feat!: remove independent-leaves=true support

PR #2571
2025-12-24 07:38:12 -05:00 · 2020-05-22 11:09:05 +03:00
parent 4f5801b1c0
commit 802d145fcd
59 changed files with 53 additions and 722 deletions
--- a/.changeset/pretty-tips-crash.md
+++ b/.changeset/pretty-tips-crash.md
@@ -0,0 +1,18 @@
+---
+"@pnpm/config": major
+"@pnpm/get-context": major
+"@pnpm/headless": major
+"@pnpm/hoist": major
+"@pnpm/modules-yaml": major
+"@pnpm/plugin-commands-installation": major
+"@pnpm/plugin-commands-listing": major
+"@pnpm/plugin-commands-outdated": major
+"@pnpm/plugin-commands-rebuild": major
+"@pnpm/plugin-commands-store": major
+"pnpm": major
+"@pnpm/read-projects-context": major
+"@pnpm/resolve-dependencies": major
+"supi": minor
+---
+
+Remove `independent-leaves` support.
--- a/.changeset/sharp-crabs-change.md
+++ b/.changeset/sharp-crabs-change.md
@@ -0,0 +1,8 @@
+---
+"@pnpm/package-requester": major
+"@pnpm/package-store": major
+"@pnpm/server": major
+"@pnpm/store-controller-types": major
+---
+
+`getPackageLocation()` removed from store. Remove `inStoreLocation` from the result of `fetchPackage()`.
--- a/packages/audit/tsconfig.json
+++ b/packages/audit/tsconfig.json
@@ -24,6 +24,9 @@
    {
      "path": "../types"
    },
+    {
+      "path": "../constants"
+    },
    {
      "path": "../lockfile-file"
    }
--- a/packages/config/src/Config.ts
+++ b/packages/config/src/Config.ts
@@ -96,7 +96,6 @@ export interface Config {
  repeatInstallDepth?: number,
  ignorePnpmfile?: boolean,
  pnpmfile: string,
-  independentLeaves?: boolean,
  packageImportMethod?: 'auto' | 'hardlink' | 'copy' | 'clone',
  hoistPattern?: string[],
  useStoreServer?: boolean,
--- a/packages/config/src/index.ts
+++ b/packages/config/src/index.ts
@@ -44,7 +44,6 @@ export const types = Object.assign({
  'hoist-pattern': Array,
  'ignore-pnpmfile': Boolean,
  'ignore-workspace-root-check': Boolean,
-  'independent-leaves': Boolean,
  'link-workspace-packages': [Boolean, 'deep'],
  'lockfile': Boolean,
  'lockfile-dir': String,
@@ -230,19 +229,11 @@ export default async (
    pnpmConfig.saveProd = true
    pnpmConfig.saveDev = false
    pnpmConfig.saveOptional = false
-    if (pnpmConfig.independentLeaves) {
-      if (opts.cliOptions['independent-leaves']) {
-        throw new PnpmError('CONFIG_CONFLICT_INDEPENDENT_LEAVES_WITH_GLOBAL',
-          'Configuration conflict. "independent-leaves" may not be used with "global"')
-      }
-      pnpmConfig.independentLeaves = false
-    }
    if (pnpmConfig.hoistPattern && (pnpmConfig.hoistPattern.length > 1 || pnpmConfig.hoistPattern[0] !== '*')) {
      if (opts.cliOptions['hoist-pattern']) {
        throw new PnpmError('CONFIG_CONFLICT_HOIST_PATTERN_WITH_GLOBAL',
          'Configuration conflict. "hoist-pattern" may not be used with "global"')
      }
-      pnpmConfig.independentLeaves = false
    }
    if (pnpmConfig.linkWorkspacePackages) {
      if (opts.cliOptions['link-workspace-packages']) {
@@ -320,9 +311,6 @@ export default async (
  }
  if (pnpmConfig['hoist'] === false) {
    delete pnpmConfig.hoistPattern
-  } else if (pnpmConfig.independentLeaves === true) {
-    throw new PnpmError('CONFIG_CONFLICT_INDEPENDENT_LEAVES_AND_HOIST',
-      '"independent-leaves=true" can only be used when hoisting is off, so "hoist=false"')
  }
  if (typeof pnpmConfig['color'] === 'boolean') {
    switch (pnpmConfig['color']) {
--- a/packages/config/test/index.ts
+++ b/packages/config/test/index.ts
@@ -11,7 +11,6 @@ import './findBestGlobalPrefixOnWindows'
 // To override any local settings,
 // we force the default values of config
 delete process.env['npm_config_depth']
-process.env['npm_config_independent_leaves'] = 'false'
 process.env['npm_config_hoist'] = 'true'
 delete process.env['npm_config_registry']
 delete process.env['npm_config_virtual_store_dir']
@@ -90,25 +89,6 @@ test('throw error if --lockfile-dir is used with --global', async (t) => {
  }
 })

-test('throw error if --independent-leaves is used with --global', async (t) => {
-  try {
-    await getConfig({
-      cliOptions: {
-        'global': true,
-        'independent-leaves': true,
-      },
-      packageManager: {
-        name: 'pnpm',
-        version: '1.0.0',
-      },
-    })
-  } catch (err) {
-    t.equal(err.message, 'Configuration conflict. "independent-leaves" may not be used with "global"')
-    t.equal((err as PnpmError).code, 'ERR_PNPM_CONFIG_CONFLICT_INDEPENDENT_LEAVES_WITH_GLOBAL')
-    t.end()
-  }
-})
-
 test('throw error if --hoist-pattern is used with --global', async (t) => {
  try {
    await getConfig({
@@ -442,47 +422,13 @@ test('throw error if --no-hoist is used with --hoist-pattern', async (t) => {
  }
 })

-test('throw error if --independent-leaves is used without --no-hoist', async (t) => {
-  try {
-    await getConfig({
-      cliOptions: {
-        'independent-leaves': true,
-      },
-      packageManager: {
-        name: 'pnpm',
-        version: '1.0.0',
-      },
-    })
-  } catch (err) {
-    t.equal(err.message, '"independent-leaves=true" can only be used when hoisting is off, so "hoist=false"')
-    t.equal((err as PnpmError).code, 'ERR_PNPM_CONFIG_CONFLICT_INDEPENDENT_LEAVES_AND_HOIST')
-    t.end()
-  }
-})
-
-test('do not throw error if --independent-leaves is used with --no-hoist', async (t) => {
-  const { config } = await getConfig({
-    cliOptions: {
-      'hoist': false,
-      'independent-leaves': true,
-    },
-    packageManager: {
-      name: 'pnpm',
-      version: '1.0.0',
-    },
-  })
-  t.ok(config.independentLeaves)
-  t.notOk(config.hoistPattern)
-  t.end()
-})
-
 test('rawLocalConfig in a workspace', async (t) => {
  const tmp = tempy.directory()
  t.comment(`temp dir created: ${tmp}`)

  process.chdir(tmp)
  const workspaceDir = process.cwd()
-  await fs.writeFile('.npmrc', 'independent-leaves=true\nhoist-pattern=*', 'utf8')
+  await fs.writeFile('.npmrc', 'hoist-pattern=*', 'utf8')
  await fs.mkdir('package')
  process.chdir('package')
  await fs.writeFile('.npmrc', 'hoist-pattern=eslint-*', 'utf8')
@@ -501,7 +447,6 @@ test('rawLocalConfig in a workspace', async (t) => {

    t.deepEqual(config.rawLocalConfig, {
      'hoist-pattern': 'eslint-*',
-      'independent-leaves': true,
      'save-exact': true,
    })
  }
@@ -523,7 +468,6 @@ test('rawLocalConfig in a workspace', async (t) => {

    t.deepEqual(config.rawLocalConfig, {
      'hoist-pattern': '*',
-      'independent-leaves': true,
      'save-exact': true,
    })
  }
@@ -535,7 +479,7 @@ test('rawLocalConfig', async (t) => {
  t.comment(`temp dir created: ${tmp}`)

  process.chdir(tmp)
-  await fs.writeFile('.npmrc', 'independent-leaves=true', 'utf8')
+  await fs.writeFile('.npmrc', 'modules-dir=modules', 'utf8')

  const { config } = await getConfig({
    cliOptions: {
@@ -548,7 +492,7 @@ test('rawLocalConfig', async (t) => {
  })

  t.deepEqual(config.rawLocalConfig, {
-    'independent-leaves': true,
+    'modules-dir': 'modules',
    'save-exact': true,
  })
  t.end()
--- a/packages/dependencies-hierarchy/example/node_modules/.modules.yaml
+++ b/packages/dependencies-hierarchy/example/node_modules/.modules.yaml
@@ -1,4 +1,3 @@
-independentLeaves: false
 layoutVersion: 1
 packageManager: pnpm@1.4.0
 skipped: []
--- a/packages/dependencies-hierarchy/fixtureMonorepo/node_modules/.modules.yaml
+++ b/packages/dependencies-hierarchy/fixtureMonorepo/node_modules/.modules.yaml
@@ -6,7 +6,6 @@ included:
  dependencies: true
  devDependencies: true
  optionalDependencies: true
-independentLeaves: true
 layoutVersion: 1
 packageManager: pnpm@2.25.5
 pendingBuilds: []
--- a/packages/get-context/src/index.ts
+++ b/packages/get-context/src/index.ts
@@ -28,7 +28,6 @@ export interface PnpmContext<T> {
  extraBinPaths: string[],
  hoistedAliases: {[depPath: string]: string[]}
  include: IncludedDependencies,
-  independentLeaves: boolean,
  modulesFile: Modules | null,
  pendingBuilds: string[],
  projects: Array<{
@@ -72,9 +71,6 @@ export default async function getContext<T> (
    useLockfile: boolean,
    virtualStoreDir?: string,

-    independentLeaves?: boolean,
-    forceIndependentLeaves?: boolean,
-
    hoistPattern?: string[] | undefined,
    forceHoistPattern?: boolean,

@@ -97,9 +93,6 @@ export default async function getContext<T> (
      storeDir: opts.storeDir,
      virtualStoreDir,

