@nirvana-labs/nirvana 1.31.0 → 1.32.0

package/oidc/node_modules/npm/node_modules/@npmcli/arborist/lib/arborist/reify.js

@@ -0,0 +1,1516 @@
+// mixin implementing the reify method
+const PackageJson = require('@npmcli/package-json')
+const hgi = require('hosted-git-info')
+const npa = require('npm-package-arg')
+const packageContents = require('@npmcli/installed-package-contents')
+const pacote = require('pacote')
+const promiseAllRejectLate = require('promise-all-reject-late')
+const runScript = require('@npmcli/run-script')
+const { callLimit: promiseCallLimit } = require('promise-call-limit')
+const { depth: dfwalk } = require('treeverse')
+const { dirname, resolve, relative, join } = require('node:path')
+const { log, time } = require('proc-log')
+const { lstat, mkdir, rm, symlink } = require('node:fs/promises')
+const { moveFile } = require('@npmcli/fs')
+const { subset, intersects } = require('semver')
+const { walkUp } = require('walk-up-path')
+
+const AuditReport = require('../audit-report.js')
+const Diff = require('../diff.js')
+const calcDepFlags = require('../calc-dep-flags.js')
+const debug = require('../debug.js')
+const onExit = require('../signal-handling.js')
+const optionalSet = require('../optional-set.js')
+const relpath = require('../relpath.js')
+const retirePath = require('../retire-path.js')
+const treeCheck = require('../tree-check.js')
+const { defaultLockfileVersion } = require('../shrinkwrap.js')
+const { saveTypeMap, hasSubKey } = require('../add-rm-pkg-deps.js')
+
+// Part of steps (steps need refactoring before we can do anything about these)
+const _retireShallowNodes = Symbol.for('retireShallowNodes')
+const _loadBundlesAndUpdateTrees = Symbol.for('loadBundlesAndUpdateTrees')
+const _submitQuickAudit = Symbol('submitQuickAudit')
+const _unpackNewModules = Symbol.for('unpackNewModules')
+const _build = Symbol.for('build')
+
+// shared by rebuild mixin
+const _trashList = Symbol.for('trashList')
+const _handleOptionalFailure = Symbol.for('handleOptionalFailure')
+const _loadTrees = Symbol.for('loadTrees')
+// defined by rebuild mixin
+const _checkBins = Symbol.for('checkBins')
+
+// shared symbols for swapping out when testing
+// TODO tests should not be this deep into internals
+const _diffTrees = Symbol.for('diffTrees')
+const _createSparseTree = Symbol.for('createSparseTree')
+const _loadShrinkwrapsAndUpdateTrees = Symbol.for('loadShrinkwrapsAndUpdateTrees')
+const _reifyNode = Symbol.for('reifyNode')
+const _updateAll = Symbol.for('updateAll')
+const _updateNames = Symbol.for('updateNames')
+const _moveContents = Symbol.for('moveContents')
+const _moveBackRetiredUnchanged = Symbol.for('moveBackRetiredUnchanged')
+const _removeTrash = Symbol.for('removeTrash')
+const _renamePath = Symbol.for('renamePath')
+const _rollbackRetireShallowNodes = Symbol.for('rollbackRetireShallowNodes')
+const _rollbackCreateSparseTree = Symbol.for('rollbackCreateSparseTree')
+const _rollbackMoveBackRetiredUnchanged = Symbol.for('rollbackMoveBackRetiredUnchanged')
+const _saveIdealTree = Symbol.for('saveIdealTree')
+const _reifyPackages = Symbol.for('reifyPackages')
+
+// defined by build-ideal-tree mixin
+const _resolvedAdd = Symbol.for('resolvedAdd')
+const _usePackageLock = Symbol.for('usePackageLock')
+// used by build-ideal-tree mixin
+const _addNodeToTrashList = Symbol.for('addNodeToTrashList')
+
+const _createIsolatedTree = Symbol.for('createIsolatedTree')
+
+module.exports = cls => class Reifier extends cls {
+  #bundleMissing = new Set() // child nodes we'd EXPECT to be included in a bundle, but aren't
+  #bundleUnpacked = new Set() // the nodes we unpack to read their bundles
+  #dryRun
+  #nmValidated = new Set()
+  #omit
+  #retiredPaths = {}
+  #retiredUnchanged = {}
+  #savePrefix
+  #shrinkwrapInflated = new Set()
+  #sparseTreeDirs = new Set()
+  #sparseTreeRoots = new Set()
+
+  constructor (options) {
+    super(options)
+
+    this[_trashList] = new Set()
+  }
+
+  // public method
+  async reify (options = {}) {
+    const linked = (options.installStrategy || this.options.installStrategy) === 'linked'
+
+    if (this.options.packageLockOnly && this.options.global) {
+      const er = new Error('cannot generate lockfile for global packages')
+      er.code = 'ESHRINKWRAPGLOBAL'
+      throw er
+    }
+
+    this.#omit = new Set(options.omit)
+
+    // start tracker block
+    this.addTracker('reify')
+    const timeEnd = time.start('reify')
+    // don't create missing dirs on dry runs
+    if (!this.options.packageLockOnly && !this.options.dryRun) {
+      // we do NOT want to set ownership on this folder, especially
+      // recursively, because it can have other side effects to do that
+      // in a project directory.  We just want to make it if it's missing.
+      await mkdir(resolve(this.path), { recursive: true })
+
+      // do not allow the top-level node_modules to be a symlink
+      await this.#validateNodeModules(resolve(this.path, 'node_modules'))
+    }
+    await this[_loadTrees](options)
+
+    const oldTree = this.idealTree
+    if (linked) {
+      // swap out the tree with the isolated tree
+      // this is currently technical debt which will be resolved in a refactor
+      // of Node/Link trees
+      log.warn('reify', 'The "linked" install strategy is EXPERIMENTAL and may contain bugs.')
+      this.idealTree = await this[_createIsolatedTree]()
+    }
+    await this[_diffTrees]()
+    await this[_reifyPackages]()
+    if (linked) {
+      // swap back in the idealTree
+      // so that the lockfile is preserved
+      this.idealTree = oldTree
+    }
+    await this[_saveIdealTree](options)
+    // clean inert
+    for (const node of this.idealTree.inventory.values()) {
+      if (node.inert) {
+        node.parent = null
+      }
+    }
+    // clean up any trash that is still in the tree
+    for (const path of this[_trashList]) {
+      const loc = relpath(this.idealTree.realpath, path)
+      const node = this.idealTree.inventory.get(loc)
+      if (node && node.root === this.idealTree) {
+        node.parent = null
+      }
+    }
+
+    // if we filtered to only certain nodes, then anything ELSE needs
+    // to be untouched in the resulting actual tree, even if it differs
+    // in the idealTree.  Copy over anything that was in the actual and
+    // was not changed, delete anything in the ideal and not actual.
+    // Then we move the entire idealTree over to this.actualTree, and
+    // save the hidden lockfile.
