fca-shankar-bot 19.0.0 → 20.1.0

package/.config/npm/node_global/lib/node_modules/npm/node_modules/@npmcli/arborist/lib/arborist/build-ideal-tree.js

@@ -0,0 +1,1561 @@
+// mixin implementing the buildIdealTree method
+const localeCompare = require('@isaacs/string-locale-compare')('en')
+const rpj = require('read-package-json-fast')
+const npa = require('npm-package-arg')
+const pacote = require('pacote')
+const cacache = require('cacache')
+const { callLimit: promiseCallLimit } = require('promise-call-limit')
+const realpath = require('../../lib/realpath.js')
+const { resolve, dirname } = require('node:path')
+const treeCheck = require('../tree-check.js')
+const { readdirScoped } = require('@npmcli/fs')
+const { lstat, readlink } = require('node:fs/promises')
+const { depth } = require('treeverse')
+const { log, time } = require('proc-log')
+const { redact } = require('@npmcli/redact')
+const semver = require('semver')
+
+const {
+  OK,
+  REPLACE,
+  CONFLICT,
+} = require('../can-place-dep.js')
+const PlaceDep = require('../place-dep.js')
+
+const debug = require('../debug.js')
+const fromPath = require('../from-path.js')
+const calcDepFlags = require('../calc-dep-flags.js')
+const Shrinkwrap = require('../shrinkwrap.js')
+const { defaultLockfileVersion } = Shrinkwrap
+const Node = require('../node.js')
+const Link = require('../link.js')
+const addRmPkgDeps = require('../add-rm-pkg-deps.js')
+const optionalSet = require('../optional-set.js')
+const { checkEngine, checkPlatform } = require('npm-install-checks')
+const relpath = require('../relpath.js')
+const resetDepFlags = require('../reset-dep-flags.js')
+
+// note: some of these symbols are shared so we can hit
+// them with unit tests and reuse them across mixins
+const _updateAll = Symbol.for('updateAll')
+const _flagsSuspect = Symbol.for('flagsSuspect')
+const _setWorkspaces = Symbol.for('setWorkspaces')
+const _updateNames = Symbol.for('updateNames')
+const _resolvedAdd = Symbol.for('resolvedAdd')
+const _usePackageLock = Symbol.for('usePackageLock')
+const _rpcache = Symbol.for('realpathCache')
+const _stcache = Symbol.for('statCache')
+
+// used by Reify mixin
+const _addNodeToTrashList = Symbol.for('addNodeToTrashList')
+
+// Push items in, pop them sorted by depth and then path
+// Sorts physically shallower deps up to the front of the queue, because
+// they'll affect things deeper in, then alphabetical for consistency between
+// installs
+class DepsQueue {
+  #deps = []
+  #sorted = true
+
+  get length () {
+    return this.#deps.length
+  }
+
+  push (item) {
+    if (!this.#deps.includes(item)) {
+      this.#sorted = false
+      this.#deps.push(item)
+    }
+  }
+
+  pop () {
+    if (!this.#sorted) {
+      this.#deps.sort((a, b) => (a.depth - b.depth) || localeCompare(a.path, b.path))
+      this.#sorted = true
+    }
+    return this.#deps.shift()
+  }
+}
+
+module.exports = cls => class IdealTreeBuilder extends cls {
+  #complete
+  #currentDep = null
+  #depsQueue = new DepsQueue()
+  #depsSeen = new Set()
+  #explicitRequests = new Set()
+  #follow
+  #installStrategy
+  #linkNodes = new Set()
+  #loadFailures = new Set()
+  #manifests = new Map()
+  #mutateTree = false
+  // a map of each module in a peer set to the thing that depended on
+  // that set of peers in the first place.  Use a WeakMap so that we
+  // don't hold onto references for nodes that are garbage collected.
+  #peerSetSource = new WeakMap()
+  #preferDedupe = false
+  #prune
+  #strictPeerDeps
+  #virtualRoots = new Map()
+
+  constructor (options) {
+    super(options)
+
+    // normalize trailing slash
+    const registry = options.registry || 'https://registry.npmjs.org'
+    options.registry = this.registry = registry.replace(/\/+$/, '') + '/'
+
+    const {
+      follow = false,
+      installStrategy = 'hoisted',
+      idealTree = null,
+      installLinks = false,
+      legacyPeerDeps = false,
+      packageLock = true,
+      strictPeerDeps = false,
+      workspaces,
+      global,
+    } = options
+
+    this.#strictPeerDeps = !!strictPeerDeps
+
+    this.idealTree = idealTree
+    this.installLinks = installLinks
+    this.legacyPeerDeps = legacyPeerDeps
+
+    this[_usePackageLock] = packageLock
+    this.#installStrategy = global ? 'shallow' : installStrategy
+    this.#follow = !!follow
+
+    if (workspaces?.length && global) {
+      throw new Error('Cannot operate on workspaces in global mode')
+    }
+
+    this[_updateAll] = false
+    this[_updateNames] = []
+    this[_resolvedAdd] = []
+  }
+
+  get explicitRequests () {
+    return new Set(this.#explicitRequests)
+  }
+
+  // public method
+  async buildIdealTree (options = {}) {
+    if (this.idealTree) {
+      return this.idealTree
+    }
+
+    // allow the user to set reify options on the ctor as well.
+    // XXX: deprecate separate reify() options object.
+    options = { ...this.options, ...options }
+
+    // an empty array or any falsey value is the same as null
+    if (!options.add || options.add.length === 0) {
+      options.add = null
+    }
+    if (!options.rm || options.rm.length === 0) {
+      options.rm = null
+    }
+
+    const timeEnd = time.start('idealTree')
+
+    if (!options.add && !options.rm && !options.update && this.options.global) {
+      throw new Error('global requires add, rm, or update option')
+    }
+
+    // first get the virtual tree, if possible.  If there's a lockfile, then
+    // that defines the ideal tree, unless the root package.json is not
+    // satisfied by what the ideal tree provides.
+    // from there, we start adding nodes to it to satisfy the deps requested
+    // by the package.json in the root.
