@ -1,7 +1,7 @@
 import fs from 'fs'
 import path from 'path'
 import { STORE_VERSION } from '@pnpm/constants'
-import { prepare, preparePackages } from '@pnpm/prepare'
+import { preparePackages } from '@pnpm/prepare'
 import { type LockfileFile } from '@pnpm/lockfile.types'
 import { sync as readYamlFile } from 'read-yaml-file'
 import { isCI } from 'ci-info'
@@ -77,7 +77,8 @@ test('workspace .npmrc is always read', async () => {
   ])
 
   const storeDir = path.resolve('../store')
-  fs.writeFileSync('pnpm-workspace.yaml', '', 'utf8')
+  fs.writeFileSync('pnpm-workspace.yaml', `packages:
+  - workspace/*`, 'utf8')
   fs.writeFileSync('.npmrc', 'shamefully-flatten = true\nshared-workspace-lockfile=false', 'utf8')
   fs.writeFileSync('workspace/project-2/.npmrc', 'hoist=false', 'utf8')
 
@@ -359,9 +360,22 @@ test('non-recursive install ignores filter from config', async () => {
 })
 
 test('adding new dependency in the root should fail if neither --workspace-root nor --ignore-workspace-root-check are used', async () => {
-  const project = prepare()
+  const project = preparePackages([
+    {
+      location: '.',
+      package: {
+        name: 'root',
+      },
+    },
+    {
+      name: 'project',
+    },
+  ])['root']
 
-  fs.writeFileSync('pnpm-workspace.yaml', '', 'utf8')
+  fs.writeFileSync('pnpm-workspace.yaml', `packages:
+  - '.'
+  - 'project'
+`, 'utf8')
 
   {
     const { status, stdout } = execPnpmSync(['add', 'is-positive'])
@@ -455,7 +469,8 @@ test('set recursive-install to false in .npmrc would disable recursive install i
   ])
 
   process.chdir('workspace')
-  fs.writeFileSync('pnpm-workspace.yaml', '', 'utf8')
+  fs.writeFileSync('pnpm-workspace.yaml', `packages:
+  - "**"`, 'utf8')
   fs.writeFileSync('.npmrc', `recursive-install = false
 dedupe-peer-dependents = false`, 'utf8')
 
@@ -493,7 +508,8 @@ test('set recursive-install to false would install as --filter {.}...', async ()
   ])
 
   process.chdir('workspace')
-  fs.writeFileSync('pnpm-workspace.yaml', '', 'utf8')
+  fs.writeFileSync('pnpm-workspace.yaml', `packages:
+  - "**"`, 'utf8')
   fs.writeFileSync('.npmrc', 'recursive-install = false', 'utf8')
 
   process.chdir('project-1')

pnpm/test/recursive/rebuild.ts

@@ -3,6 +3,14 @@ import { execPnpm } from '../utils'
 
 test('`pnpm recursive rebuild` specific dependencies', async () => {
   const projects = preparePackages([
+    {
+      location: '.',
+      package: {
+        pnpm: {
+          neverBuiltDependencies: [],
+        },
+      },
+    },
     {
       name: 'project-1',
       version: '1.0.0',

workspace/manifest-writer/README.md

@@ -0,0 +1,13 @@
+# @pnpm/workspace.manifest-writer
+
+> Updates the workspace manifest file
+
+## Install
+
+```
+pnpm add @pnpm/workspace.manifest-writer
+```
+
+## LICENSE
+
+MIT

workspace/manifest-writer/package.json

@@ -0,0 +1,44 @@
+{
+  "name": "@pnpm/workspace.manifest-writer",
+  "version": "1000.0.0-0",
+  "description": "Updates the workspace manifest file",
+  "main": "lib/index.js",
+  "types": "lib/index.d.ts",
+  "files": [
+    "lib",
+    "!*.map"
+  ],
+  "engines": {
+    "node": ">=18.12"
+  },
+  "scripts": {
+    "lint": "eslint \"src/**/*.ts\"",
+    "test": "pnpm run compile",
+    "prepublishOnly": "pnpm run compile",
+    "compile": "tsc --build && pnpm run lint --fix"
+  },
+  "repository": "https://github.com/pnpm/pnpm/blob/main/workspace/manifest-writer",
+  "keywords": [
+    "pnpm10",
+    "pnpm"
+  ],
+  "license": "MIT",
+  "bugs": {
+    "url": "https://github.com/pnpm/pnpm/issues"
+  },
+  "homepage": "https://github.com/pnpm/pnpm/blob/main/workspace/manifest-writer#readme",
+  "dependencies": {
+    "@pnpm/workspace.read-manifest": "workspace:*",
+    "write-yaml-file": "catalog:"
+  },
+  "funding": "https://opencollective.com/pnpm",
+  "devDependencies": {
+    "@pnpm/workspace.manifest-writer": "workspace:*"
+  },
+  "exports": {
+    ".": "./lib/index.js"
+  },
+  "jest": {
+    "preset": "@pnpm/jest-config"
+  }
+}