+    if (this.diff && this.diff.filterSet.size) {
+      const reroot = new Set()
+
+      const { filterSet } = this.diff
+      const seen = new Set()
+      for (const [loc, ideal] of this.idealTree.inventory.entries()) {
+        seen.add(loc)
+
+        // if it's an ideal node from the filter set, then skip it
+        // because we already made whatever changes were necessary
+        if (filterSet.has(ideal)) {
+          continue
+        }
+
+        // otherwise, if it's not in the actualTree, then it's not a thing
+        // that we actually added.  And if it IS in the actualTree, then
+        // it's something that we left untouched, so we need to record
+        // that.
+        const actual = this.actualTree.inventory.get(loc)
+        if (!actual) {
+          ideal.root = null
+        } else {
+          if ([...actual.linksIn].some(link => filterSet.has(link))) {
+            seen.add(actual.location)
+            continue
+          }
+          const { realpath, isLink } = actual
+          if (isLink && ideal.isLink && ideal.realpath === realpath) {
+            continue
+          } else {
+            reroot.add(actual)
+          }
+        }
+      }
+
+      // now find any actual nodes that may not be present in the ideal
+      // tree, but were left behind by virtue of not being in the filter
+      for (const [loc, actual] of this.actualTree.inventory.entries()) {
+        if (seen.has(loc)) {
+          continue
+        }
+        seen.add(loc)
+
+        // we know that this is something that ISN'T in the idealTree,
+        // or else we will have addressed it in the previous loop.
+        // If it's in the filterSet, that means we intentionally removed
+        // it, so nothing to do here.
+        if (filterSet.has(actual)) {
+          continue
+        }
+
+        reroot.add(actual)
+      }
+
+      // go through the rerooted actual nodes, and move them over.
+      for (const actual of reroot) {
+        actual.root = this.idealTree
+      }
+
+      // prune out any tops that lack a linkIn, they are no longer relevant.
+      for (const top of this.idealTree.tops) {
+        if (top.linksIn.size === 0) {
+          top.root = null
+        }
+      }
+
+      // need to calculate dep flags, since nodes may have been marked
+      // as extraneous or otherwise incorrect during transit.
+      calcDepFlags(this.idealTree)
+    }
+
+    // save the ideal's meta as a hidden lockfile after we actualize it
+    this.idealTree.meta.filename =
+      this.idealTree.realpath + '/node_modules/.package-lock.json'
+    this.idealTree.meta.hiddenLockfile = true
+    this.idealTree.meta.lockfileVersion = defaultLockfileVersion
+
+    this.actualTree = this.idealTree
+    this.idealTree = null
+
+    if (!this.options.global) {
+      await this.actualTree.meta.save()
+      const ignoreScripts = !!this.options.ignoreScripts
+      // if we aren't doing a dry run or ignoring scripts and we actually made changes to the dep
+      // tree, then run the dependencies scripts
+      if (!this.options.dryRun && !ignoreScripts && this.diff && this.diff.children.length) {
+        const { path, package: pkg } = this.actualTree.target
+        const stdio = this.options.foregroundScripts ? 'inherit' : 'pipe'
+        const { scripts = {} } = pkg
+        for (const event of ['predependencies', 'dependencies', 'postdependencies']) {
+          if (Object.prototype.hasOwnProperty.call(scripts, event)) {
+            log.info('run', pkg._id, event, scripts[event])
+            await time.start(`reify:run:${event}`, () => runScript({
+              event,
+              path,
+              pkg,
+              stdio,
+              scriptShell: this.options.scriptShell,
+            }))
+          }
+        }
+      }
+    }
+    // This is a very bad pattern and I can't wait to stop doing it
+    this.auditReport = await this.auditReport
+
+    this.finishTracker('reify')
+    timeEnd()
+    return treeCheck(this.actualTree)
+  }
+
+  async [_reifyPackages] () {
+    // we don't submit the audit report or write to disk on dry runs
+    if (this.options.dryRun) {
+      return
+    }
+
+    if (this.options.packageLockOnly) {
+      // we already have the complete tree, so just audit it now,
+      // and that's all we have to do here.
+      return this[_submitQuickAudit]()
+    }
+
+    // ok, we're about to start touching the fs.  need to roll back
+    // if we get an early termination.
+    let reifyTerminated = null
+    const removeHandler = onExit(({ signal }) => {
+      // only call once.  if signal hits twice, we just terminate
+      removeHandler()
+      reifyTerminated = Object.assign(new Error('process terminated'), {
+        signal,
+      })
+      return false
+    })
+
+    // [rollbackfn, [...actions]]
+    // after each step, if the process was terminated, execute the rollback
+    // note that each rollback *also* calls the previous one when it's
+    // finished, and then the first one throws the error, so we only need
+    // a new rollback step when we have a new thing that must be done to
+    // revert the install.
+    const steps = [
+      [_rollbackRetireShallowNodes, [
+        _retireShallowNodes,
+      ]],
+      [_rollbackCreateSparseTree, [
+        _createSparseTree,
+        _loadShrinkwrapsAndUpdateTrees,
+        _loadBundlesAndUpdateTrees,
+        _submitQuickAudit,
+        _unpackNewModules,
+      ]],
+      [_rollbackMoveBackRetiredUnchanged, [
+        _moveBackRetiredUnchanged,
+        _build,
+      ]],
+    ]
+    for (const [rollback, actions] of steps) {
+      for (const action of actions) {
+        try {
+          await this[action]()
+          if (reifyTerminated) {
+            throw reifyTerminated
+          }
+        } catch (er) {
+          // TODO rollbacks shouldn't be relied on to throw err
+          await this[rollback](er)
+          /* istanbul ignore next - rollback throws, should never hit this */
+          throw er
+        }
+      }
+    }
+
+    // no rollback for this one, just exit with the error, since the
+    // install completed and can't be safely recovered at this point.
+    await this[_removeTrash]()
+    if (reifyTerminated) {
+      throw reifyTerminated
+    }
+
+    // done modifying the file system, no need to keep listening for sigs
+    removeHandler()
+  }
+
+  // when doing a local install, we load everything and figure it all out.
+  // when doing a global install, we *only* care about the explicit requests.
