Fix #5165 - missing executable perms when installing with pnpm linker (#6066)

**What's the problem this PR addresses?**

This is the fix for missing executable perms when installing
dependencies like turbo and esbuild with pnpm linker
(#5165,
#5991)

Resolves #5165

<!-- Describe the rationale of your PR. -->
<!-- Link all issues that it closes. (Closes/Resolves #xxxx.) -->


**How did you fix it?**
<!-- A detailed description of your implementation. -->
Looks like the code was missing for setting permissions for the file
copied by pnpm linker into content-addressable store

I added `destinationFs.chmodPromise` to `copyFileViaIndex` in `fslib` if
the file is not in store (`if (!indexStat)` branch)

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---------

Co-authored-by: Maël Nison <nison.mael@gmail.com>

Author: fancyfractal

.yarn/versions/a5c55beb.yml

@@ -0,0 +1,37 @@
+releases:
+  "@yarnpkg/cli": patch
+  "@yarnpkg/fslib": patch
+
+declined:
+  - "@yarnpkg/plugin-compat"
+  - "@yarnpkg/plugin-constraints"
+  - "@yarnpkg/plugin-dlx"
+  - "@yarnpkg/plugin-essentials"
+  - "@yarnpkg/plugin-exec"
+  - "@yarnpkg/plugin-file"
+  - "@yarnpkg/plugin-git"
+  - "@yarnpkg/plugin-github"
+  - "@yarnpkg/plugin-init"
+  - "@yarnpkg/plugin-interactive-tools"
+  - "@yarnpkg/plugin-link"
+  - "@yarnpkg/plugin-nm"
+  - "@yarnpkg/plugin-npm"
+  - "@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"
+  - vscode-zipfs
+  - "@yarnpkg/builder"
+  - "@yarnpkg/core"
+  - "@yarnpkg/doctor"
+  - "@yarnpkg/libzip"
+  - "@yarnpkg/nm"
+  - "@yarnpkg/pnp"
+  - "@yarnpkg/pnpify"
+  - "@yarnpkg/sdks"
+  - "@yarnpkg/shell"

packages/acceptance-tests/pkg-tests-specs/sources/features/contentAddressedIndex.test.ts

@@ -2,6 +2,25 @@ import {Filename, ppath, xfs} from '@yarnpkg/fslib';
 
 describe(`Features`, () => {
   describe(`Content-Addressed Index`, () => {
+    if (process.platform !== `win32`) {
+      test(
+        `it should preserve executable mode when installing`,
+        makeTemporaryEnv({
+          dependencies: {
+            [`has-bin-entries`]: `1.0.0`,
+          },
+        }, {
+          nodeLinker: `pnpm`,
+        }, async ({path, run, source}) => {
+          await run(`install`);
+
+          const stat = await xfs.statPromise(ppath.join(path, `node_modules/has-bin-entries/bin-with-exit-code.js`));
+          const executableBits = 0o111;
+          expect(stat.mode & executableBits).toEqual(executableBits);
+        }),
+      );
+    }
+
     test(
       `it should use the exact same device/inode for the same file from the same package`,
       makeTemporaryEnv({
@@ -23,7 +42,7 @@ describe(`Features`, () => {
           await run(`install`, {cwd: path2});
 
           const statA = await xfs.statPromise(ppath.join(path, `node_modules/no-deps/package.json`));
-          const statB = await xfs.statPromise(ppath.join(path, `node_modules/no-deps/package.json`));
+          const statB = await xfs.statPromise(ppath.join(path2, `node_modules/no-deps/package.json`));
 
           expect({
             dev: statA.dev,
@@ -57,7 +76,7 @@ describe(`Features`, () => {
           await run(`install`, {cwd: path2});
 
           const statA = await xfs.statPromise(ppath.join(path, `node_modules/no-deps/index.js`));
-          const statB = await xfs.statPromise(ppath.join(path, `node_modules/no-deps/index.js`));
+          const statB = await xfs.statPromise(ppath.join(path2, `node_modules/no-deps/index.js`));
 
           expect({
             dev: statA.dev,
@@ -79,20 +98,18 @@ describe(`Features`, () => {
       }, {
         nodeLinker: `pnpm`,
       }, async ({path, run, source}) => {
-        await xfs.mktempPromise(async path2 => {
-          await run(`install`);
+        await run(`install`);
 