-      forceIndependentLeaves: opts.forceIndependentLeaves,
-      independentLeaves: opts.independentLeaves,
-
      forceHoistPattern: opts.forceHoistPattern,
      hoistPattern: opts.hoistPattern,

@@ -144,7 +137,6 @@ export default async function getContext<T> (
    hoistedModulesDir,
    hoistPattern: opts.hoistPattern,
    include: opts.include || importersContext.include,
-    independentLeaves: Boolean(typeof importersContext.independentLeaves === 'undefined' ? opts.independentLeaves : importersContext.independentLeaves),
    lockfileDir: opts.lockfileDir,
    modulesFile: importersContext.modules,
    pendingBuilds: importersContext.pendingBuilds,
@@ -189,9 +181,6 @@ async function validateModules (
    storeDir: string,
    virtualStoreDir: string,

-    independentLeaves?: boolean,
-    forceIndependentLeaves?: boolean,
-
    hoistPattern?: string[] | undefined,
    forceHoistPattern?: boolean,

@@ -218,30 +207,6 @@ async function validateModules (
      + ' You must remove that option, or else "pnpm install" to recreate the modules directory.'
    )
  }
-  if (opts.forceIndependentLeaves && Boolean(modules.independentLeaves) !== opts.independentLeaves) {
-    if (opts.forceNewModules) {
-      await Promise.all(projects.map(purgeModulesDirsOfImporter))
-      if (!rootProject) {
-        await purgeModulesDirsOfImporter({
-          modulesDir: path.join(opts.lockfileDir, opts.modulesDir),
-          rootDir: opts.lockfileDir,
-        })
-      }
-      return { purged: true }
-    }
-    if (modules.independentLeaves) {
-      throw new PnpmError(
-        'INDEPENDENT_LEAVES_WANTED',
-        'This modules directory was created using the --independent-leaves option.'
-        + ' You must add that option, or else run "pnpm install" to recreate the modules directory.'
-      )
-    }
-    throw new PnpmError(
-      'INDEPENDENT_LEAVES_NOT_WANTED',
-      'This modules directory was created without the --independent-leaves option.'
-      + ' You must remove that option, or else "pnpm install" to recreate the modules directory.'
-    )
-  }
  let purged = false
  if (opts.forceHoistPattern && rootProject) {
    try {
@@ -338,7 +303,6 @@ export interface PnpmSingleContext {
  importerId: string,
  prefix: string,
  include: IncludedDependencies,
-  independentLeaves: boolean,
  modulesFile: Modules | null,
  pendingBuilds: string[],
  registries: Registries,
@@ -375,9 +339,6 @@ export async function getContextForSingleImporter (

    shamefullyHoist?: boolean,
    forceShamefullyHoist?: boolean,
-
-    independentLeaves?: boolean,
-    forceIndependentLeaves?: boolean,
  },
  alreadyPurged: boolean = false
 ): Promise<PnpmSingleContext> {
@@ -386,7 +347,6 @@ export async function getContextForSingleImporter (
    hoistedAliases,
    projects,
    include,
-    independentLeaves,
    modules,
    pendingBuilds,
    registries,
@@ -426,9 +386,6 @@ export async function getContextForSingleImporter (
      forceHoistPattern: opts.forceHoistPattern,
      hoistPattern: opts.hoistPattern,

-      forceIndependentLeaves: opts.forceIndependentLeaves,
-      independentLeaves: opts.independentLeaves,
-
      forceShamefullyHoist: opts.forceShamefullyHoist,
      shamefullyHoist: opts.shamefullyHoist,
    })
@@ -454,7 +411,6 @@ export async function getContextForSingleImporter (
    hoistPattern: opts.hoistPattern,
    importerId,
    include: opts.include || include,
-    independentLeaves: Boolean(typeof independentLeaves === 'undefined' ? opts.independentLeaves : independentLeaves),
    lockfileDir: opts.lockfileDir,
    manifest: opts.hooks?.readPackage?.(manifest) ?? manifest,
    modulesDir,
--- a/packages/headless/src/index.ts
+++ b/packages/headless/src/index.ts
@@ -30,7 +30,6 @@ import {
 import {
  nameVerFromPkgSnapshot,
  packageIdFromSnapshot,
-  packageIsIndependent,
  pkgSnapshotToResolution,
  satisfiesPackageManifest,
 } from '@pnpm/lockfile-utils'
@@ -76,7 +75,6 @@ export interface HeadlessOptions {
  extraBinPaths?: string[],
  ignoreScripts: boolean,
  include: IncludedDependencies,
-  independentLeaves: boolean,
  projects: Array<{
    binsDir: string,
    buildIndex: number,
@@ -246,15 +244,6 @@ export default async (opts: HeadlessOptions) => {
  let newHoistedAliases!: {[depPath: string]: string[]}
  if (rootImporterWithFlatModules) {
    newHoistedAliases = await hoist(matcher(opts.hoistPattern!), {
-      getIndependentPackageLocation: opts.independentLeaves
-        ? async (packageId: string, packageName: string) => {
-          const { dir } = await opts.storeController.getPackageLocation(packageId, packageName, {
-            lockfileDir,
-            targetEngine: opts.sideEffectsCacheRead && ENGINE_NAME || undefined,
-          })
-          return dir
-        }
-        : undefined,
      lockfile: filteredLockfile,
      lockfileDir,
      modulesDir: hoistedModulesDir,
@@ -341,7 +330,6 @@ export default async (opts: HeadlessOptions) => {
    hoistedAliases: newHoistedAliases,
    hoistPattern: opts.hoistPattern,
    included: opts.include,
-    independentLeaves: !!opts.independentLeaves,
    layoutVersion: LAYOUT_VERSION,
    packageManager: `${opts.packageManager.name}@${opts.packageManager.version}`,
    pendingBuilds: opts.pendingBuilds,
@@ -468,7 +456,6 @@ async function linkRootPackages (
 interface LockfileToDepGraphOptions {
  force: boolean,
  include: IncludedDependencies,
-  independentLeaves: boolean,
  importerIds: string[],
  lockfileDir: string,
  skipped: Set<string>,
@@ -497,15 +484,8 @@ async function lockfileToDepGraph (
        const pkgName = nameVerFromPkgSnapshot(depPath, pkgSnapshot).name
        const modules = path.join(opts.virtualStoreDir, pkgIdToFilename(depPath, opts.lockfileDir), 'node_modules')
        const packageId = packageIdFromSnapshot(depPath, pkgSnapshot, opts.registries)
-        const pkgLocation = await opts.storeController.getPackageLocation(packageId, pkgName, {
-          lockfileDir: opts.lockfileDir,
-          targetEngine: opts.sideEffectsCacheRead && !opts.force && ENGINE_NAME || undefined,
-        })

-        const independent = opts.independentLeaves && packageIsIndependent(pkgSnapshot)
-        const peripheralLocation = !independent
-          ? path.join(modules, pkgName)
-          : pkgLocation.dir
+        const peripheralLocation = path.join(modules, pkgName)
        if (
          currentPackages[depPath] && R.equals(currentPackages[depPath].dependencies, lockfile.packages![depPath].dependencies) &&
          R.equals(currentPackages[depPath].optionalDependencies, lockfile.packages![depPath].optionalDependencies)
@@ -551,7 +531,6 @@ async function lockfileToDepGraph (
          finishing: fetchResponse.finishing,
          hasBin: pkgSnapshot.hasBin === true,
          hasBundledDependencies: !!pkgSnapshot.bundledDependencies,
-          independent,
          modules,
          name: pkgName,
          optional: !!pkgSnapshot.optional,
@@ -567,7 +546,6 @@ async function lockfileToDepGraph (
    const ctx = {
      force: opts.force,
      graph,
-      independentLeaves: opts.independentLeaves,
      lockfileDir: opts.lockfileDir,
      pkgSnapshotsByDepPaths: lockfile.packages,
      registries: opts.registries,
@@ -605,7 +583,6 @@ async function getChildrenPaths (
    force: boolean,
    registries: Registries,
    virtualStoreDir: string,
-    independentLeaves: boolean,
    storeDir: string,
    skipped: Set<string>,
    pkgSnapshotsByDepPaths: Record<string, PackageSnapshot>,
@@ -627,18 +604,8 @@ async function getChildrenPaths (
    if (ctx.graph[childRelDepPath]) {
      children[alias] = ctx.graph[childRelDepPath].peripheralLocation
    } else if (childPkgSnapshot) {
-      if (ctx.independentLeaves && packageIsIndependent(childPkgSnapshot)) {
-        const pkgId = childPkgSnapshot.id || childDepPath
-        const pkgName = nameVerFromPkgSnapshot(childRelDepPath, childPkgSnapshot).name
-        const pkgLocation = await ctx.storeController.getPackageLocation(pkgId, pkgName, {
-          lockfileDir: ctx.lockfileDir,
-          targetEngine: ctx.sideEffectsCacheRead && !ctx.force && ENGINE_NAME || undefined,
-        })
-        children[alias] = pkgLocation.dir
-      } else {
-        const pkgName = nameVerFromPkgSnapshot(childRelDepPath, childPkgSnapshot).name
-        children[alias] = path.join(ctx.virtualStoreDir, pkgIdToFilename(childRelDepPath, ctx.lockfileDir), 'node_modules', pkgName)
-      }
+      const pkgName = nameVerFromPkgSnapshot(childRelDepPath, childPkgSnapshot).name
+      children[alias] = path.join(ctx.virtualStoreDir, pkgIdToFilename(childRelDepPath, ctx.lockfileDir), 'node_modules', pkgName)
    } else if (allDeps[alias].indexOf('file:') === 0) {
      children[alias] = path.resolve(ctx.lockfileDir, allDeps[alias].substr(5))
    } else if (!ctx.skipped.has(childRelDepPath)) {
@@ -656,9 +623,6 @@ export interface DependenciesGraphNode {
  finishing: () => Promise<void>,
  peripheralLocation: string,
  children: {[alias: string]: string},
-  // an independent package is a package that
-  // has neither regular nor peer dependencies
-  independent: boolean,
  optionalDependencies: Set<string>,
  optional: boolean,
  depPath: string, // this option is only needed for saving pendingBuild when running with --ignore-scripts flag
@@ -754,7 +718,6 @@ async function linkAllModules (
 ) {
  return Promise.all(
    depNodes
-      .filter(({ independent }) => !independent)
      .map(async (depNode) => {
        const childrenToLink = opts.optional
          ? depNode.children
--- a/packages/headless/test/index.ts
+++ b/packages/headless/test/index.ts
@@ -42,8 +42,7 @@ test('installing a simple project', async (t) => {
  t.ok(project.requireModule('is-negative'), 'dev dep installed')
  t.ok(project.requireModule('colors'), 'optional dep installed')