+  [_loadTrees] (options) {
+    const timeEnd = time.start('reify:loadTrees')
+    const bitOpt = {
+      ...options,
+      complete: this.options.packageLockOnly || this.options.dryRun,
+    }
+
+    // if we're only writing a package lock, then it doesn't matter what's here
+    if (this.options.packageLockOnly) {
+      return this.buildIdealTree(bitOpt).then(timeEnd)
+    }
+
+    const actualOpt = this.options.global ? {
+      ignoreMissing: true,
+      global: true,
+      filter: (node, kid) => {
+        // if it's not the project root, and we have no explicit requests,
+        // then we're already into a nested dep, so we keep it
+        if (this.explicitRequests.size === 0 || !node.isProjectRoot) {
+          return true
+        }
+
+        // if we added it as an edgeOut, then we want it
+        if (this.idealTree.edgesOut.has(kid)) {
+          return true
+        }
+
+        // if it's an explicit request, then we want it
+        const hasExplicit = [...this.explicitRequests]
+          .some(edge => edge.name === kid)
+        if (hasExplicit) {
+          return true
+        }
+
+        // ignore the rest of the global install folder
+        return false
+      },
+    } : { ignoreMissing: true }
+
+    if (!this.options.global) {
+      return Promise.all([
+        this.loadActual(actualOpt),
+        this.buildIdealTree(bitOpt),
+      ]).then(timeEnd)
+    }
+
+    // the global install space tends to have a lot of stuff in it.  don't
+    // load all of it, just what we care about.  we won't be saving a
+    // hidden lockfile in there anyway.  Note that we have to load ideal
+    // BEFORE loading actual, so that the actualOpt can use the
+    // explicitRequests which is set during buildIdealTree
+    return this.buildIdealTree(bitOpt)
+      .then(() => this.loadActual(actualOpt))
+      .then(timeEnd)
+  }
+
+  [_diffTrees] () {
+    if (this.options.packageLockOnly) {
+      return
+    }
+
+    const timeEnd = time.start('reify:diffTrees')
+    // XXX if we have an existing diff already, there should be a way
+    // to just invalidate the parts that changed, but avoid walking the
+    // whole tree again.
+
+    const includeWorkspaces = this.options.workspacesEnabled
+    const includeRootDeps = !includeWorkspaces
+      || this.options.includeWorkspaceRoot && this.options.workspaces.length > 0
+
+    const filterNodes = []
+    if (this.options.global && this.explicitRequests.size) {
+      const idealTree = this.idealTree.target
+      const actualTree = this.actualTree.target
+      // we ONLY are allowed to make changes in the global top-level
+      // children where there's an explicit request.
+      for (const { name } of this.explicitRequests) {
+        const ideal = idealTree.children.get(name)
+        if (ideal) {
+          filterNodes.push(ideal)
+        }
+        const actual = actualTree.children.get(name)
+        if (actual) {
+          filterNodes.push(actual)
+        }
+      }
+    } else {
+      if (includeWorkspaces) {
+        // add all ws nodes to filterNodes
+        for (const ws of this.options.workspaces) {
+          const ideal = this.idealTree.children.get(ws)
+          if (ideal) {
+            filterNodes.push(ideal)
+          }
+          const actual = this.actualTree.children.get(ws)
+          if (actual) {
+            filterNodes.push(actual)
+          }
+        }
+      }
+      if (includeRootDeps) {
+        // add all non-workspace nodes to filterNodes
+        for (const tree of [this.idealTree, this.actualTree]) {
+          for (const { type, to } of tree.edgesOut.values()) {
+            if (type !== 'workspace' && to) {
+              filterNodes.push(to)
+            }
+          }
+        }
+      }
+    }
+
+    // find all the nodes that need to change between the actual
+    // and ideal trees.
+    this.diff = Diff.calculate({
+      omit: this.#omit,
+      shrinkwrapInflated: this.#shrinkwrapInflated,
+      filterNodes,
+      actual: this.actualTree,
+      ideal: this.idealTree,
+    })
+
+    // we don't have to add 'removed' folders to the trashlist, because
+    // they'll be moved aside to a retirement folder, and then the retired
+    // folder will be deleted at the end.  This is important when we have
+    // a folder like FOO being "removed" in favor of a folder like "foo",
+    // because if we remove node_modules/FOO on case-insensitive systems,
+    // it will remove the dep that we *want* at node_modules/foo.
+
+    timeEnd()
+  }
+
+  // add the node and all its bins to the list of things to be
+  // removed later on in the process.  optionally, also mark them
+  // as a retired paths, so that we move them out of the way and
+  // replace them when rolling back on failure.
+  [_addNodeToTrashList] (node, retire = false) {
+    const paths = [node.path, ...node.binPaths]
+    const moves = this.#retiredPaths
+    log.silly('reify', 'mark', retire ? 'retired' : 'deleted', paths)
+    for (const path of paths) {
+      if (retire) {
+        const retired = retirePath(path)
+        moves[path] = retired
+        this[_trashList].add(retired)
+      } else {
+        this[_trashList].add(path)
+      }
+    }
+  }
+
+  // move aside the shallowest nodes in the tree that have to be
+  // changed or removed, so that we can rollback if necessary.
+  [_retireShallowNodes] () {
+    const timeEnd = time.start('reify:retireShallow')
+    const moves = this.#retiredPaths = {}
+    for (const diff of this.diff.children) {
+      if (diff.action === 'CHANGE' || diff.action === 'REMOVE') {
+        // we'll have to clean these up at the end, so add them to the list
+        this[_addNodeToTrashList](diff.actual, true)
+      }
+    }
+    log.silly('reify', 'moves', moves)
+    const movePromises = Object.entries(moves)
+      .map(([from, to]) => this[_renamePath](from, to))
+    return promiseAllRejectLate(movePromises).then(timeEnd)
+  }
+
+  [_renamePath] (from, to, didMkdirp = false) {
+    return moveFile(from, to)
+      .catch(er => {
+        // Occasionally an expected bin file might not exist in the package,
+        // or a shim/symlink might have been moved aside.  If we've already
+        // handled the most common cause of ENOENT (dir doesn't exist yet),
+        // then just ignore any ENOENT.
+        if (er.code === 'ENOENT') {
+          return didMkdirp ? null : mkdir(dirname(to), { recursive: true }).then(() =>
+            this[_renamePath](from, to, true))
+        } else if (er.code === 'EEXIST') {
+          return rm(to, { recursive: true, force: true }).then(() => moveFile(from, to))
+        } else {
+          throw er
+        }
+      })
+  }
+
+  [_rollbackRetireShallowNodes] (er) {
+    const timeEnd = time.start('reify:rollback:retireShallow')
+    const moves = this.#retiredPaths
+    const movePromises = Object.entries(moves)
+      .map(([from, to]) => this[_renamePath](to, from))
+    return promiseAllRejectLate(movePromises)
+      // ignore subsequent rollback errors
+      .catch(() => {})
+      .then(timeEnd)
+      .then(() => {
+        throw er
+      })
+  }
+
+  [_createSparseTree] () {
+    const timeEnd = time.start('reify:createSparse')
+    // if we call this fn again, we look for the previous list
+    // so that we can avoid making the same directory multiple times
+    const leaves = this.diff.leaves
+      .filter(diff => {
+        return (diff.action === 'ADD' || diff.action === 'CHANGE') &&
+          !this.#sparseTreeDirs.has(diff.ideal.path) &&
+          !diff.ideal.isLink
+      })
+      .map(diff => diff.ideal)
+
+    // we check this in parallel, so guard against multiple attempts to
+    // retire the same path at the same time.