+
+    this.#parseSettings(options)
+
+    // start tracker block
+    this.addTracker('idealTree')
+
+    try {
+      await this.#initTree()
+      await this.#inflateAncientLockfile()
+      await this.#applyUserRequests(options)
+      await this.#buildDeps()
+      await this.#fixDepFlags()
+      await this.#pruneFailedOptional()
+      await this.#checkEngineAndPlatform()
+    } finally {
+      timeEnd()
+      this.finishTracker('idealTree')
+    }
+
+    return treeCheck(this.idealTree)
+  }
+
+  async #checkEngineAndPlatform () {
+    const { engineStrict, npmVersion, nodeVersion } = this.options
+    for (const node of this.idealTree.inventory.values()) {
+      if (!node.optional) {
+        try {
+          // if devEngines is present in the root node we ignore the engines check
+          if (!(node.isRoot && node.package.devEngines)) {
+            checkEngine(node.package, npmVersion, nodeVersion, this.options.force)
+          }
+        } catch (err) {
+          if (engineStrict) {
+            throw err
+          }
+          log.warn(err.code, err.message, {
+            package: err.pkgid,
+            required: err.required,
+            current: err.current,
+          })
+        }
+        checkPlatform(node.package, this.options.force)
+      }
+    }
+  }
+
+  #parseSettings (options) {
+    const update = options.update === true ? { all: true }
+      : Array.isArray(options.update) ? { names: options.update }
+      : options.update || {}
+
+    if (update.all || !Array.isArray(update.names)) {
+      update.names = []
+    }
+
+    this.#complete = !!options.complete
+    this.#preferDedupe = !!options.preferDedupe
+
+    // validates list of update names, they must
+    // be dep names only, no semver ranges are supported
+    for (const name of update.names) {
+      const spec = npa(name)
+      const validationError =
+        new TypeError(`Update arguments must only contain package names, eg:
+    npm update ${spec.name}`)
+      validationError.code = 'EUPDATEARGS'
+
+      // If they gave us anything other than a bare package name
+      if (spec.raw !== spec.name) {
+        throw validationError
+      }
+    }
+    this[_updateNames] = update.names
+
+    this[_updateAll] = update.all
+    // we prune by default unless explicitly set to boolean false
+    this.#prune = options.prune !== false
+
+    // set if we add anything, but also set here if we know we'll make
+    // changes and thus have to maybe prune later.
+    this.#mutateTree = !!(
+      options.add ||
+      options.rm ||
+      update.all ||
+      update.names.length
+    )
+  }
+
+  // load the initial tree, either the virtualTree from a shrinkwrap,
+  // or just the root node from a package.json
+  async #initTree () {
+    const timeEnd = time.start('idealTree:init')
+    let root
+    if (this.options.global) {
+      root = await this.#globalRootNode()
+    } else {
+      try {
+        const pkg = await rpj(this.path + '/package.json')
+        root = await this.#rootNodeFromPackage(pkg)
+      } catch (err) {
+        if (err.code === 'EJSONPARSE') {
+          throw err
+        }
+        root = await this.#rootNodeFromPackage({})
+      }
+    }
+    return this[_setWorkspaces](root)
+      // ok to not have a virtual tree.  probably initial install.
+      // When updating all, we load the shrinkwrap, but don't bother
+      // to build out the full virtual tree from it, since we'll be
+      // reconstructing it anyway.
+      .then(root => {
+        if (this.options.global) {
+          return root
+        } else if (!this[_usePackageLock] || this[_updateAll]) {
+          return Shrinkwrap.reset({
+            path: this.path,
+            lockfileVersion: this.options.lockfileVersion,
+            resolveOptions: this.options,
+          }).then(meta => Object.assign(root, { meta }))
+        } else {
+          return this.loadVirtual({ root })
+            .then(tree => {
+              this.#applyRootOverridesToWorkspaces(tree)
+              return tree
+            })
+        }
+      })
+
+      // if we don't have a lockfile to go from, then start with the
+      // actual tree, so we only make the minimum required changes.
+      // don't do this for global installs or updates, because in those
+      // cases we don't use a lockfile anyway.
+      // Load on a new Arborist object, so the Nodes aren't the same,
+      // or else it'll get super confusing when we change them!
+      .then(async root => {
+        if ((!this[_updateAll] && !this.options.global && !root.meta.loadedFromDisk) || (this.options.global && this[_updateNames].length)) {
+          await new this.constructor(this.options).loadActual({ root })
+          const tree = root.target
+          // even though we didn't load it from a package-lock.json FILE,
+          // we still loaded it "from disk", meaning we have to reset
+          // dep flags before assuming that any mutations were reflected.
+          if (tree.children.size) {
+            root.meta.loadedFromDisk = true
+            // set these so that we don't try to ancient lockfile reload it
+            root.meta.originalLockfileVersion = root.meta.lockfileVersion = this.options.lockfileVersion || defaultLockfileVersion
+          }
+        }
+        root.meta.inferFormattingOptions(root.package)
+        return root
+      })
+
+      .then(tree => {
+        // search the virtual tree for invalid edges, if any are found add their source to
+        // the depsQueue so that we'll fix it later
+        depth({
+          tree,
+          getChildren: (node) => {
+            const children = []
+            for (const edge of node.edgesOut.values()) {
+              children.push(edge.to)
+            }
+            return children
+          },
+          filter: node => node,
+          visit: node => {
+            for (const edge of node.edgesOut.values()) {
+              if (!edge.valid) {
+                this.#depsQueue.push(node)
+                break // no need to continue the loop after the first hit
+              }
+            }
+          },
+        })
+        // null the virtual tree, because we're about to hack away at it
+        // if you want another one, load another copy.
+        this.idealTree = tree
+        this.virtualTree = null
+        timeEnd()
+        return tree
+      })
+  }
+
+  async #globalRootNode () {
+    const root = await this.#rootNodeFromPackage({ dependencies: {} })
+    // this is a gross kludge to handle the fact that we don't save
+    // metadata on the root node in global installs, because the "root"
+    // node is something like /usr/local/lib.
+    const meta = new Shrinkwrap({
+      path: this.path,
+      lockfileVersion: this.options.lockfileVersion,
+      resolveOptions: this.options,
+    })
+    meta.reset()
+    root.meta = meta
+    return root
+  }
+
+  async #rootNodeFromPackage (pkg) {
+    // if the path doesn't exist, then we explode at this point. Note that
+    // this is not a problem for reify(), since it creates the root path
+    // before ever loading trees.
+    // TODO: make buildIdealTree() and loadActual handle a missing root path,
+    // or a symlink to a missing target, and let reify() create it as needed.
+    const real = await realpath(this.path, this[_rpcache], this[_stcache])
+    const Cls = real === this.path ? Node : Link
+    const root = new Cls({
+      path: this.path,
+      realpath: real,
+      pkg,
+      extraneous: false,
+      dev: false,
+      devOptional: false,
+      peer: false,
+      optional: false,
+      global: this.options.global,
+      installLinks: this.installLinks,
+      legacyPeerDeps: this.legacyPeerDeps,
+      loadOverrides: true,
+    })
+    if (root.isLink) {
+      root.target = new Node({
+        path: real,
+        realpath: real,
+        pkg,
+        extraneous: false,
+        dev: false,
+        devOptional: false,
+        peer: false,
+        optional: false,
+        global: this.options.global,
+        installLinks: this.installLinks,
+        legacyPeerDeps: this.legacyPeerDeps,
+        root,
+      })
+    }
+    return root
+  }
+
+  // process the add/rm requests by modifying the root node, and the
+  // update.names request by queueing nodes dependent on those named.