-  // test that independent leaves is false by default
-  await project.has(`.pnpm/colors@1.2.0`) // colors is not symlinked from the store
+  await project.has(`.pnpm/colors@1.2.0`)

  await project.isExecutable('.bin/rimraf')

@@ -245,70 +244,6 @@ test('not installing optional deps', async (t) => {
  t.end()
 })

-// Covers https://github.com/pnpm/pnpm/issues/1547
-test('installing with independent-leaves and hoistPattern=*', async (t) => {
-  const lockfileDir = path.join(fixtures, 'with-1-dep')
-  await rimraf(path.join(lockfileDir, 'node_modules'))
-
-  const { projects } = await readprojectsContext(
-    [
-      {
-        rootDir: lockfileDir,
-      },
-    ],
-    { lockfileDir }
-  )
-
-  await headless(await testDefaults({
-    hoistPattern: '*',
-    independentLeaves: true,
-    lockfileDir: lockfileDir,
-    projects: await Promise.all(
-      projects.map(async (project) => ({ ...project, manifest: await readPackageJsonFromDir(project.rootDir) }))
-    ),
-  }))
-
-  const project = assertProject(t, lockfileDir)
-  await project.has('rimraf')
-  await project.has('.pnpm/node_modules/glob')
-  await project.has('.pnpm/node_modules/path-is-absolute')
-
-  // wrappy is linked directly from the store
-  await project.hasNot(`.pnpm/wrappy@1.0.2`)
-  await project.storeHas('wrappy', '1.0.2')
-
-  await project.has(`.pnpm/rimraf@2.5.1`)
-
-  await project.isExecutable('.bin/rimraf')
-
-  t.end()
-})
-
-test('installing with independent-leaves when an optional subdep is skipped', async (t) => {
-  const prefix = path.join(fixtures, 'has-incompatible-optional-subdep')
-  await rimraf(path.join(prefix, 'node_modules'))
-
-  await headless(await testDefaults({
-    independentLeaves: true,
-    lockfileDir: prefix,
-  }))
-
-  const modulesInfo = await readYamlFile<{ skipped: string[] }>(path.join(prefix, 'node_modules', '.modules.yaml'))
-  t.deepEqual(
-    modulesInfo.skipped,
-    [
-      '/dep-of-optional-pkg/1.0.0',
-      '/not-compatible-with-any-os/1.0.0',
-    ],
-    'optional subdeps skipped'
-  )
-
-  const project = assertProject(t, prefix)
-  await project.has('pkg-with-optional')
-
-  t.end()
-})
-
 test('run pre/postinstall scripts', async (t) => {
  const prefix = path.join(fixtures, 'deps-have-lifecycle-scripts')
  const outputJsonPath = path.join(prefix, 'output.json')
@@ -544,53 +479,6 @@ test('installation of a dependency that has a resolved peer in subdeps', async (
  t.end()
 })

-test('independent-leaves: installing a simple project', async (t) => {
-  const prefix = path.join(fixtures, 'simple')
-  await rimraf(path.join(prefix, 'node_modules'))
-  const reporter = sinon.spy()
-
-  await headless(await testDefaults({ lockfileDir: prefix, reporter, independentLeaves: true }))
-
-  const project = assertProject(t, prefix)
-  t.ok(project.requireModule('is-positive'), 'prod dep installed')
-  t.ok(project.requireModule('rimraf'), 'prod dep installed')
-  t.ok(project.requireModule('is-negative'), 'dev dep installed')
-  t.ok(project.requireModule('colors'), 'optional dep installed')
-  await project.has(`.pnpm/rimraf@2.7.1`) // rimraf is not symlinked from the store
-  await project.hasNot(`.pnpm/colors@1.2.0`) // colors is symlinked from the store
-
-  await project.isExecutable('.bin/rimraf')
-
-  t.ok(await project.readCurrentLockfile())
-  t.ok(await project.readModulesManifest())
-
-  t.ok(reporter.calledWithMatch({
-    level: 'debug',
-    name: 'pnpm:package-manifest',
-    updated: require(path.join(prefix, 'package.json')),
-  } as PackageManifestLog), 'updated package.json logged')
-  t.ok(reporter.calledWithMatch({
-    added: 15,
-    level: 'debug',
-    name: 'pnpm:stats',
-    prefix,
-  } as StatsLog), 'added stat')
-  t.ok(reporter.calledWithMatch({
-    level: 'debug',
-    name: 'pnpm:stats',
-    prefix,
-    removed: 0,
-  } as StatsLog), 'removed stat')
-  t.ok(reporter.calledWithMatch({
-    level: 'debug',
-    name: 'pnpm:stage',
-    prefix,
-    stage: 'importing_done',
-  } as StageLog), 'importing stage done logged')
-
-  t.end()
-})
-
 test('installing with hoistPattern=*', async (t) => {
  const prefix = path.join(fixtures, 'simple-shamefully-flatten')
  const reporter = sinon.spy()
@@ -604,8 +492,7 @@ test('installing with hoistPattern=*', async (t) => {
  t.ok(project.requireModule('is-negative'), 'dev dep installed')
  t.ok(project.requireModule('colors'), 'optional dep installed')

-  // test that independent leaves is false by default
-  await project.has(`.pnpm/colors@1.2.0`) // colors is not symlinked from the store
+  await project.has(`.pnpm/colors@1.2.0`)

  await project.isExecutable('.bin/rimraf')
  await project.isExecutable('.pnpm/node_modules/.bin/hello-world-js-bin')
@@ -664,8 +551,7 @@ test('installing with hoistPattern=* and shamefullyHoist=true', async (t) => {
  t.ok(project.requireModule('is-negative'), 'dev dep installed')
  t.ok(project.requireModule('colors'), 'optional dep installed')

-  // test that independent leaves is false by default
-  await project.has(`.pnpm/colors@1.2.0`) // colors is not symlinked from the store
+  await project.has(`.pnpm/colors@1.2.0`)

  await project.isExecutable('.bin/rimraf')
  await project.isExecutable('.bin/hello-world-js-bin')
@@ -835,34 +721,3 @@ test('installing in a workspace', async (t) => {

  t.end()
 })
-
-test('independent-leaves: installing in a workspace', async (t) => {
-  const workspaceFixture = path.join(__dirname, 'workspace-fixture2')
-
-  const { projects } = await readprojectsContext(
-    [
-      {
-        rootDir: path.join(workspaceFixture, 'foo'),
-      },
-      {
-        rootDir: path.join(workspaceFixture, 'bar'),
-      },
-    ],
-    { lockfileDir: workspaceFixture }
-  )
-
-  await headless(await testDefaults({
-    independentLeaves: true,
-    lockfileDir: workspaceFixture,
-    projects: await Promise.all(
-      projects.map(async (project) => ({ ...project, manifest: await readPackageJsonFromDir(project.rootDir) }))
-    ),
-  }))
-
-  const projectBar = assertProject(t, path.join(workspaceFixture, 'bar'))
-
-  await projectBar.has('foo')
-  t.ok(await exists(path.join(workspaceFixture, `node_modules/.pnpm/express@4.16.4/node_modules/array-flatten`)), 'independent package linked')
-
-  t.end()
-})
--- a/packages/headless/test/utils/testDefaults.ts
+++ b/packages/headless/test/utils/testDefaults.ts
@@ -65,7 +65,6 @@ export default async function testDefaults (
    engineStrict: false,
    force: false,
    include,
-    independentLeaves: false,
    lockfileDir,
    packageManager: {
      name: 'pnpm',
--- a/packages/hoist/src/index.ts
+++ b/packages/hoist/src/index.ts
@@ -3,7 +3,6 @@ import linkBins, { WarnFunction } from '@pnpm/link-bins'
 import {
  Lockfile,
  nameVerFromPkgSnapshot,
-  packageIsIndependent,
 } from '@pnpm/lockfile-utils'
 import lockfileWalker, { LockfileWalkerStep } from '@pnpm/lockfile-walker'
 import logger from '@pnpm/logger'
@@ -17,7 +16,6 @@ import R = require('ramda')
 export default async function hoistByLockfile (
  match: (dependencyName: string) => boolean,
  opts: {
-    getIndependentPackageLocation?: (packageId: string, packageName: string) => Promise<string>,
    lockfile: Lockfile,
    lockfileDir: string,
    modulesDir: string,
@@ -48,7 +46,6 @@ export default async function hoistByLockfile (
      step,
      0,
      {
-        getIndependentPackageLocation: opts.getIndependentPackageLocation,
        lockfileDir: opts.lockfileDir,
        registries: opts.registries,
        virtualStoreDir: opts.virtualStoreDir,
@@ -83,7 +80,6 @@ async function getDependencies (
  step: LockfileWalkerStep,
  depth: number,
  opts: {
-    getIndependentPackageLocation?: (packageId: string, packageName: string) => Promise<string>,
    registries: Registries,
    lockfileDir: string,
    virtualStoreDir: string,
@@ -92,10 +88,8 @@ async function getDependencies (
  const deps: Dependency[] = []
  const nextSteps: LockfileWalkerStep[] = []
  for (const { pkgSnapshot, relDepPath, next } of step.dependencies) {
-    const absolutePath = dp.resolve(opts.registries, relDepPath)
    const pkgName = nameVerFromPkgSnapshot(relDepPath, pkgSnapshot).name
    const modules = path.join(opts.virtualStoreDir, pkgIdToFilename(relDepPath, opts.lockfileDir), 'node_modules')
-    const independent = opts.getIndependentPackageLocation && packageIsIndependent(pkgSnapshot)
    const allDeps = {
      ...pkgSnapshot.dependencies,
      ...pkgSnapshot.optionalDependencies,
@@ -107,9 +101,7 @@ async function getDependencies (
      }, {}),
      depPath: relDepPath,
      depth,
-      location: !independent
-        ? path.join(modules, pkgName)
-        : await opts.getIndependentPackageLocation!(pkgSnapshot.id || absolutePath, pkgName),
+      location: path.join(modules, pkgName),
    })