+    const dirsChecked = new Set()
+    return promiseAllRejectLate(leaves.map(async node => {
+      for (const d of walkUp(node.path)) {
+        if (d === node.top.path) {
+          break
+        }
+        if (dirsChecked.has(d)) {
+          continue
+        }
+        dirsChecked.add(d)
+        const st = await lstat(d).catch(() => null)
+        // this can happen if we have a link to a package with a name
+        // that the filesystem treats as if it is the same thing.
+        // would be nice to have conditional istanbul ignores here...
+        /* istanbul ignore next - defense in depth */
+        if (st && !st.isDirectory()) {
+          const retired = retirePath(d)
+          this.#retiredPaths[d] = retired
+          this[_trashList].add(retired)
+          await this[_renamePath](d, retired)
+        }
+      }
+      this.#sparseTreeDirs.add(node.path)
+      const made = await mkdir(node.path, { recursive: true })
+      // if the directory already exists, made will be undefined. if that's the case
+      // we don't want to remove it because we aren't the ones who created it so we
+      // omit it from the #sparseTreeRoots
+      if (made) {
+        this.#sparseTreeRoots.add(made)
+      }
+    })).then(timeEnd)
+  }
+
+  [_rollbackCreateSparseTree] (er) {
+    const timeEnd = time.start('reify:rollback:createSparse')
+    // cut the roots of the sparse tree that were created, not the leaves
+    const roots = this.#sparseTreeRoots
+    // also delete the moves that we retired, so that we can move them back
+    const failures = []
+    const targets = [...roots, ...Object.keys(this.#retiredPaths)]
+    const unlinks = targets
+      .map(path => rm(path, { recursive: true, force: true }).catch(er => failures.push([path, er])))
+    return promiseAllRejectLate(unlinks).then(() => {
+      // eslint-disable-next-line promise/always-return
+      if (failures.length) {
+        log.warn('cleanup', 'Failed to remove some directories', failures)
+      }
+    })
+      .then(timeEnd)
+      .then(() => this[_rollbackRetireShallowNodes](er))
+  }
+
+  // shrinkwrap nodes define their dependency branches with a file, so
+  // we need to unpack them, read that shrinkwrap file, and then update
+  // the tree by calling loadVirtual with the node as the root.
+  [_loadShrinkwrapsAndUpdateTrees] () {
+    const seen = this.#shrinkwrapInflated
+    const shrinkwraps = this.diff.leaves
+      .filter(d => (d.action === 'CHANGE' || d.action === 'ADD' || !d.action) &&
+        d.ideal.hasShrinkwrap && !seen.has(d.ideal) &&
+        !this[_trashList].has(d.ideal.path))
+
+    if (!shrinkwraps.length) {
+      return
+    }
+
+    const timeEnd = time.start('reify:loadShrinkwraps')
+
+    const Arborist = this.constructor
+    return promiseAllRejectLate(shrinkwraps.map(diff => {
+      const node = diff.ideal
+      seen.add(node)
+      return diff.action ? this[_reifyNode](node) : node
+    }))
+      .then(nodes => promiseAllRejectLate(nodes.map(node => new Arborist({
+        ...this.options,
+        path: node.path,
+      }).loadVirtual({ root: node }))))
+      // reload the diff and sparse tree because the ideal tree changed
+      .then(() => this[_diffTrees]())
+      .then(() => this[_createSparseTree]())
+      .then(() => this[_loadShrinkwrapsAndUpdateTrees]())
+      .then(timeEnd)
+  }
+
+  // create a symlink for Links, extract for Nodes
+  // return the node object, since we usually want that
+  // handle optional dep failures here
+  // If reifying fails, and the node is optional, add it and its optionalSet
+  // to the trash list
+  // Always return the node.
+  [_reifyNode] (node) {
+    const timeEnd = time.start(`reifyNode:${node.location}`)
+    this.addTracker('reify', node.name, node.location)
+
+    const p = Promise.resolve().then(async () => {
+      await this[_checkBins](node)
+      await this.#extractOrLink(node)
+      const { _id, deprecated } = node.package
+      // The .catch is in _handleOptionalFailure.  Not ideal, this should be cleaned up.
+      // eslint-disable-next-line promise/always-return
+      if (deprecated) {
+        log.warn('deprecated', `${_id}: ${deprecated}`)
+      }
+    })
+
+    return this[_handleOptionalFailure](node, p)
+      .then(() => {
+        this.finishTracker('reify', node.name, node.location)
+        timeEnd()
+        return node
+      })
+  }
+
+  // do not allow node_modules to be a symlink
+  async #validateNodeModules (nm) {
+    if (this.options.force || this.#nmValidated.has(nm)) {
+      return
+    }
+    const st = await lstat(nm).catch(() => null)
+    if (!st || st.isDirectory()) {
+      this.#nmValidated.add(nm)
+      return
+    }
+    log.warn('reify', 'Removing non-directory', nm)
+    await rm(nm, { recursive: true, force: true })
+  }
+
+  async #extractOrLink (node) {
+    const nm = resolve(node.parent.path, 'node_modules')
+    await this.#validateNodeModules(nm)
+
+    if (!node.isLink) {
+      // in normal cases, node.resolved should *always* be set by now.
+      // however, it is possible when a lockfile is damaged, or very old,
+      // or in some other race condition bugs in npm v6, that a previously
+      // bundled dependency will have just a version, but no resolved value,
+      // and no 'bundled: true' setting.
+      // Do the best with what we have, or else remove it from the tree
+      // entirely, since we can't possibly reify it.
+      let res = null
+      if (node.resolved) {
+        const registryResolved = this.#registryResolved(node.resolved)
+        if (registryResolved) {
+          res = `${node.name}@${registryResolved}`
+        }
+      } else if (node.package.name && node.version) {
+        res = `${node.package.name}@${node.version}`
+      }
+
+      // no idea what this thing is.  remove it from the tree.
+      if (!res) {
+        const warning = 'invalid or damaged lockfile detected\n' +
+          'please re-try this operation once it completes\n' +
+          'so that the damage can be corrected, or perform\n' +
+          'a fresh install with no lockfile if the problem persists.'
+        log.warn('reify', warning)
+        log.verbose('reify', 'unrecognized node in tree', node.path)
+        node.parent = null
+        node.fsParent = null
+        this[_addNodeToTrashList](node)
+        return
+      }
+      await debug(async () => {
+        const st = await lstat(node.path).catch(() => null)
+        if (st && !st.isDirectory()) {
+          debug.log('unpacking into a non-directory', node)
+          throw Object.assign(new Error('ENOTDIR: not a directory'), {
+            code: 'ENOTDIR',
+            path: node.path,
+          })
+        }
+      })
+      await pacote.extract(res, node.path, {
+        ...this.options,
+        resolved: node.resolved,
+        integrity: node.integrity,
+      })
+      // store nodes don't use Node class so node.package doesn't get updated
+      if (node.isInStore) {
+        const { content: pkg } = await PackageJson.normalize(node.path)
+        node.package.scripts = pkg.scripts
+      }
+      return
+    }
+
+    // node.isLink
+    await rm(node.path, { recursive: true, force: true })
+
+    // symlink
+    const dir = dirname(node.path)
+    const target = node.realpath
+
+    let rel
+    if (node.resolved?.startsWith('file:')) {
+      rel = this.#calculateRelativePath(node, dir, target, nm)
+    } else {
+      rel = relative(dir, target)
+    }
+
+    await mkdir(dir, { recursive: true })
+    return symlink(rel, node.path, 'junction')
+  }
+
+  // if the node is optional, then the failure of the promise is nonfatal
+  // just add it and its optional set to the trash list.
