fix(plugin-nm): set binary permissions for partial installs

.yarn/versions/944c0a3d.yml

@@ -0,0 +1,23 @@
+releases:
+  "@yarnpkg/cli": patch
+  "@yarnpkg/plugin-nm": patch
+
+declined:
+  - "@yarnpkg/plugin-compat"
+  - "@yarnpkg/plugin-constraints"
+  - "@yarnpkg/plugin-dlx"
+  - "@yarnpkg/plugin-essentials"
+  - "@yarnpkg/plugin-init"
+  - "@yarnpkg/plugin-interactive-tools"
+  - "@yarnpkg/plugin-npm-cli"
+  - "@yarnpkg/plugin-pack"
+  - "@yarnpkg/plugin-patch"
+  - "@yarnpkg/plugin-pnp"
+  - "@yarnpkg/plugin-pnpm"
+  - "@yarnpkg/plugin-stage"
+  - "@yarnpkg/plugin-typescript"
+  - "@yarnpkg/plugin-version"
+  - "@yarnpkg/plugin-workspace-tools"
+  - "@yarnpkg/builder"
+  - "@yarnpkg/core"
+  - "@yarnpkg/doctor"

packages/acceptance-tests/pkg-tests-fixtures/packages/@scoped__has-bin-entry-2.0.0/bin.js

@@ -0,0 +1,3 @@
+#!/usr/bin/env node
+
+console.log(require(`./package.json`).version);

packages/acceptance-tests/pkg-tests-fixtures/packages/@scoped__has-bin-entry-2.0.0/package.json

@@ -0,0 +1,7 @@
+{
+	"name": "@scoped/has-bin-entry",
+	"version": "2.0.0",
+	"bin": {
+		"@scoped/has-bin-entry": "./bin.js"
+	}
+}

packages/acceptance-tests/pkg-tests-specs/sources/node-modules.test.ts

@@ -1780,6 +1780,81 @@ describe(`Node_Modules`, () => {
     ),
   );
 
+  it(`should set correct permissions on binaries in installed packages`,
+    makeTemporaryEnv(
+      {
+        dependencies: {
+          [`has-bin-entries`]: `1.0.0`,
+        },
+      },
+      {
+        nodeLinker: `node-modules`,
+      },
+      async ({path, run}) => {
+        await run(`install`);
+        const {mode} = await xfs.lstatPromise(npath.toPortablePath(`${path}/node_modules/has-bin-entries/bin.js`));
+        const permissions = (mode & 0o777).toString(8);
+        expect(permissions).toBe(process.platform === `win32` ? `666` : `755`);
+      },
+    ),
+  );
+
+  it(`should set correct permissions on binaries in packages that were upgraded`,
+    makeTemporaryEnv(
+      {
+        dependencies: {
+          [`has-bin-entries`]: `1.0.0`,
+          [`scoped/has-bin-entry`]: `1.0.0`,
+        },
+      },
+      {
+        nodeLinker: `node-modules`,
+      },
+      async ({path, run}) => {
+        await run(`install`);
+        await xfs.writeJsonPromise(`${path}/package.json` as PortablePath, {
+          dependencies: {
+            'has-bin-entries': `2.0.0`,
+            '@scoped/has-bin-entry': `2.0.0`,
+          },
+        });
+        await run(`install`);
+
+        const binaries = [
+          `has-bin-entries/bin.js`,
+          `@scoped/has-bin-entry/bin.js`,
+        ];
+
+        for (const binary of binaries) {
+          const {mode} = await xfs.lstatPromise(npath.toPortablePath(`${path}/node_modules/${binary}`));
+          const permissions = (mode & 0o777).toString(8);
+          expect(permissions).toBe(process.platform === `win32` ? `666` : `755`);
+        }
+      },
+    ),
+  );
+
+  it(`should reinstall and set correct permissions on next install when packages have been deleted by the user`,
+    makeTemporaryEnv(
+      {
+        dependencies: {
+          [`has-bin-entries`]: `1.0.0`,
+        },
+      },
+      {
+        nodeLinker: `node-modules`,
+      },
+      async ({path, run}) => {
+        await run(`install`);
+        await xfs.removePromise(`${path}/node_modules/has-bin-entries` as PortablePath);
+        await run(`install`);
+        const {mode} = await xfs.lstatPromise(npath.toPortablePath(`${path}/node_modules/has-bin-entries/bin.js`));
+        const permissions = (mode & 0o777).toString(8);
+        expect(permissions).toBe(process.platform === `win32` ? `666` : `755`);
+      },
+    ),
+  );
+
   it(`should only reinstall scoped dependencies deleted by the user on the next install`,
     makeTemporaryEnv(
       {

packages/plugin-nm/sources/NodeModulesLinker.ts

@@ -1045,6 +1045,28 @@ export function getGlobalHardlinksStore(configuration: Configuration): PortableP
   return ppath.join(configuration.get(`globalFolder`), `store` as Filename);
 }
 
+/**
+ * Mutate binSymlinks by removing binaries related to the changedLocations.
+ */
+function invalidateBinSymlinks(binSymlinks: BinSymlinkMap, changedLocations: Set<PortablePath>): void {
+  const getLocationPackageRoot = (targetPath: PortablePath): PortablePath => {
+    const parts = targetPath.split(ppath.sep);
+    const nmIndex = parts.lastIndexOf(NODE_MODULES);
+    if (nmIndex < 0 || nmIndex == parts.length - 1)
+      throw new Error(`Assertion failed. Path is outside of any node_modules package ${targetPath}`);
+
+    return parts.slice(0, nmIndex + (parts[nmIndex + 1].startsWith(`@`) ? 3 : 2)).join(ppath.sep) as PortablePath;
+  };
+
+  for (const binSymlinkMap of binSymlinks.values()) {
+    for (const [binFile, binLocation] of binSymlinkMap) {
+      if (changedLocations.has(getLocationPackageRoot(binLocation))) {
+        binSymlinkMap.delete(binFile);
+      }
+    }
+  }
+}
+
 async function persistNodeModules(preinstallState: InstallState, installState: NodeModulesLocatorMap, {baseFs, project, report, loadManifest, realLocatorChecksums}: {project: Project, baseFs: FakeFS<PortablePath>, report: Report, loadManifest: LoadManifest, realLocatorChecksums: Map<LocatorHash, string | null>}) {
   const rootNmDirPath = ppath.join(project.cwd, NODE_MODULES);
 
@@ -1314,6 +1336,7 @@ async function persistNodeModules(preinstallState: InstallState, installState: N
 
     await xfs.mkdirPromise(rootNmDirPath, {recursive: true});
 
+    invalidateBinSymlinks(prevBinSymlinks, new Set(addList.map(l => l.dstDir)));
     const binSymlinks = await createBinSymlinkMap(installState, locationTree, project.cwd, {loadManifest});
     await persistBinSymlinks(prevBinSymlinks, binSymlinks, project.cwd, windowsLinkType);