+  async #applyUserRequests (options) {
+    const timeEnd = time.start('idealTree:userRequests')
+    const tree = this.idealTree.target
+
+    if (!this.options.workspaces.length) {
+      await this.#applyUserRequestsToNode(tree, options)
+    } else {
+      const nodes = this.workspaceNodes(tree, this.options.workspaces)
+      if (this.options.includeWorkspaceRoot) {
+        nodes.push(tree)
+      }
+      const appliedRequests = nodes.map(
+        node => this.#applyUserRequestsToNode(node, options)
+      )
+      await Promise.all(appliedRequests)
+    }
+
+    timeEnd()
+  }
+
+  async #applyUserRequestsToNode (tree, options) {
+    // If we have a list of package names to update, and we know it's
+    // going to update them wherever they are, add any paths into those
+    // named nodes to the buildIdealTree queue.
+    if (!this.options.global && this[_updateNames].length) {
+      this.#queueNamedUpdates()
+    }
+
+    // global updates only update the globalTop nodes, but we need to know
+    // that they're there, and not reinstall the world unnecessarily.
+    const globalExplicitUpdateNames = []
+    if (this.options.global && (this[_updateAll] || this[_updateNames].length)) {
+      const nm = resolve(this.path, 'node_modules')
+      const paths = await readdirScoped(nm).catch(() => [])
+      for (const p of paths) {
+        const name = p.replace(/\\/g, '/')
+        tree.package.dependencies = tree.package.dependencies || {}
+        const updateName = this[_updateNames].includes(name)
+        if (this[_updateAll] || updateName) {
+          if (updateName) {
+            globalExplicitUpdateNames.push(name)
+          }
+          const dir = resolve(nm, name)
+          const st = await lstat(dir)
+            .catch(/* istanbul ignore next */ () => null)
+          if (st && st.isSymbolicLink()) {
+            const target = await readlink(dir)
+            const real = resolve(dirname(dir), target)
+            tree.package.dependencies[name] = `file:${real}`
+          } else {
+            tree.package.dependencies[name] = '*'
+          }
+        }
+      }
+    }
+
+    if (this.auditReport && this.auditReport.size > 0) {
+      await this.#queueVulnDependents(options)
+    }
+
+    const { add, rm } = options
+
+    if (rm && rm.length) {
+      addRmPkgDeps.rm(tree.package, rm)
+      for (const name of rm) {
+        this.#explicitRequests.add({ from: tree, name, action: 'DELETE' })
+      }
+    }
+
+    if (add && add.length) {
+      await this.#add(tree, options)
+    }
+
+    // triggers a refresh of all edgesOut.  this has to be done BEFORE
+    // adding the edges to explicitRequests, because the package setter
+    // resets all edgesOut.
+    if (add && add.length || rm && rm.length || this.options.global) {
+      tree.package = tree.package
+    }
+
+    for (const spec of this[_resolvedAdd]) {
+      if (spec.tree === tree) {
+        this.#explicitRequests.add(tree.edgesOut.get(spec.name))
+      }
+    }
+    for (const name of globalExplicitUpdateNames) {
+      this.#explicitRequests.add(tree.edgesOut.get(name))
+    }
+
+    this.#depsQueue.push(tree)
+  }
+
+  // This returns a promise because we might not have the name yet, and need to
+  // call pacote.manifest to find the name.
+  async #add (tree, { add, saveType = null, saveBundle = false }) {
+    // If we have a link it will need to be added relative to the target's path
+    const path = tree.target.path
+
+    // get the name for each of the specs in the list.
+    // ie, doing `foo@bar` we just return foo but if it's a url or git, we
+    // don't know the name until we fetch it and look in its manifest.
+    await Promise.all(add.map(async rawSpec => {
+      // We do NOT provide the path to npa here, because user-additions need to
+      // be resolved relative to the tree being added to.
+      let spec = npa(rawSpec)
+
+      // if it's just @'' then we reload whatever's there, or get latest
+      // if it's an explicit tag, we need to install that specific tag version
+      const isTag = spec.rawSpec && spec.type === 'tag'
+
+      // look up the names of file/directory/git specs
+      if (!spec.name || isTag) {
+        const mani = await pacote.manifest(spec, { ...this.options })
+        if (isTag) {
+          // translate tag to a version
+          spec = npa(`${mani.name}@${mani.version}`)
+        }
+        spec.name = mani.name
+      }
+
+      const { name } = spec
+      if (spec.type === 'file') {
+        spec = npa(`file:${relpath(path, spec.fetchSpec)}`, path)
+        spec.name = name
+      } else if (spec.type === 'directory') {
+        try {
+          const real = await realpath(spec.fetchSpec, this[_rpcache], this[_stcache])
+          spec = npa(`file:${relpath(path, real)}`, path)
+          spec.name = name
+        } catch {
+          // TODO: create synthetic test case to simulate realpath failure
+        }
+      }
+      spec.tree = tree
+      this[_resolvedAdd].push(spec)
+    }))
+
+    // now this._resolvedAdd is a list of spec objects with names.
+    // find a home for each of them!
+    addRmPkgDeps.add({
+      pkg: tree.package,
+      add: this[_resolvedAdd],
+      saveBundle,
+      saveType,
+    })
+  }
+
+  // TODO: provide a way to fix bundled deps by exposing metadata about
+  // what's in the bundle at each published manifest.  Without that, we
+  // can't possibly fix bundled deps without breaking a ton of other stuff,
+  // and leaving the user subject to getting it overwritten later anyway.
+  async #queueVulnDependents (options) {
+    for (const vuln of this.auditReport.values()) {
+      for (const node of vuln.nodes) {
+        const bundler = node.getBundler()
+
+        // XXX this belongs in the audit report itself, not here.
+        // We shouldn't even get these things here, and they shouldn't
+        // be printed by npm-audit-report as if they can be fixed, because
+        // they can't.
+        if (bundler) {
+          log.warn(`audit fix ${node.name}@${node.version}`,
+            `${node.location}\nis a bundled dependency of\n${
+            bundler.name}@${bundler.version} at ${bundler.location}\n` +
+            'It cannot be fixed automatically.\n' +
+            `Check for updates to the ${bundler.name} package.`)
+          continue
+        }
+
+        for (const edge of node.edgesIn) {
+          this.addTracker('idealTree', edge.from.name, edge.from.location)
+          this.#depsQueue.push(edge.from)
+        }
+      }
+    }
+
+    // note any that can't be fixed at the root level without --force
+    // if there's a fix, we use that.  otherwise, the user has to remove it,
+    // find a different thing, fix the upstream, etc.
+    //
+    // XXX: how to handle top nodes that aren't the root?  Maybe the report
+    // just tells the user to cd into that directory and fix it?