+  [_handleOptionalFailure] (node, p) {
+    return (node.optional ? p.catch(() => {
+      const set = optionalSet(node)
+      for (const node of set) {
+        log.verbose('reify', 'failed optional dependency', node.path)
+        node.inert = true
+        this[_addNodeToTrashList](node)
+      }
+    }) : p).then(() => node)
+  }
+
+  #calculateRelativePath (node, dir, target) {
+    // Check if the node is affected by a root override
+    let hasRootOverride = [...node.edgesIn].some(edge => edge.from.isRoot && edge.overrides)
+    // If not set via edges, see if the root package.json explicitly lists an override
+    if (!hasRootOverride && node.root) {
+      const rootPackage = node.root.target
+      hasRootOverride = !!(rootPackage &&
+        rootPackage.package.overrides &&
+        rootPackage.package.overrides[node.name])
+    }
+    if (!hasRootOverride) {
+      return relative(dir, target)
+    }
+    // If an override is detected, attempt to retrieve the override spec from the root package.json
+    const overrideSpec = node.root?.target?.package?.overrides?.[node.name]
+    if (typeof overrideSpec === 'string' && overrideSpec.startsWith('file:')) {
+      const overridePath = overrideSpec.replace(/^file:/, '')
+      const rootDir = node.root.target.path
+      return relative(dir, resolve(rootDir, overridePath))
+    }
+
+    // Fallback: derive the file path from node.resolved in a platform-agnostic way
+    const filePath = node.resolved.replace(/^file:/, '')
+    return join(filePath)
+  }
+
+  #registryResolved (resolved) {
+    // the default registry url is a magic value meaning "the currently
+    // configured registry".
+    // `resolved` must never be falsey.
+    //
+    // XXX: use a magic string that isn't also a valid value, like
+    // ${REGISTRY} or something.  This has to be threaded through the
+    // Shrinkwrap and Node classes carefully, so for now, just treat
+    // the default reg as the magical animal that it has been.
+    try {
+      const resolvedURL = hgi.parseUrl(resolved)
+
+      if ((this.options.replaceRegistryHost === resolvedURL.hostname) ||
+           this.options.replaceRegistryHost === 'always') {
+        const registryURL = new URL(this.registry)
+
+        // Replace the host with the registry host while keeping the path intact
+        resolvedURL.hostname = registryURL.hostname
+        resolvedURL.port = registryURL.port
+        resolvedURL.protocol = registryURL.protocol
+
+        // Make sure we don't double-include the path if it's already there
+        const registryPath = registryURL.pathname.replace(/\/$/, '')
+
+        if (registryPath && registryPath !== '/' && !resolvedURL.pathname.startsWith(registryPath)) {
+          // Since hostname is changed, we need to ensure the registry path is included
+          resolvedURL.pathname = registryPath + resolvedURL.pathname
+        }
+
+        return resolvedURL.toString()
+      }
+      return resolved
+    } catch (e) {
+      // if we could not parse the url at all then returning nothing
+      // here means it will get removed from the tree in the next step
+      return undefined
+    }
+  }
+
+  // bundles are *sort of* like shrinkwraps, in that the branch is defined
+  // by the contents of the package.  however, in their case, rather than
+  // shipping a virtual tree that must be reified, they ship an entire
+  // reified actual tree that must be unpacked and not modified.
+  [_loadBundlesAndUpdateTrees] (depth = 0, bundlesByDepth) {
+    let maxBundleDepth
+    if (!bundlesByDepth) {
+      bundlesByDepth = new Map()
+      maxBundleDepth = -1
+      dfwalk({
+        tree: this.diff,
+        visit: diff => {
+          const node = diff.ideal
+          if (!node) {
+            return
+          }
+          if (node.isProjectRoot) {
+            return
+          }
+
+          const { bundleDependencies } = node.package
+          if (bundleDependencies && bundleDependencies.length) {
+            maxBundleDepth = Math.max(maxBundleDepth, node.depth)
+            if (!bundlesByDepth.has(node.depth)) {
+              bundlesByDepth.set(node.depth, [node])
+            } else {
+              bundlesByDepth.get(node.depth).push(node)
+            }
+          }
+        },
+        getChildren: diff => diff.children,
+      })
+
+      bundlesByDepth.set('maxBundleDepth', maxBundleDepth)
+    } else {
+      maxBundleDepth = bundlesByDepth.get('maxBundleDepth')
+    }
+
+    if (depth === 0) {
+      time.start('reify:loadBundles')
+    }
+
+    if (depth > maxBundleDepth) {
+      // if we did something, then prune the tree and update the diffs
+      if (maxBundleDepth !== -1) {
+        this.#pruneBundledMetadeps(bundlesByDepth)
+        this[_diffTrees]()
+      }
+      time.end('reify:loadBundles')
+      return
+    }
+
+    // skip any that have since been removed from the tree, eg by a
+    // shallower bundle overwriting them with a bundled meta-dep.
+    const set = (bundlesByDepth.get(depth) || [])
+      .filter(node => node.root === this.idealTree &&
+        node.target !== node.root &&
+        !this[_trashList].has(node.path))
+
+    if (!set.length) {
+      return this[_loadBundlesAndUpdateTrees](depth + 1, bundlesByDepth)
+    }
+
+    // extract all the nodes with bundles
+    return promiseCallLimit(set.map(node => {
+      return () => {
+        this.#bundleUnpacked.add(node)
+        return this[_reifyNode](node)
+      }
+    }), { rejectLate: true })
+    // then load their unpacked children and move into the ideal tree
+      .then(nodes =>
+        promiseAllRejectLate(nodes.map(async node => {
+          const arb = new this.constructor({
+            ...this.options,
+            path: node.path,
+          })
+          const notTransplanted = new Set(node.children.keys())
+          await arb.loadActual({
+            root: node,
+            // don't transplant any sparse folders we created
+            // loadActual will set node.package to {} for empty directories
+            // if by chance there are some empty folders in the node_modules
+            // tree for some other reason, then ok, ignore those too.
