fix: deps of linked deps in package-lock

When having optional dependencies of a dependency of
a top-level link dependency, e.g:

    root -> LINK(a)
    a -> (b)
    b -> OPTIONAL(c)

    * c marked as extraneous

Any optional dependency (and all its nested nodes) were marked
as extraneous in package-lock due to `calcDepFlags` missing
properly following the target of Link nodes.

This changeset fixes it by properly following the result of the
`treeverse.visit` method that will have already followed any
link targets at that point.

Fixes: npm/cli#2505

lib/calc-dep-flags.js

@@ -11,7 +11,7 @@ const calcDepFlags = (tree, resetRoot = true) => {
     tree,
     visit: node => calcDepFlagsStep(node),
     filter: node => node,
-    getChildren: node => [...node.edgesOut.values()].map(edge => edge.to),
+    getChildren: (node, tree) => [...tree.edgesOut.values()].map(edge => edge.to),
   })
   return ret
 }

tap-snapshots/test-arborist-build-ideal-tree.js-TAP.test.js

@@ -5,6 +5,99 @@
  * Make sure to inspect the output below.  Do not ignore changes!
  */
 'use strict'
+exports[`test/arborist/build-ideal-tree.js TAP a direct link dep has a dep with optional dependencies > should not mark children of the optional dep as extraneous 1`] = `
+ArboristNode {
+  "children": Map {
+    "a" => ArboristLink {
+      "edgesIn": Set {
+        EdgeIn {
+          "from": "",
+          "name": "a",
+          "spec": "./a",
+          "type": "prod",
+        },
+      },
+      "location": "node_modules/a",
+      "name": "a",
+      "path": "{CWD}/test/fixtures/link-dep-has-dep-with-optional-dep/node_modules/a",
+      "realpath": "{CWD}/test/fixtures/link-dep-has-dep-with-optional-dep/a",
+      "resolved": "file:../a",
+      "target": Object {
+        "location": "a",
+      },
+      "version": "1.0.0",
+    },
+    "graceful-fs" => ArboristNode {
+      "edgesIn": Set {
+        EdgeIn {
+          "from": "node_modules/rimraf",
+          "name": "graceful-fs",
+          "spec": "~2",
+          "type": "optional",
+        },
+      },
+      "location": "node_modules/graceful-fs",
+      "name": "graceful-fs",
+      "optional": true,
+      "path": "{CWD}/test/fixtures/link-dep-has-dep-with-optional-dep/node_modules/graceful-fs",
+      "resolved": "https://registry.npmjs.org/graceful-fs/-/graceful-fs-2.0.3.tgz",
+      "version": "2.0.3",
+    },
+    "rimraf" => ArboristNode {
+      "edgesIn": Set {
+        EdgeIn {
+          "from": "a",
+          "name": "rimraf",
+          "spec": "2.2.4",
+          "type": "prod",
+        },
+      },
+      "edgesOut": Map {
+        "graceful-fs" => EdgeOut {
+          "name": "graceful-fs",
+          "spec": "~2",
+          "to": "node_modules/graceful-fs",
+          "type": "optional",
+        },
+      },
+      "location": "node_modules/rimraf",
+      "name": "rimraf",
+      "path": "{CWD}/test/fixtures/link-dep-has-dep-with-optional-dep/node_modules/rimraf",
+      "resolved": "https://registry.npmjs.org/rimraf/-/rimraf-2.2.4.tgz",
+      "version": "2.2.4",
+    },
+  },
+  "edgesOut": Map {
+    "a" => EdgeOut {
+      "name": "a",
+      "spec": "./a",
+      "to": "node_modules/a",
+      "type": "prod",
+    },
+  },
+  "fsChildren": Set {
+    ArboristNode {
+      "edgesOut": Map {
+        "rimraf" => EdgeOut {
+          "name": "rimraf",
+          "spec": "2.2.4",
+          "to": "node_modules/rimraf",
+          "type": "prod",
+        },
+      },
+      "location": "a",
+      "name": "a",
+      "path": "{CWD}/test/fixtures/link-dep-has-dep-with-optional-dep/a",
+      "version": "1.0.0",
+    },
+  },
+  "location": "",
+  "name": "link-dep-has-dep-with-optional-dep",
+  "path": "{CWD}/test/fixtures/link-dep-has-dep-with-optional-dep",
+  "version": "1.0.0",
+}
+`
+
 exports[`test/arborist/build-ideal-tree.js TAP a tree with an outdated dep, missing dep, no lockfile > should not update all 1`] = `
 ArboristNode {
   "children": Map {

test/arborist/build-ideal-tree.js

@@ -174,6 +174,11 @@ t.test('bad shrinkwrap file', t => {
   return t.resolveMatchSnapshot(printIdeal(path), 'bad shrinkwrap')
 })
 
+t.test('a direct link dep has a dep with optional dependencies', t => {
+  const path = resolve(fixtures, 'link-dep-has-dep-with-optional-dep')
+  return t.resolveMatchSnapshot(printIdeal(path), 'should not mark children of the optional dep as extraneous')
+})
+
 t.test('cyclical peer deps', t => {
   const paths = [
     resolve(fixtures, 'peer-dep-cycle'),

test/fixtures/link-dep-has-dep-with-optional-dep/a/package.json

@@ -0,0 +1,7 @@
+{
+  "name": "a",
+  "version": "1.0.0",
+  "dependencies": {
+    "rimraf": "2.2.4"
+  }
+}

test/fixtures/link-dep-has-dep-with-optional-dep/package.json

@@ -0,0 +1,7 @@
+{
+  "name": "link-dep-has-dep-with-optional-dep",
+  "version": "1.0.0",
+  "dependencies": {
+    "a": "./a"
+  }
+}