workspace/manifest-writer/src/index.ts

@@ -0,0 +1,10 @@
+import { readWorkspaceManifest, type WorkspaceManifest } from '@pnpm/workspace.read-manifest'
+import writeYamlFile from 'write-yaml-file'
+
+export async function updateWorkspaceManifest (dir: string, updatedFields: Partial<WorkspaceManifest>): Promise<void> {
+  const manifest = await readWorkspaceManifest(dir)
+  await writeYamlFile(dir, {
+    ...manifest,
+    updatedFields,
+  })
+}

workspace/manifest-writer/tsconfig.json

@@ -0,0 +1,16 @@
+{
+  "extends": "@pnpm/tsconfig",
+  "compilerOptions": {
+    "outDir": "lib",
+    "rootDir": "src"
+  },
+  "include": [
+    "src/**/*.ts",
+    "../../__typings__/**/*.d.ts"
+  ],
+  "references": [
+    {
+      "path": "../read-manifest"
+    }
+  ]
+}

workspace/manifest-writer/tsconfig.lint.json

@@ -0,0 +1,8 @@
+{
+  "extends": "./tsconfig.json",
+  "include": [
+    "src/**/*.ts",
+    "test/**/*.ts",
+    "../../__typings__/**/*.d.ts"
+  ]
+}

workspace/read-manifest/package.json

@@ -31,6 +31,7 @@
   "dependencies": {
     "@pnpm/constants": "workspace:*",
     "@pnpm/error": "workspace:*",
+    "@pnpm/types": "workspace:*",
     "read-yaml-file": "catalog:"
   },
   "funding": "https://opencollective.com/pnpm",

workspace/read-manifest/src/index.ts

@@ -1,5 +1,6 @@
 import util from 'util'
 import { WORKSPACE_MANIFEST_FILENAME } from '@pnpm/constants'
+import { type PnpmSettings } from '@pnpm/types'
 import path from 'node:path'
 import readYamlFile from 'read-yaml-file'
 import {
@@ -10,7 +11,7 @@ import {
 } from './catalogs'
 import { InvalidWorkspaceManifestError } from './errors/InvalidWorkspaceManifestError'
 
-export interface WorkspaceManifest {
+export interface WorkspaceManifest extends PnpmSettings {
   packages: string[]
 
   /**
@@ -75,7 +76,7 @@ function validateWorkspaceManifest (manifest: unknown): asserts manifest is Work
 
 function assertValidWorkspaceManifestPackages (manifest: { packages?: unknown }): asserts manifest is { packages: string[] } {
   if (!manifest.packages) {
-    throw new InvalidWorkspaceManifestError('packages field missing or empty')
+    return
   }
 
   if (!Array.isArray(manifest.packages)) {

workspace/read-manifest/test/index.ts

@@ -21,10 +21,10 @@ test('readWorkspaceManifest() throws on array content', async () => {
   ).rejects.toThrow('Expected object but found - array')
 })
 
-test('readWorkspaceManifest() throws on empty packages field', async () => {
+test('readWorkspaceManifest() does not throw on empty packages field', async () => {
   await expect(
     readWorkspaceManifest(path.join(__dirname, '__fixtures__/packages-empty'))
-  ).rejects.toThrow('packages field missing or empty')
+  ).resolves.toBeTruthy()
 })
 
 test('readWorkspaceManifest() throws on string packages field', async () => {

workspace/read-manifest/tsconfig.json

@@ -14,6 +14,9 @@
     },
     {
       "path": "../../packages/error"
+    },
+    {
+      "path": "../../packages/types"
     }
   ]
 }