+    if (this.options.force && this.auditReport && this.auditReport.topVulns.size) {
+      options.add = options.add || []
+      options.rm = options.rm || []
+      const nodesTouched = new Set()
+      for (const [name, topVuln] of this.auditReport.topVulns.entries()) {
+        const {
+          simpleRange,
+          topNodes,
+          fixAvailable,
+        } = topVuln
+        for (const node of topNodes) {
+          if (!node.isProjectRoot && !node.isWorkspace) {
+            // not something we're going to fix, sorry.  have to cd into
+            // that directory and fix it yourself.
+            log.warn('audit', 'Manual fix required in linked project ' +
+              `at ./${node.location} for ${name}@${simpleRange}.\n` +
+              `'cd ./${node.location}' and run 'npm audit' for details.`)
+            continue
+          }
+
+          if (!fixAvailable) {
+            log.warn('audit', `No fix available for ${name}@${simpleRange}`)
+            continue
+          }
+
+          // name may be different if parent fixes the dep
+          // see Vuln fixAvailable setter
+          const { isSemVerMajor, version, name: fixName } = fixAvailable
+          const breakingMessage = isSemVerMajor
+            ? 'a SemVer major change'
+            : 'outside your stated dependency range'
+          log.warn('audit', `Updating ${fixName} to ${version}, ` +
+            `which is ${breakingMessage}.`)
+
+          await this.#add(node, { add: [`${fixName}@${version}`] })
+          nodesTouched.add(node)
+        }
+      }
+      for (const node of nodesTouched) {
+        node.package = node.package
+      }
+    }
+  }
+
+  #avoidRange (name) {
+    if (!this.auditReport) {
+      return null
+    }
+    const vuln = this.auditReport.get(name)
+    if (!vuln) {
+      return null
+    }
+    return vuln.range
+  }
+
+  #queueNamedUpdates () {
+    // ignore top nodes, since they are not loaded the same way, and
+    // probably have their own project associated with them.
+
+    // for every node with one of the names on the list, we add its
+    // dependents to the queue to be evaluated.  in buildDepStep,
+    // anything on the update names list will get refreshed, even if
+    // it isn't a problem.
+
+    // XXX this could be faster by doing a series of inventory.query('name')
+    // calls rather than walking over everything in the tree.
+    for (const node of this.idealTree.inventory.values()) {
+      // XXX add any invalid edgesOut to the queue
+      if (this[_updateNames].includes(node.name) &&
+        !node.isTop && !node.inDepBundle && !node.inShrinkwrap) {
+        for (const edge of node.edgesIn) {
+          this.addTracker('idealTree', edge.from.name, edge.from.location)
+          this.#depsQueue.push(edge.from)
+        }
+      }
+    }
+  }
+
+  async #inflateAncientLockfile () {
+    const { meta, inventory } = this.idealTree
+    const ancient = meta.ancientLockfile
+    const old = meta.loadedFromDisk && !(meta.originalLockfileVersion >= 2)
+
+    if (inventory.size === 0 || !ancient && !old) {
+      return
+    }
+
+    // if the lockfile is from node v5 or earlier, then we'll have to reload
+    // all the manifests of everything we encounter.  this is costly, but at
+    // least it's just a one-time hit.
+    const timeEnd = time.start('idealTree:inflate')
+
+    // don't warn if we're not gonna actually write it back anyway.
+    const heading = ancient ? 'ancient lockfile' : 'old lockfile'
+    if (ancient || !this.options.lockfileVersion ||
+        this.options.lockfileVersion >= defaultLockfileVersion) {
+      log.warn(heading,
+        `
+The ${meta.type} file was created with an old version of npm,
+so supplemental metadata must be fetched from the registry.
+
+This is a one-time fix-up, please be patient...
+`)
+    }
+
+    this.addTracker('idealTree:inflate')
+    const queue = []
+    for (const node of inventory.values()) {
+      if (node.isProjectRoot) {
+        continue
+      }
+
+      // if the node's location isn't within node_modules then this is actually
+      // a link target, so skip it. the link node itself will be queued later.
+      if (!node.location.startsWith('node_modules')) {
+        continue
+      }
+
+      queue.push(async () => {
+        log.silly('inflate', node.location)
+        const { resolved, version, path, name, location, integrity } = node
+        // don't try to hit the registry for linked deps
+        const useResolved = resolved && (
+          !version || resolved.startsWith('file:')
+        )
+        const id = useResolved ? resolved : version
+        const spec = npa.resolve(name, id, dirname(path))
+        const t = `idealTree:inflate:${location}`
+        this.addTracker(t)
+        try {
+          const mani = await pacote.manifest(spec, {
+            ...this.options,
+            resolved: resolved,
+            integrity: integrity,
+            fullMetadata: false,
+          })
+          node.package = { ...mani, _id: `${mani.name}@${mani.version}` }
+        } catch (er) {
+          const warning = `Could not fetch metadata for ${name}@${id}`
+          log.warn(heading, warning, er)
+        }
+        this.finishTracker(t)
+      })
+    }
+    await promiseCallLimit(queue)
+
+    // have to re-calc dep flags, because the nodes don't have edges
+    // until their packages get assigned, so everything looks extraneous
+    calcDepFlags(this.idealTree)
+
+    // yes, yes, this isn't the "original" version, but now that it's been
+    // upgraded, we need to make sure we don't do the work to upgrade it
+    // again, since it's now as new as can be.
+    if (!this.options.lockfileVersion && !meta.hiddenLockfile) {
+      meta.originalLockfileVersion = defaultLockfileVersion
+    }
+    this.finishTracker('idealTree:inflate')
+    timeEnd()
+  }
+
+  // at this point we have a virtual tree with the actual root node's
+  // package deps, which may be partly or entirely incomplete, invalid
+  // or extraneous.
+  #buildDeps () {
+    const timeEnd = time.start('idealTree:buildDeps')
+    const tree = this.idealTree.target
+    tree.assertRootOverrides()
+    this.#depsQueue.push(tree)
+    // XXX also push anything that depends on a node with a name
+    // in the override list
+    log.silly('idealTree', 'buildDeps')
+    this.addTracker('idealTree', tree.name, '')
+    return this.#buildDepStep().then(timeEnd)
+  }
+
+  async #buildDepStep () {
+    // removes tracker of previous dependency in the queue
+    if (this.#currentDep) {
+      const { location, name } = this.#currentDep
+      time.end(`idealTree:${location || '#root'}`)
+      this.finishTracker('idealTree', name, location)
+      this.#currentDep = null
+    }
+
+    if (!this.#depsQueue.length) {
+      return this.#resolveLinks()
+    }
+
+    const node = this.#depsQueue.pop()
+    const bd = node.package.bundleDependencies
+    const hasBundle = bd && Array.isArray(bd) && bd.length
+    const { hasShrinkwrap } = node
+
+    // if the node was already visited, or has since been removed from the
+    // tree, skip over it and process the rest of the queue.  If a node has
+    // a shrinkwrap, also skip it, because it's going to get its deps
+    // satisfied by whatever's in that file anyway.