    nextSteps.push(next())
--- a/packages/list/example/node_modules/.modules.yaml
+++ b/packages/list/example/node_modules/.modules.yaml
@@ -1,4 +1,3 @@
-independentLeaves: false
 layoutVersion: 1
 packageManager: pnpm@1.4.0
 skipped: []
--- a/packages/list/src/getPkgInfo.ts
+++ b/packages/list/src/getPkgInfo.ts
@@ -14,9 +14,7 @@ export default async function getPkgInfo (
  try {
    manifest = await readPkg(path.join(pkg.path, 'node_modules', pkg.name, 'package.json'))
  } catch (err) {
-    // This is a temporary workaround.
-    // If the package.json is not found inside node_modules, it should be read from the store.
-    // This frequently happens when the independent-leaves config is true.
+    // This will probably never happen
    manifest = {
      description: '[Could not find additional info about this dependency]',
    }
--- a/packages/list/test/fixture-with-external-shrinkwrap/node_modules/.modules.yaml
+++ b/packages/list/test/fixture-with-external-shrinkwrap/node_modules/.modules.yaml
@@ -6,7 +6,6 @@ included:
  dependencies: true
  devDependencies: true
  optionalDependencies: true
-independentLeaves: false
 layoutVersion: 1
 packageManager: pnpm@2.17.0-4
 pendingBuilds: []
--- a/packages/list/test/fixture-with-no-pkg-name-and-no-version/node_modules/.modules.yaml
+++ b/packages/list/test/fixture-with-no-pkg-name-and-no-version/node_modules/.modules.yaml
@@ -2,7 +2,6 @@ included:
  dependencies: true
  devDependencies: true
  optionalDependencies: true
-independentLeaves: true
 layoutVersion: 3
 packageManager: pnpm@3.8.1
 pendingBuilds: []
--- a/packages/list/test/fixture-with-no-pkg-version/node_modules/.modules.yaml
+++ b/packages/list/test/fixture-with-no-pkg-version/node_modules/.modules.yaml
@@ -2,7 +2,6 @@ included:
  dependencies: true
  devDependencies: true
  optionalDependencies: true
-independentLeaves: true
 layoutVersion: 3
 packageManager: pnpm@3.8.1
 pendingBuilds: []
--- a/packages/list/test/fixture/node_modules/.modules.yaml
+++ b/packages/list/test/fixture/node_modules/.modules.yaml
@@ -2,7 +2,6 @@ included:
  dependencies: true
  devDependencies: true
  optionalDependencies: true
-independentLeaves: true
 layoutVersion: 3
 packageManager: pnpm@3.8.1
 pendingBuilds: []
--- a/packages/list/test/with-aliased-dep/node_modules/.modules.yaml
+++ b/packages/list/test/with-aliased-dep/node_modules/.modules.yaml
@@ -2,7 +2,6 @@ included:
  dependencies: true
  devDependencies: true
  optionalDependencies: true
-independentLeaves: true
 layoutVersion: 3
 packageManager: pnpm@3.8.1
 pendingBuilds: []
--- a/packages/modules-yaml/README.md
+++ b/packages/modules-yaml/README.md
@@ -19,13 +19,12 @@ import {write, read} from '@pnpm/modules-yaml'

 await write('node_modules', {
  hoistedAliases: {}
-  independentLeaves: false,
  layoutVersion: 1,
  packageManager: 'pnpm@1.0.0',
  pendingBuilds: [],
  shamefullyFlatten: false,
  skipped: [],
-  store: '/home/user/.pnpm-store',
+  storeDir: '/home/user/.pnpm-store',
 })

 const modulesYaml = await read(`node_modules`)
--- a/packages/modules-yaml/src/index.ts
+++ b/packages/modules-yaml/src/index.ts
@@ -16,7 +16,6 @@ export interface Modules {
  hoistedAliases: {[depPath: string]: string[]}
  hoistPattern?: string[]
  included: IncludedDependencies,
-  independentLeaves: boolean,
  layoutVersion: number,
  packageManager: string,
  pendingBuilds: string[],
--- a/packages/modules-yaml/test/index.ts
+++ b/packages/modules-yaml/test/index.ts
@@ -15,7 +15,6 @@ test('write() and read()', async (t) => {
      devDependencies: true,
      optionalDependencies: true,
    },
-    independentLeaves: false,
    layoutVersion: 1,
    packageManager: 'pnpm@2',
    pendingBuilds: [],
--- a/packages/package-requester/src/index.ts
+++ b/packages/package-requester/src/index.ts
@@ -1,9 +1,5 @@
 import packageRequester from './packageRequester'

-export {
-  getCacheByEngine,
-} from './packageRequester'
-
 export default packageRequester

 export { PackageResponse, PackageFilesResponse } from '@pnpm/store-controller-types'
--- a/packages/package-requester/src/packageRequester.ts
+++ b/packages/package-requester/src/packageRequester.ts
@@ -198,7 +198,6 @@ async function resolveAndFetch (
      return {
        body: {
          id,
-          inStoreLocation: path.join(ctx.storeDir, pkgIdToFilename(id, options.lockfileDir)),
          isLocal: false as const,
          latest,
          manifest,
@@ -221,7 +220,6 @@ async function resolveAndFetch (
    return {
      body: {
        id,
-        inStoreLocation: fetchResult.inStoreLocation,
        isLocal: false as const,
        latest,
        manifest,
@@ -245,7 +243,6 @@ type FetchLock = {
  files: Promise<PackageFilesResponse>,
  filesIndexFile: string,
  finishing: Promise<void>,
-  inStoreLocation: string,
 }

 function fetchToStore (
@@ -278,7 +275,6 @@ function fetchToStore (
  filesIndexFile: string,
  files: () => Promise<PackageFilesResponse>,
  finishing: () => Promise<void>,
-  inStoreLocation: string,
 } {
  const targetRelative = pkgIdToFilename(opts.pkgId, opts.lockfileDir)
  const target = path.join(ctx.storeDir, targetRelative)
@@ -299,14 +295,12 @@ function fetchToStore (
        files: removeKeyOnFail(files.promise),
        filesIndexFile,
        finishing: removeKeyOnFail(finishing.promise),
-        inStoreLocation: target,
      })
    } else {
      ctx.fetchingLocker.set(opts.pkgId, {
        files: removeKeyOnFail(files.promise),
        filesIndexFile,
        finishing: removeKeyOnFail(finishing.promise),
-        inStoreLocation: target,
      })
    }

@@ -358,7 +352,6 @@ function fetchToStore (
    files: pShare(result.files),
    filesIndexFile: result.filesIndexFile,
    finishing: pShare(result.finishing),
-    inStoreLocation: result.inStoreLocation,
  }

  async function removeKeyOnFail<T> (p: Promise<T>): Promise<T> {
@@ -551,24 +544,3 @@ async function fetcher (
    throw err
  }
 }
-
-// TODO: cover with tests
-export async function getCacheByEngine (storeDir: string, id: string): Promise<Map<string, string>> {
-  const map = new Map<string, string>()
-
-  const cacheRoot = path.join(storeDir, id, 'side_effects')
-  if (!await fs.exists(cacheRoot)) {
-    return map
-  }
-
-  const dirContents = (await fs.readdir(cacheRoot)).map((content: string) => path.join(cacheRoot, content))
-  await Promise.all(dirContents.map(async (dir: string) => {
-    if (!(await fs.lstat(dir)).isDirectory()) {
-      return
-    }
-    const engineName = path.basename(dir)
-    map[engineName] = path.join(dir, 'package')
-  }))
-
-  return map
-}
--- a/packages/package-requester/test/index.ts
+++ b/packages/package-requester/test/index.ts
@@ -61,7 +61,6 @@ test('request package', async t => {

  t.equal(pkgResponse.body.id, 'registry.npmjs.org/is-positive/1.0.0', 'responded with correct package ID')
  t.equal(pkgResponse.body.resolvedVia, 'npm-registry', 'responded with correct resolvedVia')
-  t.equal(pkgResponse.body.inStoreLocation, path.join(storeDir, 'registry.npmjs.org', 'is-positive@1.0.0'), 'package location in store returned')
  t.equal(pkgResponse.body.isLocal, false, 'package is not local')
  t.equal(typeof pkgResponse.body.latest, 'string', 'latest is returned')
  t.equal(pkgResponse.body.manifest.name, 'is-positive', 'package manifest returned')
@@ -104,7 +103,6 @@ test('request package but skip fetching', async t => {
  t.ok(pkgResponse.body, 'response has body')

  t.equal(pkgResponse.body.id, 'registry.npmjs.org/is-positive/1.0.0', 'responded with correct package ID')
-  t.equal(pkgResponse.body.inStoreLocation, path.join('.store', 'registry.npmjs.org', 'is-positive@1.0.0'), 'package location in store returned')
  t.equal(pkgResponse.body.isLocal, false, 'package is not local')
  t.equal(typeof pkgResponse.body.latest, 'string', 'latest is returned')
  t.equal(pkgResponse.body.manifest.name, 'is-positive', 'package manifest returned')
@@ -146,7 +144,6 @@ test('request package but skip fetching, when resolution is already available',
    update: false,
  }) as PackageResponse & {
    body: {
-      inStoreLocation: string,
      latest: string,
      manifest: {name: string},
    },
@@ -158,7 +155,6 @@ test('request package but skip fetching, when resolution is already available',
  t.ok(pkgResponse.body, 'response has body')