-          const referenceFile = ppath.join(path, `node_modules/no-deps/index.js`);
+        const referenceFile = ppath.join(path, `node_modules/no-deps/index.js`);
 
-          const originalContent = await xfs.readFilePromise(referenceFile, `utf8`);
-          const newContent = `${originalContent}// oh no, modified\n`;
+        const originalContent = await xfs.readFilePromise(referenceFile, `utf8`);
+        const newContent = `${originalContent}// oh no, modified\n`;
 
-          await xfs.writeFilePromise(referenceFile, newContent);
+        await xfs.writeFilePromise(referenceFile, newContent);
 
-          await run(`install`);
+        await run(`install`);
 
-          await expect(xfs.readFilePromise(referenceFile, `utf8`)).resolves.toEqual(originalContent);
-        });
+        await expect(xfs.readFilePromise(referenceFile, `utf8`)).resolves.toEqual(originalContent);
       }),
     );
 
@@ -117,7 +134,7 @@ describe(`Features`, () => {
           await run(`install`, {cwd: path2});
 
           const referenceFileA = ppath.join(path, `node_modules/no-deps/index.js`);
-          const referenceFileB = ppath.join(path, `node_modules/no-deps/index.js`);
+          const referenceFileB = ppath.join(path2, `node_modules/no-deps/index.js`);
 
           const originalContent = await xfs.readFilePromise(referenceFileA, `utf8`);
           const newContent = `${originalContent}// oh no, modified\n`;

packages/yarnpkg-fslib/sources/algorithms/copyPromise.ts

@@ -95,7 +95,7 @@ async function copyImpl<P1 extends Path, P2 extends Path>(prelayout: Operations,
 
     default: {
       throw new Error(`Unsupported file type (${sourceStat.mode})`);
-    } break;
+    }
   }
 
   // We aren't allowed to modify the destination if we work with the index,
@@ -173,7 +173,13 @@ async function copyFolder<P1 extends Path, P2 extends Path>(prelayout: Operation
 
 async function copyFileViaIndex<P1 extends Path, P2 extends Path>(prelayout: Operations, postlayout: Operations, destinationFs: FakeFS<P1>, destination: P1, destinationStat: Stats | null, sourceFs: FakeFS<P2>, source: P2, sourceStat: Stats, opts: CopyOptions<P1>, linkStrategy: HardlinkFromIndexStrategy<P1>) {
   const sourceHash = await sourceFs.checksumFilePromise(source, {algorithm: `sha1`});
-  const indexPath = destinationFs.pathUtils.join(linkStrategy.indexPath, sourceHash.slice(0, 2) as P1, `${sourceHash}.dat` as P1);
+
+  const defaultMode = 0o644;
+  const sourceMode = sourceStat.mode & 0o777;
+
+  // add mode to the index file name if it's not the default b/c different packages could have the file with same content, but different modes
+  const indexFileName = `${sourceHash}${sourceMode !== defaultMode ? sourceMode.toString(8) : ``}`;
+  const indexPath = destinationFs.pathUtils.join(linkStrategy.indexPath, sourceHash.slice(0, 2) as P1, `${indexFileName}.dat` as P1);
 
   enum AtomicBehavior {
     Lock,
@@ -263,8 +269,12 @@ async function copyFileViaIndex<P1 extends Path, P2 extends Path>(prelayout: Ope
   });
 
   postlayout.push(async () => {
-    if (!indexStat)
+    if (!indexStat) {
       await destinationFs.lutimesPromise(indexPath, defaultTime, defaultTime);
+      if (sourceMode !== defaultMode) {
+        await destinationFs.chmodPromise(indexPath, sourceMode);
+      }
+    }
 
     if (tempPath && !tempPathCleaned) {
       await destinationFs.unlinkPromise(tempPath);