+            transplantFilter: node => {
+              if (node.package._id) {
+                // it's actually in the bundle if it gets transplanted
+                notTransplanted.delete(node.name)
+                return true
+              } else {
+                return false
+              }
+            },
+          })
+          for (const name of notTransplanted) {
+            this.#bundleMissing.add(node.children.get(name))
+          }
+        })))
+    // move onto the next level of bundled items
+      .then(() => this[_loadBundlesAndUpdateTrees](depth + 1, bundlesByDepth))
+  }
+
+  // https://github.com/npm/cli/issues/1597#issuecomment-667639545
+  #pruneBundledMetadeps (bundlesByDepth) {
+    const bundleShadowed = new Set()
+
+    // Example dep graph:
+    // root -> (a, c)
+    // a -> BUNDLE(b)
+    // b -> c
+    // c -> b
+    //
+    // package tree:
+    // root
+    // +-- a
+    // |   +-- b(1)
+    // |   +-- c(1)
+    // +-- b(2)
+    // +-- c(2)
+    // 1. mark everything that's shadowed by anything in the bundle.  This
+    //    marks b(2) and c(2).
+    // 2. anything with edgesIn from outside the set, mark not-extraneous,
+    //    remove from set.  This unmarks c(2).
+    // 3. continue until no change
+    // 4. remove everything in the set from the tree.  b(2) is pruned
+
+    // create the list of nodes shadowed by children of bundlers
+    for (const bundles of bundlesByDepth.values()) {
+      // skip the 'maxBundleDepth' item
+      if (!Array.isArray(bundles)) {
+        continue
+      }
+      for (const node of bundles) {
+        for (const name of node.children.keys()) {
+          const shadow = node.parent.resolve(name)
+          if (!shadow) {
+            continue
+          }
+          bundleShadowed.add(shadow)
+          shadow.extraneous = true
+        }
+      }
+    }
+
+    // lib -> (a@1.x) BUNDLE(a@1.2.3 (b@1.2.3))
+    // a@1.2.3 -> (b@1.2.3)
+    // a@1.3.0 -> (b@2)
+    // b@1.2.3 -> ()
+    // b@2 -> (c@2)
+    //
+    // root
+    // +-- lib
+    // |   +-- a@1.2.3
+    // |   +-- b@1.2.3
+    // +-- b@2 <-- shadowed, now extraneous
+    // +-- c@2 <-- also shadowed, because only dependent is shadowed
+    for (const shadow of bundleShadowed) {
+      for (const shadDep of shadow.edgesOut.values()) {
+        /* istanbul ignore else - pretty unusual situation, just being
+         * defensive here. Would mean that a bundled dep has a dependency
+         * that is unmet. which, weird, but if you bundle it, we take
+         * whatever you put there and assume the publisher knows best. */
+        if (shadDep.to) {
+          bundleShadowed.add(shadDep.to)
+          shadDep.to.extraneous = true
+        }
+      }
+    }
+
+    let changed
+    do {
+      changed = false
+      for (const shadow of bundleShadowed) {
+        for (const edge of shadow.edgesIn) {
+          if (!bundleShadowed.has(edge.from)) {
+            shadow.extraneous = false
+            bundleShadowed.delete(shadow)
+            changed = true
+            break
+          }
+        }
+      }
+    } while (changed)
+
+    for (const shadow of bundleShadowed) {
+      this[_addNodeToTrashList](shadow)
+      shadow.root = null
+    }
+  }
+
+  async [_submitQuickAudit] () {
+    if (this.options.audit === false) {
+      this.auditReport = null
+      return
+    }
+
+    // we submit the quick audit at this point in the process, as soon as
+    // we have all the deps resolved, so that it can overlap with the other
+    // actions as much as possible.  Stash the promise, which we resolve
+    // before finishing the reify() and returning the tree.  Thus, we do
+    // NOT return the promise, as the intent is for this to run in parallel
+    // with the reification, and be resolved at a later time.
+    const timeEnd = time.start('reify:audit')
+    const options = { ...this.options }
+    const tree = this.idealTree
+
+    // if we're operating on a workspace, only audit the workspace deps
+    if (this.options.workspaces.length) {
+      options.filterSet = this.workspaceDependencySet(
+        tree,
+        this.options.workspaces,
+        this.options.includeWorkspaceRoot
+      )
+    }
+
+    this.auditReport = AuditReport.load(tree, options).then(res => {
+      timeEnd()
+      return res
+    })
+  }
+
+  // ok!  actually unpack stuff into their target locations!
+  // The sparse tree has already been created, so we walk the diff
+  // kicking off each unpack job.  If any fail, we rm the sparse
+  // tree entirely and try to put everything back where it was.
+  [_unpackNewModules] () {
+    const timeEnd = time.start('reify:unpack')
+    const unpacks = []
+    dfwalk({
+      tree: this.diff,
+      visit: diff => {
+        // no unpacking if we don't want to change this thing
+        if (diff.action !== 'CHANGE' && diff.action !== 'ADD') {
+          return
+        }
+
+        const node = diff.ideal
+        const bd = this.#bundleUnpacked.has(node)
+        const sw = this.#shrinkwrapInflated.has(node)
+        const bundleMissing = this.#bundleMissing.has(node)
+
+        // check whether we still need to unpack this one.
+        // test the inDepBundle last, since that's potentially a tree walk.
+        const doUnpack = node && // can't unpack if removed!
+          // root node already exists
+          !node.isRoot &&
+          // already unpacked to read bundle
+          !bd &&
+          // already unpacked to read sw
+          !sw &&
+          // already unpacked by another dep's bundle
+          (bundleMissing || !node.inDepBundle)
+
+        if (doUnpack) {
+          unpacks.push(this[_reifyNode](node))
+        }
+      },
+      getChildren: diff => diff.children,
+    })
+    return promiseAllRejectLate(unpacks).then(timeEnd)
+  }
+
+  // This is the part where we move back the unchanging nodes that were
+  // the children of a node that did change.  If this fails, the rollback
+  // is a three-step process.  First, we try to move the retired unchanged
+  // nodes BACK to their retirement folders, then delete the sparse tree,
+  // then move everything out of retirement.
+  [_moveBackRetiredUnchanged] () {
+    // get a list of all unchanging children of any shallow retired nodes
+    // if they are not the ancestor of any node in the diff set, then the
+    // directory won't already exist, so just rename it over.
+    // This is sort of an inverse diff tree, of all the nodes where
+    // the actualTree and idealTree _don't_ differ, starting from the
+    // shallowest nodes that we moved aside in the first place.