  t.equal(pkgResponse.body.id, 'registry.npmjs.org/is-positive/1.0.0', 'responded with correct package ID')
-  t.equal(pkgResponse.body.inStoreLocation, path.join('.store', 'registry.npmjs.org', 'is-positive@1.0.0'), 'package location in store returned')
  t.equal(pkgResponse.body.isLocal, false, 'package is not local')
  t.equal(typeof pkgResponse.body.latest, 'string', 'latest is returned')
  t.equal(pkgResponse.body.manifest.name, 'is-positive', 'package manifest returned')
--- a/packages/package-store/package.json
+++ b/packages/package-store/package.json
@@ -20,7 +20,6 @@
    "@pnpm/core-loggers": "workspace:4.0.2-alpha.0",
    "@pnpm/fetcher-base": "workspace:7.0.0-alpha.3",
    "@pnpm/package-requester": "workspace:12.0.0-alpha.5",
-    "@pnpm/pkgid-to-filename": "3.0.0",
    "@pnpm/resolver-base": "workspace:7.0.1-alpha.0",
    "@pnpm/store-controller-types": "workspace:8.0.0-alpha.4",
    "@pnpm/types": "workspace:6.0.0-alpha.0",
--- a/packages/package-store/src/storeController/index.ts
+++ b/packages/package-store/src/storeController/index.ts
@@ -4,8 +4,7 @@ import {
  PackageFilesIndex,
 } from '@pnpm/cafs'
 import { FetchFunction } from '@pnpm/fetcher-base'
-import createPackageRequester, { getCacheByEngine } from '@pnpm/package-requester'
-import pkgIdToFilename from '@pnpm/pkgid-to-filename'
+import createPackageRequester from '@pnpm/package-requester'
 import { ResolveFunction } from '@pnpm/resolver-base'
 import {
  ImportPackageFunction,
@@ -64,37 +63,12 @@ export default async function (
  return {
    close: async () => {}, // tslint:disable-line:no-empty
    fetchPackage: packageRequester.fetchPackageToStore,
-    getPackageLocation,
    importPackage,
    prune: prune.bind(null, storeDir),
    requestPackage: packageRequester.requestPackage,
    upload,
  }

-  async function getPackageLocation (
-    packageId: string,
-    packageName: string,
-    opts: {
-      lockfileDir: string,
-      targetEngine?: string,
-    }
-  ) {
-    if (opts.targetEngine) {
-      const sideEffectsCacheLocation = (await getCacheByEngine(initOpts.storeDir, packageId))[opts.targetEngine]
-      if (sideEffectsCacheLocation) {
-        return {
-          dir: sideEffectsCacheLocation,
-          isBuilt: true,
-        }
-      }
-    }
-
-    return {
-      dir: path.join(initOpts.storeDir, pkgIdToFilename(packageId, opts.lockfileDir), 'node_modules', packageName),
-      isBuilt: false,
-    }
-  }
-
  async function upload (builtPkgLocation: string, opts: {filesIndexFile: string, engine: string}) {
    const sideEffectsIndex = await packageRequester.cafs.addFilesFromDir(builtPkgLocation)
    // TODO: move this to a function
--- a/packages/plugin-commands-installation/src/add.ts
+++ b/packages/plugin-commands-installation/src/add.ts
@@ -21,7 +21,6 @@ export function rcOptionsTypes () {
    'ignore-pnpmfile',
    'ignore-scripts',
    'ignore-workspace-root-check',
-    'independent-leaves',
    'link-workspace-packages',
    'lockfile-dir',
    'lockfile-directory',
--- a/packages/plugin-commands-installation/src/install.ts
+++ b/packages/plugin-commands-installation/src/install.ts
@@ -22,7 +22,6 @@ export function rcOptionsTypes () {
    'hoist-pattern',
    'ignore-pnpmfile',
    'ignore-scripts',
-    'independent-leaves',
    'link-workspace-packages',
    'lockfile-dir',
    'lockfile-directory',
@@ -158,10 +157,6 @@ export function help () {
            description: 'Disable pnpm hooks defined in pnpmfile.js',
            name: '--ignore-pnpmfile',
          },
-          {
-            description: 'Symlinks leaf dependencies directly from the global store',
-            name: '--independent-leaves',
-          },
          {
            description: "If false, doesn't check whether packages in the store were mutated",
            name: '--[no-]verify-store-integrity',
@@ -260,7 +255,6 @@ export type InstallCommandOptions = Pick<Config,
  | 'globalPnpmfile'
  | 'ignorePnpmfile'
  | 'ignoreScripts'
-  | 'independentLeaves'
  | 'linkWorkspacePackages'
  | 'rawLocalConfig'
  | 'lockfileDir'
--- a/packages/plugin-commands-installation/src/installDeps.ts
+++ b/packages/plugin-commands-installation/src/installDeps.ts
@@ -38,7 +38,6 @@ export type InstallDepsOptions = Pick<Config,
  | 'globalPnpmfile'
  | 'ignorePnpmfile'
  | 'ignoreScripts'
-  | 'independentLeaves'
  | 'linkWorkspacePackages'
  | 'lockfileDir'
  | 'lockfileOnly'
@@ -146,7 +145,6 @@ export default async function handler (
    workspacePackages,

    forceHoistPattern: typeof opts.rawLocalConfig['hoist-pattern'] !== 'undefined' || typeof opts.rawLocalConfig['hoist'] !== 'undefined',
-    forceIndependentLeaves: typeof opts.rawLocalConfig['independent-leaves'] !== 'undefined',
    forceShamefullyHoist: typeof opts.rawLocalConfig['shamefully-hoist'] !== 'undefined',
  }
  if (!opts.ignorePnpmfile) {
--- a/packages/plugin-commands-installation/src/recursive.ts
+++ b/packages/plugin-commands-installation/src/recursive.ts
@@ -120,7 +120,6 @@ export default async function recursive (
    workspacePackages,

    forceHoistPattern: typeof opts.rawLocalConfig['hoist-pattern'] !== 'undefined' || typeof opts.rawLocalConfig['hoist'] !== 'undefined',
-    forceIndependentLeaves: typeof opts.rawLocalConfig['independent-leaves'] !== 'undefined',
    forceShamefullyHoist: typeof opts.rawLocalConfig['shamefully-hoist'] !== 'undefined',
  }) as InstallOptions

--- a/packages/plugin-commands-listing/test/index.ts
+++ b/packages/plugin-commands-listing/test/index.ts
@@ -81,40 +81,6 @@ test('listing packages', async (t) => {
  t.end()
 })

-test('independent-leaves=true: pnpm list --long', async (t) => {
-  prepare(t, {
-    dependencies: {
-      'is-positive': '1.0.0',
-    },
-    devDependencies: {
-      'is-negative': '1.0.0',
-    },
-  })
-
-  await execa('node', [pnpmBin, 'install', '--independent-leaves', '--no-hoist'])
-
-  const output = await list.handler({
-    dir: process.cwd(),
-    long: true,
-  }, [])
-
-  // TODO: the --long flag should work with --independent-leaves
-  t.equal(stripAnsi(output), stripIndent`
-    Legend: production dependency, optional only, dev only
-
-    project@0.0.0 ${process.cwd()}
-
-    dependencies:
-    is-positive 1.0.0
-      [Could not find additional info about this dependency]
-
-    devDependencies:
-    is-negative 1.0.0
-      [Could not find additional info about this dependency]
-  `)
-  t.end()
-})
-
 test(`listing packages of a project that has an external ${WANTED_LOCKFILE}`, async (t) => {
  preparePackages(t, [
    {
--- a/packages/plugin-commands-outdated/src/outdated.ts
+++ b/packages/plugin-commands-outdated/src/outdated.ts
@@ -138,7 +138,6 @@ export type OutdatedCommandOptions = {
  | 'fetchRetryMintimeout'
  | 'global'
  | 'httpsProxy'
-  | 'independentLeaves'
  | 'key'
  | 'localAddress'
  | 'lockfileDir'
--- a/packages/plugin-commands-outdated/test/index.ts
+++ b/packages/plugin-commands-outdated/test/index.ts
@@ -27,7 +27,6 @@ const OUTDATED_OPTIONS = {
  fetchRetryMaxtimeout: 60,
  fetchRetryMintimeout: 10,
  global: false,
-  independentLeaves: false,
  networkConcurrency: 16,
  offline: false,
  rawConfig: { registry: REGISTRY_URL },
--- a/packages/plugin-commands-outdated/test/utils.ts
+++ b/packages/plugin-commands-outdated/test/utils.ts
@@ -23,7 +23,6 @@ export const DEFAULT_OPTS = {
    devDependencies: true,
    optionalDependencies: true,
  },
-  independentLeaves: false,
  key: undefined,
  linkWorkspacePackages: true,
  localAddress: undefined,
--- a/packages/plugin-commands-rebuild/src/implementation/index.ts
+++ b/packages/plugin-commands-rebuild/src/implementation/index.ts
@@ -175,7 +175,6 @@ export async function rebuild (
    hoistedAliases: ctx.hoistedAliases,
    hoistPattern: ctx.hoistPattern,
    included: ctx.include,
-    independentLeaves: ctx.independentLeaves,
    layoutVersion: LAYOUT_VERSION,
    packageManager: `${opts.packageManager.name}@${opts.packageManager.version}`,
    pendingBuilds: ctx.pendingBuilds,
@@ -224,7 +223,6 @@ async function _rebuild (
    rootModulesDir: string,
    currentLockfile: Lockfile,
    projects: Array<{ id: string, rootDir: string }>,
-    independentLeaves: boolean,
    extraBinPaths: string[],
  },
  opts: StrictRebuildOptions
@@ -268,24 +266,11 @@ async function _rebuild (
      const pkgSnapshot = pkgSnapshots[relDepPath]
      const depPath = dp.resolve(opts.registries, relDepPath)
      const pkgInfo = nameVerFromPkgSnapshot(relDepPath, pkgSnapshot)
-      const independent = ctx.independentLeaves && packageIsIndependent(pkgSnapshot)
-      const pkgRoot = !independent
-        ? path.join(ctx.virtualStoreDir, pkgIdToFilename(relDepPath, opts.lockfileDir), 'node_modules', pkgInfo.name)
-        : await (
-          async () => {
-            const { dir } = await opts.storeController.getPackageLocation(pkgSnapshot.id || depPath, pkgInfo.name, {
-              lockfileDir: opts.lockfileDir,
-              targetEngine: opts.sideEffectsCacheRead && !opts.force && ENGINE_NAME || undefined,
-            })
-            return dir
-          }
-        )()
+      const pkgRoot = path.join(ctx.virtualStoreDir, pkgIdToFilename(relDepPath, opts.lockfileDir), 'node_modules', pkgInfo.name)
      try {
-        if (!independent) {
-          const modules = path.join(ctx.virtualStoreDir, pkgIdToFilename(relDepPath, opts.lockfileDir), 'node_modules')
-          const binPath = path.join(pkgRoot, 'node_modules', '.bin')
-          await linkBins(modules, binPath, { warn })
-        }
+        const modules = path.join(ctx.virtualStoreDir, pkgIdToFilename(relDepPath, opts.lockfileDir), 'node_modules')
+        const binPath = path.join(pkgRoot, 'node_modules', '.bin')
+        await linkBins(modules, binPath, { warn })
        await runPostinstallHooks({
          depPath,
          extraBinPaths: ctx.extraBinPaths,
@@ -325,7 +310,6 @@ async function _rebuild (
      .keys(pkgSnapshots)
      .filter((relDepPath) => !packageIsIndependent(pkgSnapshots[relDepPath]))
      .map((relDepPath) => limitLinking(() => {
-        const depPath = dp.resolve(opts.registries, relDepPath)
        const pkgSnapshot = pkgSnapshots[relDepPath]
        const pkgInfo = nameVerFromPkgSnapshot(relDepPath, pkgSnapshot)
        const modules = path.join(ctx.virtualStoreDir, pkgIdToFilename(relDepPath, opts.lockfileDir), 'node_modules')
--- a/packages/plugin-commands-rebuild/src/rebuild.ts
+++ b/packages/plugin-commands-rebuild/src/rebuild.ts
@@ -70,7 +70,6 @@ export async function handler (
    | 'allProjects'
    | 'dir'
    | 'engineStrict'
-    | 'independentLeaves'
    | 'rawLocalConfig'
    | 'registries'
    | 'selectedProjectsGraph'
--- a/packages/plugin-commands-rebuild/test/index.ts
+++ b/packages/plugin-commands-rebuild/test/index.ts
@@ -235,46 +235,6 @@ test('rebuild dependencies in correct order', async (t) => {
  t.end()
 })