+    if (this.#depsSeen.has(node) ||
+        node.root !== this.idealTree ||
+        hasShrinkwrap && !this.#complete) {
+      return this.#buildDepStep()
+    }
+
+    this.#depsSeen.add(node)
+    this.#currentDep = node
+    time.start(`idealTree:${node.location || '#root'}`)
+
+    // if we're loading a _complete_ ideal tree, for a --package-lock-only
+    // installation for example, we have to crack open the tarball and
+    // look inside if it has bundle deps or shrinkwraps.  note that this is
+    // not necessary during a reification, because we just update the
+    // ideal tree by reading bundles/shrinkwraps in place.
+    // Don't bother if the node is from the actual tree and hasn't
+    // been resolved, because we can't fetch it anyway, could be anything!
+    const crackOpen = this.#complete &&
+      node !== this.idealTree &&
+      node.resolved &&
+      (hasBundle || hasShrinkwrap) &&
+      !node.ideallyInert
+    if (crackOpen) {
+      const Arborist = this.constructor
+      const opt = { ...this.options }
+      await cacache.tmp.withTmp(this.cache, opt, async path => {
+        await pacote.extract(node.resolved, path, {
+          ...opt,
+          Arborist,
+          resolved: node.resolved,
+          integrity: node.integrity,
+        })
+
+        if (hasShrinkwrap) {
+          await new Arborist({ ...this.options, path })
+            .loadVirtual({ root: node })
+        }
+
+        if (hasBundle) {
+          await new Arborist({ ...this.options, path })
+            .loadActual({ root: node, ignoreMissing: true })
+        }
+      })
+    }
+
+    // if any deps are missing or invalid, then we fetch the manifest for
+    // the thing we want, and build a new dep node from that.
+    // Then, find the ideal placement for that node.  The ideal placement
+    // searches from the node's deps (or parent deps in the case of non-root
+    // peer deps), and walks up the tree until it finds the highest spot
+    // where it doesn't cause any conflicts.
+    //
+    // A conflict can be:
+    // - A node by that name already exists at that location.
+    // - The parent has a peer dep on that name
+    // - One of the node's peer deps conflicts at that location, unless the
+    //   peer dep is met by a node at that location, which is fine.
+    //
+    // If we create a new node, then build its ideal deps as well.
+    //
+    // Note: this is the same "maximally naive" deduping tree-building
+    // algorithm that npm has used since v3.  In a case like this:
+    //
+    // root -> (a@1, b@1||2)
+    // a -> (b@1)
+    //
+    // You'll end up with a tree like this:
+    //
+    // root
+    // +-- a@1
+    // |   +-- b@1
+    // +-- b@2
+    //
+    // rather than this, more deduped, but just as correct tree:
+    //
+    // root
+    // +-- a@1
+    // +-- b@1
+    //
+    // Another way to look at it is that this algorithm favors getting higher
+    // version deps at higher levels in the tree, even if that reduces
+    // potential deduplication.
+    //
+    // Set `preferDedupe: true` in the options to replace the shallower
+    // dep if allowed.
+
+    const tasks = []
+    const peerSource = this.#peerSetSource.get(node) || node
+    for (const edge of this.#problemEdges(node)) {
+      if (edge.peerConflicted) {
+        continue
+      }
+
+      // peerSetSource is only relevant when we have a peerEntryEdge
+      // otherwise we're setting regular non-peer deps as if they have
+      // a virtual root of whatever brought in THIS node.
+      // so we VR the node itself if the edge is not a peer
+      const source = edge.peer ? peerSource : node
+
+      const virtualRoot = this.#virtualRoot(source, true)
+      // reuse virtual root if we already have one, but don't
+      // try to do the override ahead of time, since we MAY be able
+      // to create a more correct tree than the virtual root could.
+      const vrEdge = virtualRoot && virtualRoot.edgesOut.get(edge.name)
+      const vrDep = vrEdge && vrEdge.valid && vrEdge.to
+      // only re-use the virtualRoot if it's a peer edge we're placing.
+      // otherwise, we end up in situations where we override peer deps that
+      // we could have otherwise found homes for.  Eg:
+      // xy -> (x, y)
+      // x -> PEER(z@1)
+      // y -> PEER(z@2)
+      // If xy is a dependency, we can resolve this like:
+      // project
+      // +-- xy
+      // |   +-- y
+      // |   +-- z@2
+      // +-- x
+      // +-- z@1
+      // But if x and y are loaded in the same virtual root, then they will
+      // be forced to agree on a version of z.
+      const required = new Set([edge.from])
+      const parent = edge.peer ? virtualRoot : null
+      const dep = vrDep && vrDep.satisfies(edge) ? vrDep
+        : await this.#nodeFromEdge(edge, parent, null, required)
+
+      /* istanbul ignore next */
+      debug(() => {
+        if (!dep) {
+          throw new Error('no dep??')
+        }
+      })
+
+      tasks.push({ edge, dep })
+    }
+
+    const placeDeps = tasks.sort((a, b) => localeCompare(a.edge.name, b.edge.name))
+
+    const promises = []
+    for (const { edge, dep } of placeDeps) {
+      const pd = new PlaceDep({
+        edge,
+        dep,
+
+        auditReport: this.auditReport,
+        explicitRequest: this.#explicitRequests.has(edge),
+        force: this.options.force,
+        installLinks: this.installLinks,
+        installStrategy: this.#installStrategy,
+        legacyPeerDeps: this.legacyPeerDeps,
+        preferDedupe: this.#preferDedupe,
+        strictPeerDeps: this.#strictPeerDeps,
+        updateNames: this[_updateNames],
+      })
+      // placing a dep is actually a tree of placing the dep itself
+      // and all of its peer group that aren't already met by the tree
+      depth({
+        tree: pd,
+        getChildren: pd => pd.children,
+        visit: pd => {
+          const { placed, edge, canPlace: cpd } = pd
+          // if we didn't place anything, nothing to do here
+          if (!placed) {
+            return
+          }
+
+          // we placed something, that means we changed the tree
+          if (placed.errors.length) {
+            this.#loadFailures.add(placed)
+          }
+          this.#mutateTree = true
+          if (cpd.canPlaceSelf === OK) {
+            for (const edgeIn of placed.edgesIn) {
+              if (edgeIn === edge) {
+                continue
+              }
+              const { from, valid, peerConflicted } = edgeIn
+              if (!peerConflicted && !valid && !this.#depsSeen.has(from)) {
+                this.addTracker('idealTree', from.name, from.location)
+                this.#depsQueue.push(edgeIn.from)
+              }
+            }
+          } else {
+            /* istanbul ignore else - should be only OK or REPLACE here */
+            if (cpd.canPlaceSelf === REPLACE) {
+              // this may also create some invalid edges, for example if we're
+              // intentionally causing something to get nested which was
+              // previously placed in this location.