+    const timeEnd = time.start('reify:unretire')
+    const moves = this.#retiredPaths
+    this.#retiredUnchanged = {}
+    return promiseAllRejectLate(this.diff.children.map(diff => {
+      // skip if nothing was retired
+      if (diff.action !== 'CHANGE' && diff.action !== 'REMOVE') {
+        return
+      }
+
+      const { path: realFolder } = diff.actual
+      const retireFolder = moves[realFolder]
+      /* istanbul ignore next - should be impossible */
+      debug(() => {
+        if (!retireFolder) {
+          const er = new Error('trying to un-retire but not retired')
+          throw Object.assign(er, {
+            realFolder,
+            retireFolder,
+            actual: diff.actual,
+            ideal: diff.ideal,
+            action: diff.action,
+          })
+        }
+      })
+
+      this.#retiredUnchanged[retireFolder] = []
+      return promiseAllRejectLate(diff.unchanged.map(node => {
+        // no need to roll back links, since we'll just delete them anyway
+        if (node.isLink) {
+          return mkdir(dirname(node.path), { recursive: true, force: true })
+            .then(() => this[_reifyNode](node))
+        }
+
+        // will have been moved/unpacked along with bundler
+        if (node.inDepBundle && !this.#bundleMissing.has(node)) {
+          return
+        }
+
+        this.#retiredUnchanged[retireFolder].push(node)
+
+        const rel = relative(realFolder, node.path)
+        const fromPath = resolve(retireFolder, rel)
+        // if it has bundleDependencies, then make node_modules.  otherwise
+        // skip it.
+        const bd = node.package.bundleDependencies
+        const dir = bd && bd.length ? node.path + '/node_modules' : node.path
+        return mkdir(dir, { recursive: true }).then(() => this[_moveContents](node, fromPath))
+      }))
+    })).then(timeEnd)
+  }
+
+  // move the contents from the fromPath to the node.path
+  [_moveContents] (node, fromPath) {
+    return packageContents({
+      path: fromPath,
+      depth: 1,
+      packageJsonCache: new Map([[fromPath + '/package.json', node.package]]),
+    }).then(res => promiseAllRejectLate(res.map(path => {
+      const rel = relative(fromPath, path)
+      const to = resolve(node.path, rel)
+      return this[_renamePath](path, to)
+    })))
+  }
+
+  [_rollbackMoveBackRetiredUnchanged] (er) {
+    const moves = this.#retiredPaths
+    // flip the mapping around to go back
+    const realFolders = new Map(Object.entries(moves).map(([k, v]) => [v, k]))
+    const promises = Object.entries(this.#retiredUnchanged)
+      .map(([retireFolder, nodes]) => promiseAllRejectLate(nodes.map(node => {
+        const realFolder = realFolders.get(retireFolder)
+        const rel = relative(realFolder, node.path)
+        const fromPath = resolve(retireFolder, rel)
+        return this[_moveContents]({ ...node, path: fromPath }, node.path)
+      })))
+    return promiseAllRejectLate(promises)
+      .then(() => this[_rollbackCreateSparseTree](er))
+  }
+
+  [_build] () {
+    const timeEnd = time.start('reify:build')
+
+    // for all the things being installed, run their appropriate scripts
+    // run in tip->root order, so as to be more likely to build a node's
+    // deps before attempting to build it itself
+    const nodes = []
+    dfwalk({
+      tree: this.diff,
+      leave: diff => {
+        if (!diff.ideal.isProjectRoot) {
+          nodes.push(diff.ideal)
+        }
+      },
+      // process adds before changes, ignore removals
+      getChildren: diff => diff && diff.children,
+      filter: diff => diff.action === 'ADD' || diff.action === 'CHANGE',
+    })
+
+    // pick up link nodes from the unchanged list as we want to run their
+    // scripts in every install despite of having a diff status change
+    for (const node of this.diff.unchanged) {
+      const tree = node.root.target
+
+      // skip links that only live within node_modules as they are most
+      // likely managed by packages we installed, we only want to rebuild
+      // unchanged links we directly manage
+      const linkedFromRoot = (node.parent === tree && !node.inert) || node.target.fsTop === tree
+      if (node.isLink && linkedFromRoot) {
+        nodes.push(node)
+      }
+    }
+
+    return this.rebuild({ nodes, handleOptionalFailure: true }).then(timeEnd)
+  }
+
+  // the tree is pretty much built now, so it's cleanup time.
+  // remove the retired folders, and any deleted nodes
+  // If this fails, there isn't much we can do but tell the user about it.
+  // Thankfully, it's pretty unlikely that it'll fail, since rm is a node builtin.
+  async [_removeTrash] () {
+    const timeEnd = time.start('reify:trash')
+    const promises = []
+    const failures = []
+    const _rm = path => rm(path, { recursive: true, force: true }).catch(er => failures.push([path, er]))
+
+    for (const path of this[_trashList]) {
+      promises.push(_rm(path))
+    }
+
+    await promiseAllRejectLate(promises)
+    if (failures.length) {
+      log.warn('cleanup', 'Failed to remove some directories', failures)
+    }
+
+    timeEnd()
+  }
+
+  // last but not least, we save the ideal tree metadata to the package-lock
+  // or shrinkwrap file, and any additions or removals to package.json
+  async [_saveIdealTree] (options) {
+    // the ideal tree is actualized now, hooray!
+    // it still contains all the references to optional nodes that were removed
+    // for install failures.  Those still end up in the shrinkwrap, so we
+    // save it first, then prune out the optional trash, and then return it.
+
+    const save = !(options.save === false)
+
+    // we check for updates in order to make sure we run save ideal tree
+    // even though save=false since we want `npm update` to be able to
+    // write to package-lock files by default
+    const hasUpdates = this[_updateAll] || this[_updateNames].length
+
+    // we're going to completely skip save ideal tree in case of a global or
+    // dry-run install and also if the save option is set to false, EXCEPT for
+    // update since the expected behavior for npm7+ is for update to
+    // NOT save to package.json, we make that exception since we still want
+    // saveIdealTree to be able to write the lockfile by default.
+    const saveIdealTree = !(
+      (!save && !hasUpdates)
+      || this.options.global
+      || this.options.dryRun
+    )
+
+    if (!saveIdealTree) {
+      return false
+    }
+
+    const timeEnd = time.start('reify:save')
+
+    const updatedTrees = new Set()
+    const updateNodes = nodes => {
+      for (const { name, tree: addTree } of nodes) {
+        // addTree either the root, or a workspace
+        const edge = addTree.edgesOut.get(name)
+        const pkg = addTree.package
+        const req = npa.resolve(name, edge.spec, addTree.realpath)
+        const { rawSpec, subSpec } = req
+
+        const spec = subSpec ? subSpec.rawSpec : rawSpec
+        const child = edge.to
+
+        // if we tried to install an optional dep, but it was a version
+        // that we couldn't resolve, this MAY be missing.  if we haven't
+        // blown up by now, it's because it was not a problem, though, so
+        // just move on.
+        if (!child || !addTree.isTop) {
+          continue
+        }
+
+        let newSpec
+        // True if the dependency is getting installed from a local file path
+        // In this case it is not possible to do the normal version comparisons
+        // as the new version will be a file path
+        const isLocalDep = req.type === 'directory' || req.type === 'file'
+        if (req.registry) {
+          const version = child.version
+          const prefixRange = version ? this.options.savePrefix + version : '*'
+          // if we installed a range, then we save the range specified
+          // if it is not a subset of the ^x.y.z.  eg, installing a range
+          // of `1.x <1.2.3` will not be saved as `^1.2.0`, because that
+          // would allow versions outside the requested range.  Tags and
+          // specific versions save with the save-prefix.