-test('rebuild dependencies in correct order when node_modules uses independent-leaves', async (t) => {
-  const project = prepareEmpty(t)
-  const storeDir = path.resolve('store')
-
-  await execa('node', [
-    pnpmBin,
-    'add',
-    'with-postinstall-a',
-    '--registry',
-    REGISTRY,
-    '--store-dir',
-    storeDir,
-    '--ignore-scripts',
-    '--independent-leaves',
-    '--no-hoist',
-  ])
-
-  let modules = await project.readModulesManifest()
-  t.ok(modules)
-  t.doesNotEqual(modules!.pendingBuilds.length, 0)
-
-  await project.hasNot(`.pnpm/with-postinstall-b@1.0.0/node_modules/with-postinstall-b/output.json`)
-  await project.hasNot('with-postinstall-a/output.json')
-
-  await rebuild.handler({
-    ...DEFAULT_OPTS,
-    dir: process.cwd(),
-    independentLeaves: true,
-    pending: true,
-    storeDir,
-  }, [])
-
-  modules = await project.readModulesManifest()
-  t.ok(modules)
-  t.equal(modules!.pendingBuilds.length, 0)
-
-  t.ok(+project.requireModule(`.pnpm/with-postinstall-b@1.0.0/node_modules/with-postinstall-b/output.json`)[0] < +project.requireModule('with-postinstall-a/output.json')[0])
-  t.end()
-})
-
 test('rebuild links bins', async (t) => {
  const project = prepareEmpty(t)
  const storeDir = path.resolve('store')
--- a/packages/plugin-commands-store/src/storeStatus/extendStoreStatusOptions.ts
+++ b/packages/plugin-commands-store/src/storeStatus/extendStoreStatusOptions.ts
@@ -7,7 +7,6 @@ export interface StrictStoreStatusOptions {
  lockfileDir: string,
  dir: string,
  storeDir: string,
-  independentLeaves: boolean,
  force: boolean,
  forceSharedLockfile: boolean,
  useLockfile: boolean,
@@ -32,7 +31,6 @@ const defaults = async (opts: StoreStatusOptions) => {
    dir,
    force: false,
    forceSharedLockfile: false,
-    independentLeaves: false,
    lockfileDir,
    registries: DEFAULT_REGISTRIES,
    shamefullyHoist: false,
--- a/packages/pnpm/src/cmd/root.ts
+++ b/packages/pnpm/src/cmd/root.ts
@@ -29,7 +29,7 @@ export function help () {
        ],
      },
    ],
-    usages: ['pnpm root [-g [--independent-leaves]]'],
+    usages: ['pnpm root [-g]'],
  })
 }

--- a/packages/pnpm/test/cli.ts
+++ b/packages/pnpm/test/cli.ts
@@ -94,18 +94,6 @@ test('command fails when an unsupported flag is used', async (t) => {
  t.ok(stderr.toString().includes("Unknown option 'save-dev'"))
 })

-test('adding new dep does not fail if node_modules was created with --no-hoist and --independent-leaves', async (t: tape.Test) => {
-  const project = prepare(t)
-
-  await execPnpm(['add', 'is-positive', '--no-hoist', '--independent-leaves'])
-
-  t.equal(execPnpmSync(['add', 'is-negative', '--hoist']).status, 1)
-  t.equal(execPnpmSync(['add', 'is-negative', '--no-independent-leaves']).status, 1)
-  t.equal(execPnpmSync(['add', 'is-negative']).status, 0)
-
-  await project.has('is-negative')
-})
-
 test('adding new dep does not fail if node_modules was created with --hoist-pattern=eslint-* and --shamefully-hoist', async (t: tape.Test) => {
  const project = prepare(t)

--- a/packages/pnpm/test/utils/execPnpm.ts
+++ b/packages/pnpm/test/utils/execPnpm.ts
@@ -86,7 +86,6 @@ function createEnv (opts?: {storeDir?: string}): NodeJS.ProcessEnv {
  const env = {
    npm_config_fetch_retries: '4',
    npm_config_hoist: 'true',
-    npm_config_independent_leaves: 'false',
    npm_config_registry: `http://localhost:${REGISTRY_MOCK_PORT}/`,
    npm_config_silent: 'true',
    npm_config_store_dir: opts && opts.storeDir || '../store',
--- a/packages/read-projects-context/src/index.ts
+++ b/packages/read-projects-context/src/index.ts
@@ -25,7 +25,6 @@ export default async function <T>(
    id: string,
  } & T & Required<ProjectOptions>>,
  include: Record<DependenciesField, boolean>,
-  independentLeaves: boolean | undefined,
  modules: Modules | null,
  pendingBuilds: string[],
  registries: Registries | null | undefined,
@@ -41,7 +40,6 @@ export default async function <T>(
    hoist: !modules ? undefined : Boolean(modules.hoistPattern),
    hoistedAliases: modules?.hoistedAliases || {},
    include: modules?.included || { dependencies: true, devDependencies: true, optionalDependencies: true },
-    independentLeaves: modules?.independentLeaves || undefined,
    modules,
    pendingBuilds: modules?.pendingBuilds || [],
    projects: await Promise.all(
--- a/packages/resolve-dependencies/src/resolveDependencies.ts
+++ b/packages/resolve-dependencies/src/resolveDependencies.ts
@@ -175,14 +175,12 @@ export interface ResolvedPackage {
  fetchingBundledManifest?: () => Promise<DependencyManifest>,
  filesIndexFile: string,
  finishing: () => Promise<void>,
-  path: string,
  name: string,
  version: string,
  peerDependencies: Dependencies,
  optionalDependencies: Set<string>,
  hasBin: boolean,
  hasBundledDependencies: boolean,
-  independent: boolean,
  prepare: boolean,
  depPath: string,
  requiresBuild: boolean | undefined, // added to fix issue #1201
@@ -784,13 +782,9 @@ function getResolvedPackage (
    hasBin: options.hasBin,
    hasBundledDependencies: !!(options.pkg.bundledDependencies || options.pkg.bundleDependencies),
    id: options.pkgResponse.body.id,
-    independent: (options.pkg.dependencies === undefined || R.isEmpty(options.pkg.dependencies)) &&
-      (options.pkg.optionalDependencies === undefined || R.isEmpty(options.pkg.optionalDependencies)) &&
-      (options.pkg.peerDependencies === undefined || R.isEmpty(options.pkg.peerDependencies)),
    name: options.pkg.name,
    optional: options.wantedDependency.optional,
    optionalDependencies: new Set(R.keys(options.pkg.optionalDependencies)),
-    path: options.pkgResponse.body.inStoreLocation!,
    peerDependencies: peerDependencies ?? {},
    prepare: options.prepare,
    prod: !options.wantedDependency.dev && !options.wantedDependency.optional,
--- a/packages/server/src/connectStoreController.ts
+++ b/packages/server/src/connectStoreController.ts
@@ -30,20 +30,6 @@ export default function (
    resolve({
      close: async () => { return },
      fetchPackage: fetchPackage.bind(null, remotePrefix, limitedFetch),
-      getPackageLocation: async (
-        packageId: string,
-        packageName: string,
-        opts: {
-          lockfileDir: string,
-          targetEngine?: string,
-        }
-      ): Promise<{ dir: string, isBuilt: boolean }> => {
-        return await limitedFetch(`${remotePrefix}/getPackageLocation`, {
-          opts,
-          packageId,
-          packageName,
-        }) as { dir: string, isBuilt: boolean }
-      },
      importPackage: async (to: string, opts: {
        filesResponse: PackageFilesResponse,
        force: boolean,
--- a/packages/server/src/createServer.ts
+++ b/packages/server/src/createServer.ts
@@ -103,7 +103,7 @@ export default function (
            if (pkgResponse['files']) { // tslint:disable-line
              filesPromises[body.msgId] = pkgResponse['files'] // tslint:disable-line
            }
-            res.end(JSON.stringify({ inStoreLocation: pkgResponse.inStoreLocation }))
+            res.end(JSON.stringify({ filesIndexFile: pkgResponse.filesIndexFile }))
          } catch (err) {
            res.end(JSON.stringify({
              error: {
@@ -158,12 +158,6 @@ export default function (
          res.end(JSON.stringify('OK'))
          globalInfo('Server stopped')
          break
-        case '/getPackageLocation': {
-          const { packageId, packageName, opts } = (await bodyPromise) as any // tslint:disable-line:no-any
-          const pkgLocation = await store.getPackageLocation(packageId, packageName, opts)
-          res.end(JSON.stringify(pkgLocation))
-          break
-        }
        default:
          res.statusCode = 404
          const error = { error: `${req.url} does not match any route` }
--- a/packages/server/test/index.ts
+++ b/packages/server/test/index.ts
@@ -103,7 +103,7 @@ test('fetchPackage', async t => {
    },
  })