+              for (const edgeIn of placed.edgesIn) {
+                if (edgeIn === edge) {
+                  continue
+                }
+
+                const { valid, peerConflicted } = edgeIn
+                if (!valid && !peerConflicted) {
+                  // if it's already been visited, we have to re-visit
+                  // otherwise, just enqueue normally.
+                  this.#depsSeen.delete(edgeIn.from)
+                  this.#depsQueue.push(edgeIn.from)
+                }
+              }
+            }
+          }
+
+          /* istanbul ignore if - should be impossible */
+          if (cpd.canPlaceSelf === CONFLICT) {
+            debug(() => {
+              const er = new Error('placed with canPlaceSelf=CONFLICT')
+              throw Object.assign(er, { placeDep: pd })
+            })
+            return
+          }
+
+          // lastly, also check for the missing deps of the node we placed,
+          // and any holes created by pruning out conflicted peer sets.
+          this.#depsQueue.push(placed)
+          for (const dep of pd.needEvaluation) {
+            this.#depsSeen.delete(dep)
+            this.#depsQueue.push(dep)
+          }
+
+          // pre-fetch any problem edges, since we'll need these soon
+          // if it fails at this point, though, dont' worry because it
+          // may well be an optional dep that has gone missing.  it'll
+          // fail later anyway.
+          for (const e of this.#problemEdges(placed)) {
+            // XXX This is somehow load bearing.  This makes tests that print
+            // the ideal tree of a tree with tarball dependencies fail. This
+            // can't be changed or removed till we figure out why
+            // The test is named "tarball deps with transitive tarball deps"
+            promises.push(() =>
+              this.#fetchManifest(npa.resolve(e.name, e.spec, fromPath(placed, e)))
+                .catch(() => null)
+            )
+          }
+        },
+      })
+    }
+
+    for (const { to } of node.edgesOut.values()) {
+      if (to && to.isLink && to.target) {
+        this.#linkNodes.add(to)
+      }
+    }
+
+    await promiseCallLimit(promises)
+    return this.#buildDepStep()
+  }
+
+  // loads a node from an edge, and then loads its peer deps (and their
+  // peer deps, on down the line) into a virtual root parent.
+  async #nodeFromEdge (edge, parent_, secondEdge, required) {
+    // create a virtual root node with the same deps as the node that
+    // is requesting this one, so that we can get all the peer deps in
+    // a context where they're likely to be resolvable.
+    // Note that the virtual root will also have virtual copies of the
+    // targets of any child Links, so that they resolve appropriately.
+    const parent = parent_ || this.#virtualRoot(edge.from)
+
+    const spec = npa.resolve(edge.name, edge.spec, edge.from.path)
+    const first = await this.#nodeFromSpec(edge.name, spec, parent, edge)
+
+    // we might have a case where the parent has a peer dependency on
+    // `foo@*` which resolves to v2, but another dep in the set has a
+    // peerDependency on `foo@1`.  In that case, if we force it to be v2,
+    // we're unnecessarily triggering an ERESOLVE.
+    // If we have a second edge to worry about, and it's not satisfied
+    // by the first node, try a second and see if that satisfies the
+    // original edge here.
+    const spec2 = secondEdge && npa.resolve(
+      edge.name,
+      secondEdge.spec,
+      secondEdge.from.path
+    )
+    const second = secondEdge && !secondEdge.valid
+      ? await this.#nodeFromSpec(edge.name, spec2, parent, secondEdge)
+      : null
+
+    // pick the second one if they're both happy with that, otherwise first
+    const node = second && edge.valid ? second : first
+    // ensure the one we want is the one that's placed
+    node.parent = parent
+
+    if (required.has(edge.from) && edge.type !== 'peerOptional' ||
+        secondEdge && (
+          required.has(secondEdge.from) && secondEdge.type !== 'peerOptional')) {
+      required.add(node)
+    }
+
+    // keep track of the thing that caused this node to be included.
+    const src = parent.sourceReference
+    this.#peerSetSource.set(node, src)
+
+    // do not load the peers along with the set if this is a global top pkg
+    // otherwise we'll be tempted to put peers as other top-level installed
+    // things, potentially clobbering what's there already, which is not
+    // what we want.  the missing edges will be picked up on the next pass.
+    if (this.options.global && edge.from.isProjectRoot) {
+      return node
+    }
+
+    // otherwise, we have to make sure that our peers can go along with us.
+    return this.#loadPeerSet(node, required)
+  }
+
+  #virtualRoot (node, reuse = false) {
+    if (reuse && this.#virtualRoots.has(node)) {
+      return this.#virtualRoots.get(node)
+    }
+
+    const vr = new Node({
+      path: node.realpath,
+      sourceReference: node,
+      installLinks: this.installLinks,
+      legacyPeerDeps: this.legacyPeerDeps,
+      overrides: node.overrides,
+    })
+
+    // also need to set up any targets from any link deps, so that
+    // they are properly reflected in the virtual environment
+    for (const child of node.children.values()) {
+      if (child.isLink) {
+        new Node({
+          path: child.realpath,
+          sourceReference: child.target,
+          root: vr,
+        })
+      }
+    }
+
+    this.#virtualRoots.set(node, vr)
+    return vr
+  }
+
+  #problemEdges (node) {
+    // skip over any bundled deps, they're not our problem.
+    // Note that this WILL fetch bundled meta-deps which are also dependencies
+    // but not listed as bundled deps.  When reifying, we first unpack any
+    // nodes that have bundleDependencies, then do a loadActual on them, move
+    // the nodes into the ideal tree, and then prune.  So, fetching those
+    // possibly-bundled meta-deps at this point doesn't cause any worse
+    // problems than a few unnecessary packument fetches.
+
+    // also skip over any nodes in the tree that failed to load, since those
+    // will crash the install later on anyway.
+    const bd = node.isProjectRoot || node.isWorkspace ? null
+      : node.package.bundleDependencies
+    const bundled = new Set(bd || [])
+
+    const problems = []
+    for (const edge of node.edgesOut.values()) {
+      // If it's included in a bundle, we take whatever is specified.
+      if (bundled.has(edge.name)) {
+        continue
+      }
+
+      // If it's already been logged as a load failure, skip it.
+      if (edge.to && this.#loadFailures.has(edge.to)) {
+        continue
+      }
+
+      // If it's shrinkwrapped, we use what the shrinkwap wants.
+      if (edge.to && edge.to.inShrinkwrap) {
+        continue
+      }
+
+      // If the edge has no destination, that's a problem, unless
+      // if it's peerOptional and not explicitly requested.
+      if (!edge.to) {
+        if (edge.type !== 'peerOptional' ||
+          this.#explicitRequests.has(edge)) {
+          problems.push(edge)
+        }
+        continue
+      }
+
+      // If the edge has an error, there's a problem.
