Reset flags when initializing ideal from actual

lib/arborist/build-ideal-tree.js

@@ -312,8 +312,14 @@ module.exports = cls => class IdealTreeBuilder extends cls {
       // 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[_global] && !root.meta.loadedFromDisk)
+        if (!this[_updateAll] && !this[_global] && !root.meta.loadedFromDisk) {
           await new this.constructor(this.options).loadActual({ root })
+          // 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 (root.children.size)
+            root.meta.loadedFromDisk = true
+        }
         return root
       })
 

test/arborist/build-ideal-tree.js

@@ -2317,3 +2317,20 @@ t.test('peer dep override with dep sets being replaced', async t => {
   await t.rejects(printIdeal(path), { code: 'ERESOLVE' })
   t.matchSnapshot(await printIdeal(path, { force: true }))
 })
+
+t.test('remove deps when initializing tree from actual tree', async t => {
+  const path = t.testdir({
+    node_modules: {
+      foo: {
+        'package.json': JSON.stringify({
+          name: 'foo',
+          version: '1.2.3',
+        }),
+      },
+    },
+  })
+
+  const arb = new Arborist({ path, ...OPT })
+  const tree = await arb.buildIdealTree({ rm: ['foo'] })
+  t.equal(tree.children.get('foo'), undefined, 'removed foo child')
+})