-  t.equal(typeof response.inStoreLocation, 'string', 'location in store returned')
+  t.equal(typeof response.filesIndexFile, 'string', 'index file location in store returned')

  t.ok(await response.bundledManifest!())

@@ -116,16 +116,6 @@ test('fetchPackage', async t => {

  t.comment('getPackageLocation()')

-  t.deepEqual(
-    await storeCtrl.getPackageLocation(pkgId, 'is-positive', {
-      lockfileDir: process.cwd(),
-    }),
-    {
-      dir: path.join(storeDir, 'registry.npmjs.org/is-positive@1.0.0/node_modules/is-positive'),
-      isBuilt: false,
-    }
-  )
-
  await server.close()
  await storeCtrl.close()
  t.end()
--- a/packages/store-controller-types/src/index.ts
+++ b/packages/store-controller-types/src/index.ts
@@ -29,14 +29,6 @@ export type BundledManifest = Pick<
 >

 export interface StoreController {
-  getPackageLocation (
-    packageId: string,
-    packageName: string,
-    opts: {
-      lockfileDir: string,
-      targetEngine?: string,
-    }
-  ): Promise<{ dir: string, isBuilt: boolean }>,
  requestPackage: RequestPackageFunction,
  fetchPackage: FetchPackageToStoreFunction,
  importPackage: ImportPackageFunction,
@@ -52,7 +44,6 @@ export type FetchPackageToStoreFunction = (
  filesIndexFile: string,
  files: () => Promise<PackageFilesResponse>,
  finishing: () => Promise<void>,
-  inStoreLocation: string,
 }

 export interface FetchPackageToStoreOptions {
@@ -118,7 +109,6 @@ export type PackageResponse = {
    normalizedPref?: string,
    updated: boolean,
    resolvedVia?: string,
-    inStoreLocation?: string,
    // This is useful for recommending updates.
    // If latest does not equal the version of the
    // resolved package, it is out-of-date.
--- a/packages/supi/src/install/extendInstallOptions.ts
+++ b/packages/supi/src/install/extendInstallOptions.ts
@@ -71,9 +71,6 @@ export interface StrictInstallOptions {
  shamefullyHoist: boolean,
  forceShamefullyHoist: boolean,

-  independentLeaves: boolean,
-  forceIndependentLeaves: boolean,
-
  global: boolean,
 }

@@ -106,7 +103,6 @@ const defaults = async (opts: InstallOptions) => {
      devDependencies: true,
      optionalDependencies: true,
    },
-    independentLeaves: false,
    lockfileDir: opts.lockfileDir || opts.dir || process.cwd(),
    lockfileOnly: false,
    nodeVersion: process.version,
--- a/packages/supi/src/install/index.ts
+++ b/packages/supi/src/install/index.ts
@@ -194,7 +194,6 @@ export async function mutateModules (
            hoistPattern: ctx.hoistPattern,
            ignoreScripts: opts.ignoreScripts,
            include: opts.include,
-            independentLeaves: opts.independentLeaves,
            lockfileDir: ctx.lockfileDir,
            modulesDir: opts.modulesDir,
            ownLifecycleHooksStdio: opts.ownLifecycleHooksStdio,
@@ -428,9 +427,7 @@ export async function mutateModules (
 async function isExternalLink (storeDir: string, modules: string, pkgName: string) {
  const link = await isInnerLink(modules, pkgName)

-  // checking whether the link is pointing to the store is needed
-  // because packages are linked to store when independent-leaves = true
-  return !link.isInner && !isSubdir(storeDir, link.target)
+  return !link.isInner
 }

 function pkgHasDependencies (manifest: ProjectManifest) {
@@ -712,7 +709,6 @@ async function installInContext (
      hoistedModulesDir: ctx.hoistedModulesDir,
      hoistPattern: ctx.hoistPattern,
      include: opts.include,
-      independentLeaves: opts.independentLeaves,
      lockfileDir: opts.lockfileDir,
      makePartialCurrentLockfile: opts.makePartialCurrentLockfile,
      outdatedDependencies,
@@ -818,7 +814,6 @@ async function installInContext (
          hoistedAliases: result.newHoistedAliases,
          hoistPattern: ctx.hoistPattern,
          included: ctx.include,
-          independentLeaves: ctx.independentLeaves,
          layoutVersion: LAYOUT_VERSION,
          packageManager: `${opts.packageManager.name}@${opts.packageManager.version}`,
          pendingBuilds: ctx.pendingBuilds,
--- a/packages/supi/src/install/link.ts
+++ b/packages/supi/src/install/link.ts
@@ -64,7 +64,6 @@ export default async function linkPackages (
    hoistedModulesDir: string,
    hoistPattern?: string[],
    include: IncludedDependencies,
-    independentLeaves: boolean,
    lockfileDir: string,
    makePartialCurrentLockfile: boolean,
    outdatedDependencies: {[pkgId: string]: string},
@@ -94,7 +93,6 @@ export default async function linkPackages (
  // logger.info(`Creating dependency graph`)
  const { depGraph, projectsDirectPathsByAlias } = resolvePeers({
    dependenciesTree,
-    independentLeaves: opts.independentLeaves,
    lockfileDir: opts.lockfileDir,
    projects,
    strictPeerDependencies: opts.strictPeerDependencies,
@@ -308,15 +306,6 @@ export default async function linkPackages (
  let newHoistedAliases: Record<string, string[]> = {}
  if (opts.hoistPattern && (newDepPaths.length > 0 || removedDepPaths.size > 0)) {
    newHoistedAliases = await hoist(matcher(opts.hoistPattern!), {
-      getIndependentPackageLocation: opts.independentLeaves
-        ? async (packageId: string, packageName: string) => {
-          const { dir } = await opts.storeController.getPackageLocation(packageId, packageName, {
-            lockfileDir: opts.lockfileDir,
-            targetEngine: opts.sideEffectsCacheRead && ENGINE_NAME || undefined,
-          })
-          return dir
-        }
-        : undefined,
      lockfile: currentLockfile,
      lockfileDir: opts.lockfileDir,
      modulesDir: opts.hoistedModulesDir,
@@ -501,7 +490,6 @@ async function linkAllModules (
 ) {
  return Promise.all(
    depNodes
-      .filter(({ independent }) => !independent)
      .map(async ({ children, optionalDependencies, name, modules }) => {
        const childrenToLink = opts.optional
          ? children
--- a/packages/supi/src/install/resolvePeers.ts
+++ b/packages/supi/src/install/resolvePeers.ts
@@ -31,9 +31,6 @@ export interface DependenciesGraphNode {
  resolution: Resolution,
  peripheralLocation: string,
  children: {[alias: string]: string},
-  // an independent package is a package that
-  // has neither regular nor peer dependencies
-  independent: boolean,
  optionalDependencies: Set<string>,
  depth: number,
  depPath: string,
@@ -75,7 +72,6 @@ export default function (
      id: string,
    }>,
    dependenciesTree: DependenciesTree,
-    independentLeaves: boolean,
    virtualStoreDir: string,
    lockfileDir: string,
    strictPeerDependencies: boolean,
@@ -112,7 +108,6 @@ export default function (
    resolvePeersOfChildren(directNodeIdsByAlias, pkgsByName, {
      dependenciesTree: opts.dependenciesTree,
      depGraph,
-      independentLeaves: opts.independentLeaves,
      lockfileDir: opts.lockfileDir,
      pathsByNodeId,
      purePkgs: new Set(),
@@ -149,7 +144,6 @@ function resolvePeersOfNode (
    dependenciesTree: DependenciesTree,
    pathsByNodeId: {[nodeId: string]: string},
    depGraph: DependenciesGraph,
-    independentLeaves: boolean,
    virtualStoreDir: string,
    purePkgs: Set<string>, // pure packages are those that don't rely on externally resolved peers
    rootDir: string,
@@ -216,11 +210,7 @@ function resolvePeersOfNode (

  ctx.pathsByNodeId[nodeId] = depPath
  if (!ctx.depGraph[depPath] || ctx.depGraph[depPath].depth > node.depth) {
-    const independent = ctx.independentLeaves && resolvedPackage.independent
-    const centralLocation = path.join(resolvedPackage.path, 'node_modules', resolvedPackage.name)
-    const peripheralLocation = !independent
-      ? path.join(modules, resolvedPackage.name)
-      : centralLocation
+    const peripheralLocation = path.join(modules, resolvedPackage.name)