+      if (!edge.valid) {
+        problems.push(edge)
+        continue
+      }
+
+      // If the edge is a workspace, and it's valid, leave it alone
+      if (edge.to.isWorkspace) {
+        continue
+      }
+
+      // user explicitly asked to update this package by name, problem
+      if (this[_updateNames].includes(edge.name)) {
+        problems.push(edge)
+        continue
+      }
+
+      // fixing a security vulnerability with this package, problem
+      if (this.auditReport && this.auditReport.isVulnerable(edge.to)) {
+        problems.push(edge)
+        continue
+      }
+
+      // user has explicitly asked to install this package, problem
+      if (this.#explicitRequests.has(edge)) {
+        problems.push(edge)
+        continue
+      }
+    }
+    return problems
+  }
+
+  async #fetchManifest (spec) {
+    const options = {
+      ...this.options,
+      avoid: this.#avoidRange(spec.name),
+      fullMetadata: true,
+    }
+    // get the intended spec and stored metadata from yarn.lock file,
+    // if available and valid.
+    spec = this.idealTree.meta.checkYarnLock(spec, options)
+
+    if (this.#manifests.has(spec.raw)) {
+      return this.#manifests.get(spec.raw)
+    } else {
+      log.silly('fetch manifest', spec.raw.replace(spec.rawSpec, redact(spec.rawSpec)))
+      const mani = await pacote.manifest(spec, options)
+      this.#manifests.set(spec.raw, mani)
+      return mani
+    }
+  }
+
+  #nodeFromSpec (name, spec, parent, edge) {
+    // pacote will slap integrity on its options, so we have to clone
+    // the object so it doesn't get mutated.
+    // Don't bother to load the manifest for link deps, because the target
+    // might be within another package that doesn't exist yet.
+    const { installLinks, legacyPeerDeps } = this
+    const isWorkspace = this.idealTree.workspaces && this.idealTree.workspaces.has(spec.name)
+
+    // spec is a directory, link it unless installLinks is set or it's a workspace
+    // TODO post arborist refactor, will need to check for installStrategy=linked
+    if (spec.type === 'directory' && (isWorkspace || !installLinks)) {
+      return this.#linkFromSpec(name, spec, parent, edge)
+    }
+
+    // if the spec matches a workspace name, then see if the workspace node will
+    // satisfy the edge. if it does, we return the workspace node to make sure it
+    // takes priority.
+    if (isWorkspace) {
+      const existingNode = this.idealTree.edgesOut.get(spec.name).to
+      if (existingNode && existingNode.isWorkspace && existingNode.satisfies(edge)) {
+        return existingNode
+      }
+    }
+
+    // spec isn't a directory, and either isn't a workspace or the workspace we have
+    // doesn't satisfy the edge. try to fetch a manifest and build a node from that.
+    return this.#fetchManifest(spec)
+      .then(pkg => new Node({ name, pkg, parent, installLinks, legacyPeerDeps }), error => {
+        error.requiredBy = edge.from.location || '.'
+
+        // failed to load the spec, either because of enotarget or
+        // fetch failure of some other sort.  save it so we can verify
+        // later that it's optional, otherwise the error is fatal.
+        const n = new Node({
+          name,
+          parent,
+          error,
+          installLinks,
+          legacyPeerDeps,
+        })
+        this.#loadFailures.add(n)
+        return n
+      })
+  }
+
+  #linkFromSpec (name, spec, parent) {
+    const realpath = spec.fetchSpec
+    const { installLinks, legacyPeerDeps } = this
+    return rpj(realpath + '/package.json').catch(() => ({})).then(pkg => {
+      const link = new Link({ name, parent, realpath, pkg, installLinks, legacyPeerDeps })
+      this.#linkNodes.add(link)
+      return link
+    })
+  }
+
+  // load all peer deps and meta-peer deps into the node's parent
+  // At the end of this, the node's peer-type outward edges are all
+  // resolved, and so are all of theirs, but other dep types are not.
+  // We prefer to get peer deps that meet the requiring node's dependency,
+  // if possible, since that almost certainly works (since that package was
+  // developed with this set of deps) and will typically be more restrictive.
+  // Note that the peers in the set can conflict either with each other,
+  // or with a direct dependency from the virtual root parent!  In strict
+  // mode, this is always an error.  In force mode, it never is, and we
+  // prefer the parent's non-peer dep over a peer dep, or the version that
+  // gets placed first.  In non-strict mode, we behave strictly if the
+  // virtual root is based on the root project, and allow non-peer parent
+  // deps to override, but throw if no preference can be determined.
+  async #loadPeerSet (node, required) {
+    const peerEdges = [...node.edgesOut.values()]
+      // we typically only install non-optional peers, but we have to
+      // factor them into the peerSet so that we can avoid conflicts
+      .filter(e => e.peer && !(e.valid && e.to))
+      .sort(({ name: a }, { name: b }) => localeCompare(a, b))
+
+    for (const edge of peerEdges) {
+      // already placed this one, and we're happy with it.
+      if (edge.valid && edge.to) {
+        continue
+      }
+
+      const parentEdge = node.parent.edgesOut.get(edge.name)
+      const { isProjectRoot, isWorkspace } = node.parent.sourceReference
+      const isMine = isProjectRoot || isWorkspace
+      const conflictOK = this.options.force || !isMine && !this.#strictPeerDeps
+
+      if (!edge.to) {
+        if (!parentEdge) {
+          // easy, just put the thing there
+          await this.#nodeFromEdge(edge, node.parent, null, required)
+          continue
+        } else {
+          // if the parent's edge is very broad like >=1, and the edge in
+          // question is something like 1.x, then we want to get a 1.x, not
+          // a 2.x.  pass along the child edge as an advisory guideline.
+          // if the parent edge doesn't satisfy the child edge, and the
+          // child edge doesn't satisfy the parent edge, then we have
+          // a conflict.  this is always a problem in strict mode, never
+          // in force mode, and a problem in non-strict mode if this isn't
+          // on behalf of our project.  in all such cases, we warn at least.
+          const dep = await this.#nodeFromEdge(
+            parentEdge,
+            node.parent,
+            edge,
+            required
+          )
+
+          // hooray! that worked!
+          if (edge.valid) {
+            continue
+          }
+
+          // allow it.  either we're overriding, or it's not something
+          // that will be installed by default anyway, and we'll fail when
+          // we get to the point where we need to, if we need to.
+          if (conflictOK || !required.has(dep)) {
+            edge.peerConflicted = true
+            continue
+          }
+
+          // problem
+          this.#failPeerConflict(edge, parentEdge)
+        }
+      }
+
+      // There is something present already, and we're not happy about it
+      // See if the thing we WOULD be happy with is also going to satisfy
+      // the other dependents on the current node.