+          const isRange = (subSpec || req).type === 'range'
+
+          let range = spec
+          if (
+            !isRange ||
+            spec === '*' ||
+            subset(prefixRange, spec, { loose: true })
+          ) {
+            range = prefixRange
+          }
+
+          const pname = child.packageName
+          const alias = name !== pname
+          newSpec = alias ? `npm:${pname}@${range}` : range
+        } else if (req.hosted) {
+          // save the git+https url if it has auth; otherwise, shortcut
+          const h = req.hosted
+          const opt = { noCommittish: false }
+          if (h.https && h.auth) {
+            newSpec = `git+${h.https(opt)}`
+          } else {
+            newSpec = h.shortcut(opt)
+          }
+        } else if (isLocalDep) {
+          // when finding workspace nodes, make sure that
+          // we save them using their version instead of
+          // using their relative path
+          if (edge.type === 'workspace') {
+            const { version } = edge.to.target
+            const prefixRange = version ? this.options.savePrefix + version : '*'
+            newSpec = prefixRange
+          } else {
+            // save the relative path in package.json
+            // Normally saveSpec is updated with the proper relative
+            // path already, but it's possible to specify a full absolute
+            // path initially, in which case we can end up with the wrong
+            // thing, so just get the ultimate fetchSpec and relativize it.
+            const p = req.fetchSpec.replace(/^file:/, '')
+            const rel = relpath(addTree.realpath, p)
+            newSpec = `file:${rel}`
+          }
+        } else {
+          newSpec = req.saveSpec
+        }
+
+        if (options.saveType) {
+          const depType = saveTypeMap.get(options.saveType)
+          pkg[depType][name] = newSpec
+          // PackageJson.normalize will have moved it here if it was in both, if it is empty it will be deleted later
+          if (options.saveType === 'prod' && pkg.optionalDependencies) {
+            delete pkg.optionalDependencies[name]
+          }
+        } else {
+          if (hasSubKey(pkg, 'dependencies', name)) {
+            pkg.dependencies[name] = newSpec
+          }
+
+          if (hasSubKey(pkg, 'devDependencies', name)) {
+            pkg.devDependencies[name] = newSpec
+            // don't update peer or optional if we don't have to
+            if (hasSubKey(pkg, 'peerDependencies', name) && (isLocalDep || !intersects(newSpec, pkg.peerDependencies[name]))) {
+              pkg.peerDependencies[name] = newSpec
+            }
+
+            if (hasSubKey(pkg, 'optionalDependencies', name) && (isLocalDep || !intersects(newSpec, pkg.optionalDependencies[name]))) {
+              pkg.optionalDependencies[name] = newSpec
+            }
+          } else {
+            if (hasSubKey(pkg, 'peerDependencies', name)) {
+              pkg.peerDependencies[name] = newSpec
+            }
+
+            if (hasSubKey(pkg, 'optionalDependencies', name)) {
+              pkg.optionalDependencies[name] = newSpec
+            }
+          }
+        }
+
+        updatedTrees.add(addTree)
+      }
+    }
+
+    // Returns true if any of the edges from this node has a semver
+    // range definition that is an exact match to the version installed
+    // e.g: should return true if for a given and installed version 1.0.0,
+    // range is either =1.0.0 or 1.0.0
+    const exactVersion = node => {
+      for (const edge of node.edgesIn) {
+        try {
+          if (subset(edge.spec, node.version)) {
+            return false
+          }
+        } catch {
+          // ignore errors
+        }
+      }
+      return true
+    }
+
+    // helper that retrieves an array of nodes that were
+    // potentially updated during the reify process, in order
+    // to limit the number of nodes to check and update, only
+    // select nodes from the inventory that are direct deps
+    // of a given package.json (project root or a workspace)
+    // and in ase of using a list of `names`, restrict nodes
+    // to only names that are found in this list
+    const retrieveUpdatedNodes = names => {
+      const filterDirectDependencies = node =>
+        !node.isRoot && node.resolveParent && node.resolveParent.isRoot
+        && (!names || names.includes(node.name))
+        && exactVersion(node) // skip update for exact ranges
+
+      const directDeps = this.idealTree.inventory
+        .filter(filterDirectDependencies)
+
+      // traverses the list of direct dependencies and collect all nodes
+      // to be updated, since any of them might have changed during reify
+      const nodes = []
+      for (const node of directDeps) {
+        for (const edgeIn of node.edgesIn) {
+          nodes.push({
+            name: node.name,
+            tree: edgeIn.from.target,
+          })
+        }
+      }
+      return nodes
+    }
+
+    if (save) {
+      // when using update all alongside with save, we'll make
+      // sure to refresh every dependency of the root idealTree
+      if (this[_updateAll]) {
+        const nodes = retrieveUpdatedNodes()
+        updateNodes(nodes)
+      } else {
+        // resolvedAdd is the list of user add requests, but with names added
+        // to things like git repos and tarball file/urls.  However, if the
+        // user requested 'foo@', and we have a foo@file:../foo, then we should
+        // end up saving the spec we actually used, not whatever they gave us.
+        if (this[_resolvedAdd].length) {
+          updateNodes(this[_resolvedAdd])
+        }
+
+        // if updating given dependencies by name, restrict the list of
+        // nodes to check to only those currently in _updateNames
+        if (this[_updateNames].length) {
+          const nodes = retrieveUpdatedNodes(this[_updateNames])
+          updateNodes(nodes)
+        }
+
+        // grab any from explicitRequests that had deps removed
+        for (const { from: tree } of this.explicitRequests) {
+          updatedTrees.add(tree)
+        }
+      }
+    }
+
+    if (save) {
+      for (const tree of updatedTrees) {
+        // refresh the edges so they have the correct specs
+        tree.package = tree.package
+        const pkgJson = await PackageJson.load(tree.path, { create: true })
+        const {
+          dependencies = {},
+          devDependencies = {},
+          optionalDependencies = {},
+          peerDependencies = {},
+          // bundleDependencies is not required by PackageJson like the other
+          // fields here PackageJson also doesn't omit an empty array for this
+          // field so defaulting this to an empty array would add that field to
+          // every package.json file.
+          bundleDependencies,
+        } = tree.package
+
+        pkgJson.update({
+          dependencies,
+          devDependencies,
+          optionalDependencies,
+          peerDependencies,
+          bundleDependencies,
+        })
+        await pkgJson.save()
+      }
+    }
+
+    // before now edge specs could be changing, affecting the `requires` field
+    // in the package lock, so we hold off saving to the very last action
+    if (this[_usePackageLock]) {
+      // preserve indentation, if possible
+      let format = this.idealTree.package[Symbol.for('indent')]
+      if (format === undefined) {
+        format = '  '
+      }
+
+      // TODO this ignores options.save
+      await this.idealTree.meta.save({
+        format: (this.options.formatPackageLock && format) ? format
+        : this.options.formatPackageLock,
+      })
+    }
+
+    timeEnd()
+    return true
+  }
+}