    const unknownPeers = Object.keys(unknownResolvedPeersOfChildren)
    if (unknownPeers.length) {
@@ -244,7 +234,6 @@ function resolvePeersOfNode (
      filesIndexFile: resolvedPackage.filesIndexFile,
      hasBin: resolvedPackage.hasBin,
      hasBundledDependencies: resolvedPackage.hasBundledDependencies,
-      independent,
      installable: node.installable,
      isPure,
      modules,
@@ -270,7 +259,6 @@ function resolvePeersOfChildren (
  parentPkgs: ParentRefs,
  ctx: {
    pathsByNodeId: {[nodeId: string]: string},
-    independentLeaves: boolean,
    virtualStoreDir: string,
    purePkgs: Set<string>,
    depGraph: DependenciesGraph,
--- a/packages/supi/src/link/options.ts
+++ b/packages/supi/src/link/options.ts
@@ -28,9 +28,6 @@ interface StrictLinkOptions {

  shamefullyHoist: boolean,
  forceShamefullyHoist: boolean,
-
-  independentLeaves: boolean,
-  forceIndependentLeaves: boolean,
 }

 export type LinkOptions = Partial<StrictLinkOptions> &
@@ -58,7 +55,6 @@ async function defaults (opts: LinkOptions) {
    force: false,
    forceSharedLockfile: false,
    hoistPattern: undefined,
-    independentLeaves: false,
    lockfileDir: opts.lockfileDir || dir,
    registries: DEFAULT_REGISTRIES,
    shamefullyHoist: false,
--- a/packages/supi/test/breakingChanges.ts
+++ b/packages/supi/test/breakingChanges.ts
@@ -52,7 +52,7 @@ test("don't fail on non-compatible node_modules when forced in a workspace", asy

  process.chdir('..')

-  await fs.writeFile('node_modules/.modules.yaml', `packageManager: pnpm@${3}\nstore: ${opts.storeDir}\nindependentLeaves: false\nlayoutVersion: 1`)
+  await fs.writeFile('node_modules/.modules.yaml', `packageManager: pnpm@${3}\nstore: ${opts.storeDir}\nlayoutVersion: 1`)

  await install(manifest, { ...opts, dir: path.resolve('pkg'), lockfileDir: process.cwd() })

@@ -108,7 +108,7 @@ test('do not fail on non-compatible store when forced during named installation'

 async function saveModulesYaml (pnpmVersion: string, storeDir: string) {
  await fs.mkdir('node_modules')
-  await fs.writeFile('node_modules/.modules.yaml', `packageManager: pnpm@${pnpmVersion}\nstoreDir: ${storeDir}\nindependentLeaves: false`)
+  await fs.writeFile('node_modules/.modules.yaml', `packageManager: pnpm@${pnpmVersion}\nstoreDir: ${storeDir}`)
 }

 test(`fail on non-compatible ${WANTED_LOCKFILE}`, async (t: tape.Test) => {
--- a/packages/supi/test/install/independentLeaves.ts
+++ b/packages/supi/test/install/independentLeaves.ts
@@ -1,83 +0,0 @@
-import { prepareEmpty } from '@pnpm/prepare'
-import { REGISTRY_MOCK_PORT } from '@pnpm/registry-mock'
-import isSubdir = require('is-subdir')
-import path = require('path')
-import resolveLinkTarget = require('resolve-link-target')
-import { addDependenciesToPackage, install } from 'supi'
-import tape = require('tape')
-import promisifyTape from 'tape-promise'
-import { testDefaults } from '../utils'
-
-const test = promisifyTape(tape)
-
-test('install with --independent-leaves', async (t: tape.Test) => {
-  const project = prepareEmpty(t)
-  const manifest = await addDependenciesToPackage({}, ['pkg-with-1-dep@100.0.0'], await testDefaults({ independentLeaves: true }))
-
-  await project.has('pkg-with-1-dep')
-
-  await install(manifest, await testDefaults({ independentLeaves: true, preferFrozenLockfile: false }))
-
-  t.ok(isSubdir(path.resolve('node_modules'), await resolveLinkTarget(path.resolve('node_modules/pkg-with-1-dep'))), 'non-independent package is not symlinked directly from store')
-})
-
-test('--independent-leaves throws exception when executed on node_modules installed w/o the option', async (t: tape.Test) => {
-  const project = prepareEmpty(t)
-  const opts = await testDefaults({ independentLeaves: false })
-  const manifest = await addDependenciesToPackage({}, ['is-positive'], opts)
-
-  try {
-    await addDependenciesToPackage(manifest, ['is-negative'], {
-      ...opts,
-      forceIndependentLeaves: true,
-      independentLeaves: true,
-    })
-    t.fail('installation should have failed')
-  } catch (err) {
-    t.equal(err['code'], 'ERR_PNPM_INDEPENDENT_LEAVES_NOT_WANTED') // tslint:disable-line:no-string-literal
-    t.ok(err.message.indexOf('This modules directory was created without the --independent-leaves option.') === 0)
-  }
-
-  // Install doesn't fail if independentLeaves is not forced
-  await addDependenciesToPackage(manifest, ['is-negative'], {
-    ...opts,
-    forceIndependentLeaves: false,
-    independentLeaves: true,
-  })
-
-  await project.has('is-negative')
-})
-
-test('--no-independent-leaves throws exception when executed on node_modules installed with --independent-leaves', async (t: tape.Test) => {
-  prepareEmpty(t)
-  const manifest = await addDependenciesToPackage({}, ['is-positive'], await testDefaults({ independentLeaves: true }))
-
-  try {
-    await addDependenciesToPackage(manifest, ['is-negative'], await testDefaults({
-      forceIndependentLeaves: true,
-      independentLeaves: false,
-    }))
-    t.fail('installation should have failed')
-  } catch (err) {
-    t.equal(err['code'], 'ERR_PNPM_INDEPENDENT_LEAVES_WANTED') // tslint:disable-line:no-string-literal
-    t.ok(err.message.indexOf('This modules directory was created using the --independent-leaves option.') === 0)
-  }
-})
-
-// Covers https://github.com/pnpm/pnpm/issues/1547
-test('installing with independent-leaves and hoistPattern', async (t) => {
-  const project = prepareEmpty(t)
-  await addDependenciesToPackage({}, ['pkg-with-1-dep@100.0.0'], await testDefaults({
-    hoistPattern: '*',
-    independentLeaves: true,
-  }))
-
-  await project.has('pkg-with-1-dep')
-  await project.has('.pnpm/node_modules/dep-of-pkg-with-1-dep')
-
-  // wrappy is linked directly from the store
-  await project.hasNot(`.pnpm/dep-of-pkg-with-1-dep@100.0.0`)
-  await project.storeHas('dep-of-pkg-with-1-dep', '100.0.0')
-
-  await project.has(`.pnpm/pkg-with-1-dep@100.0.0`)
-})
--- a/packages/supi/test/install/index.ts
+++ b/packages/supi/test/install/index.ts
@@ -6,7 +6,6 @@ import './fromTarball'
 import './frozenLockfile'
 import './hoist'
 import './hooks'
-import './independentLeaves'
 import './installationChecks'
 import './lifecycleScripts'
 import './local'
--- a/packages/supi/test/unlink.ts
+++ b/packages/supi/test/unlink.ts
@@ -282,28 +282,3 @@ test("don't unlink package that is not a link", async (t: tape.Test) => {
    message: 'is-positive is not an external link',
  }), 'reported warning')
 })
-
-test("don't unlink package that is not a link when independent-leaves = true", async (t: tape.Test) => {
-  prepareEmpty(t)
-
-  const reporter = sinon.spy()
-
-  const manifest = await addDependenciesToPackage({}, ['is-positive'], await testDefaults({ independentLeaves: true }))
-
-  await mutateModules(
-    [
-      {
-        dependencyNames: ['is-positive'],
-        manifest,
-        mutation: 'unlinkSome',
-        rootDir: process.cwd(),
-      },
-    ],
-    await testDefaults({ independentLeaves: true, reporter })
-  )
-
-  t.ok(reporter.calledWithMatch({
-    level: 'warn',
-    message: 'is-positive is not an external link',
-  }), 'reported warning')
-})
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -1300,7 +1300,6 @@ importers:
      '@pnpm/core-loggers': 'link:../core-loggers'
      '@pnpm/fetcher-base': 'link:../fetcher-base'
      '@pnpm/package-requester': 'link:../package-requester'
-      '@pnpm/pkgid-to-filename': 3.0.0
      '@pnpm/resolver-base': 'link:../resolver-base'
      '@pnpm/store-controller-types': 'link:../store-controller-types'
      '@pnpm/types': 'link:../types'
@@ -1337,7 +1336,6 @@ importers:
      '@pnpm/npm-resolver': 'workspace:*'
      '@pnpm/package-requester': 'workspace:12.0.0-alpha.5'
      '@pnpm/package-store': 'link:'
-      '@pnpm/pkgid-to-filename': 3.0.0
      '@pnpm/resolver-base': 'workspace:7.0.1-alpha.0'
      '@pnpm/store-controller-types': 'workspace:8.0.0-alpha.4'
      '@pnpm/tarball-fetcher': 'workspace:*'
@@ -3862,7 +3860,6 @@ packages:
    dependencies:
      async-retry: 1.3.1
      debug: 3.2.6
-      node-fetch: 2.6.0
    dev: false
    peerDependencies:
      node-fetch: '*'
@@ -11928,7 +11925,6 @@ packages:
      diff: 4.0.2
      make-error: 1.3.6
      source-map-support: 0.5.19
-      typescript: 3.9.3
      yn: 3.1.1
    dev: true
    engines:
@@ -11978,7 +11974,6 @@ packages:
      semver: 5.7.1
      tslib: 1.13.0
      tsutils: 2.29.0_typescript@3.9.3
-      typescript: 3.9.3
    deprecated: 'TSLint has been deprecated in favor of ESLint. Please see https://github.com/palantir/tslint/issues/4534 for more information.'
    dev: true
    engines: