Fix: Reimplements part of the integrity check

**Summary**

The integrity file doesn't currently support workspaces, which leads
to #3863 (removing a workspace node_modules folder and running yarn
doesn't do anything, because Yarn incorrectly assumes that everything
is already done).

This PR rewrites a good chunk of the integrity logic to support and
fix this behavior.

**Test plan**

Tests are passing, I still have to write an automated test before
merging this PR.

src/cli/commands/install.js

@@ -351,7 +351,7 @@ export class Install {
     if (!patterns.length && !match.integrityFileMissing) {
       this.reporter.success(this.reporter.lang('nothingToInstall'));
       await this.createEmptyManifestFolders();
-      await this.saveLockfileAndIntegrity(patterns);
+      await this.saveLockfileAndIntegrity(patterns, workspaceLayout);
       return true;
     }
 
@@ -674,7 +674,7 @@ export class Install {
       patterns,
       lockfileBasedOnResolver,
       this.flags,
-      this.resolver.usedRegistries,
+      workspaceLayout,
       this.scripts.getArtifacts(),
     );