+      const current = edge.to
+      const dep = await this.#nodeFromEdge(edge, null, null, required)
+      if (dep.canReplace(current)) {
+        await this.#nodeFromEdge(edge, node.parent, null, required)
+        continue
+      }
+
+      // at this point we know that there is a dep there, and
+      // we don't like it.  always fail strictly, always allow forcibly or
+      // in non-strict mode if it's not our fault.  don't warn here, because
+      // we are going to warn again when we place the deps, if we end up
+      // overriding for something else.  If the thing that has this dep
+      // isn't also required, then there's a good chance we won't need it,
+      // so allow it for now and let it conflict if it turns out to actually
+      // be necessary for the installation.
+      if (conflictOK || !required.has(edge.from)) {
+        continue
+      }
+
+      // ok, it's the root, or we're in unforced strict mode, so this is bad
+      this.#failPeerConflict(edge, parentEdge)
+    }
+    return node
+  }
+
+  #failPeerConflict (edge, currentEdge) {
+    const expl = this.#explainPeerConflict(edge, currentEdge)
+    throw Object.assign(new Error('unable to resolve dependency tree'), expl)
+  }
+
+  #explainPeerConflict (edge, currentEdge) {
+    const node = edge.from
+    const curNode = node.resolve(edge.name)
+    const current = curNode.explain()
+    return {
+      code: 'ERESOLVE',
+      current,
+      // it SHOULD be impossible to get here without a current node in place,
+      // but this at least gives us something report on when bugs creep into
+      // the tree handling logic.
+      currentEdge: currentEdge ? currentEdge.explain() : null,
+      edge: edge.explain(),
+      strictPeerDeps: this.#strictPeerDeps,
+      force: this.options.force,
+    }
+  }
+
+  // go through all the links in the this.#linkNodes set
+  // for each one:
+  // - if outside the root, ignore it, assume it's fine, it's not our problem
+  // - if a node in the tree already, assign the target to that node.
+  // - if a path under an existing node, then assign that as the fsParent,
+  //   and add it to the _depsQueue
+  //
+  // call buildDepStep if anything was added to the queue, otherwise we're done
+  #resolveLinks () {
+    for (const link of this.#linkNodes) {
+      this.#linkNodes.delete(link)
+
+      // link we never ended up placing, skip it
+      if (link.root !== this.idealTree) {
+        continue
+      }
+
+      const tree = this.idealTree.target
+      const external = !link.target.isDescendantOf(tree)
+
+      // outside the root, somebody else's problem, ignore it
+      if (external && !this.#follow) {
+        continue
+      }
+
+      // didn't find a parent for it or it has not been seen yet
+      // so go ahead and process it.
+      const unseenLink = (link.target.parent || link.target.fsParent) &&
+        !this.#depsSeen.has(link.target)
+
+      if (this.#follow &&
+          !link.target.parent &&
+          !link.target.fsParent ||
+          unseenLink) {
+        this.addTracker('idealTree', link.target.name, link.target.location)
+        this.#depsQueue.push(link.target)
+      }
+    }
+
+    if (this.#depsQueue.length) {
+      return this.#buildDepStep()
+    }
+  }
+
+  #fixDepFlags () {
+    const timeEnd = time.start('idealTree:fixDepFlags')
+    const metaFromDisk = this.idealTree.meta.loadedFromDisk
+    const flagsSuspect = this[_flagsSuspect]
+    const mutateTree = this.#mutateTree
+    // if the options set prune:false, then we don't prune, but we still
+    // mark the extraneous items in the tree if we modified it at all.
+    // If we did no modifications, we just iterate over the extraneous nodes.
+    // if we started with an empty tree, then the dep flags are already
+    // all set to true, and there can be nothing extraneous, so there's
+    // nothing to prune, because we built it from scratch.  if we didn't
+    // add or remove anything, then also nothing to do.
+    if (metaFromDisk && mutateTree) {
+      resetDepFlags(this.idealTree)
+    }
+
+    // update all the dev/optional/etc flags in the tree
+    // either we started with a fresh tree, or we
+    // reset all the flags to find the extraneous nodes.
+    //
+    // if we started from a blank slate, or changed something, then
+    // the dep flags will be all set to true.
+    if (!metaFromDisk || mutateTree) {
+      calcDepFlags(this.idealTree)
+    } else {
+      // otherwise just unset all the flags on the root node
+      // since they will sometimes have the default value
+      this.idealTree.extraneous = false
+      this.idealTree.dev = false
+      this.idealTree.optional = false
+      this.idealTree.devOptional = false
+      this.idealTree.peer = false
+    }
+
+    // at this point, any node marked as extraneous should be pruned.
+    // if we started from a shrinkwrap, and then added/removed something,
+    // then the tree is suspect.  Prune what is marked as extraneous.
+    // otherwise, don't bother.
+    const needPrune = metaFromDisk && (mutateTree || flagsSuspect)
+    if (this.#prune && needPrune) {
+      this.#idealTreePrune()
+      for (const node of this.idealTree.inventory.values()) {
+        if (node.extraneous) {
+          node.parent = null
+        }
+      }
+    }
+
+    timeEnd()
+  }
+
+  #applyRootOverridesToWorkspaces (tree) {
+    const rootOverrides = tree.root.package.overrides || {}
+
+    for (const node of tree.root.inventory.values()) {
+      if (!node.isWorkspace) {
+        continue
+      }
+
+      for (const depName of Object.keys(rootOverrides)) {
+        const edge = node.edgesOut.get(depName)
+        const rootNode = tree.root.children.get(depName)
+
+        // safely skip if either edge or rootNode doesn't exist yet
+        if (!edge || !rootNode) {
+          continue
+        }
+
+        const resolvedRootVersion = rootNode.package.version
+        if (!semver.satisfies(resolvedRootVersion, edge.spec)) {
+          edge.detach()
+          node.children.delete(depName)
+        }
+      }
+    }
+  }
+
+  #idealTreePrune () {
+    for (const node of this.idealTree.inventory.values()) {
+      if (node.extraneous) {
+        node.parent = null
+      }
+    }
+  }
+
+  #pruneFailedOptional () {
+    for (const node of this.#loadFailures) {
+      if (!node.optional) {
+        throw node.errors[0]
+      }
+
+      const set = optionalSet(node)
+      for (const node of set) {
+        node.ideallyInert = true
+      }
+    }
+  }
+
+  async prune (options = {}) {
+    // allow the user to set options on the ctor as well.
+    // XXX: deprecate separate method options objects.
+    options = { ...this.options, ...options }
+
+    await this.buildIdealTree(options)
+
+    this.#idealTreePrune()
+
+    if (!this.options.workspacesEnabled) {
+      const excludeNodes = this.excludeWorkspacesDependencySet(this.idealTree)
+      for (const node of this.idealTree.inventory.values()) {
+        if (
+          node.parent !== null
+          && !node.isProjectRoot
+          && !excludeNodes.has(node)
+          && !node.ideallyInert
+        ) {
+          this[_addNodeToTrashList](node)
+        }
+      }
+    }
+
+    return this.reify(options)
+  }
+}