install: remove files deleted from a folder dependency on reinstall with the isolated linker

src/install/isolated_install/Installer.rs

@@ -902,6 +902,29 @@
                             };
                             let _folder_dir_guard = sys::CloseOnDrop::new(folder_dir);
 
+                            // The hardlink/copy walk below only visits names
+                            // present in the source folder, so rebuilding in
+                            // place merges: a file deleted from the folder
+                            // dependency would survive in the store entry
+                            // forever. Delete to replace, matching the hoisted
+                            // linker's uninstall-before-install. (Lifecycle
+                            // scripts re-run on every install for folder
+                            // entries, so artifacts they write are recreated.)
+                            //
+                            // Root entries only reach LinkPackage as a
+                            // dependency on the root package (`"x": "file:."`);
+                            // for those `append_store_path` yields the store
+                            // entry's package dir, never the project dir.
+                            debug_assert!(
+                                pkg_res.tag != ResolutionTag::Root
+                                    || dep_id != invalid_dependency_id
+                            );
+                            let mut prev_build = AutoPath::init_top_level_dir();
+                            installer.append_store_path(&mut prev_build, self.entry_id);
+                            if let Some(e) = Fd::cwd().delete_tree(prev_build.slice()).err() {
+                                return Ok(Yield::failure(TaskError::LinkPackage(e)));
+                            }
+
                             let mut backend = InstallMethod::Hardlink;
                             'backend: loop {
                                 match backend {

test/cli/install/isolated-install.test.ts

@@ -327,6 +327,64 @@ test("can install folder dependencies", async () => {
   ).toBe("module.exports = 'hello from pkg-1';");
 });
 
+test("file deleted from a folder dependency is removed on reinstall", async () => {
+  const { packageJson, packageDir } = await registry.createTestDir({ bunfigOpts: { linker: "isolated" } });
+
+  await Promise.all([
+    write(
+      packageJson,
+      JSON.stringify({
+        name: "test-pkg-folder-dep-prune",
+        dependencies: {
+          "folder-dep": "file:./pkg-1",
+        },
+      }),
+    ),
+    write(
+      join(packageDir, "pkg-1", "package.json"),
+      JSON.stringify({
+        name: "folder-dep",
+        version: "1.0.0",
+        dependencies: { "no-deps": "1.0.0" },
+      }),
+    ),
+    write(join(packageDir, "pkg-1", "index.js"), "module.exports = 1;"),
+    write(join(packageDir, "pkg-1", "extra.js"), "module.exports = 2;"),
+    write(join(packageDir, "pkg-1", "nested", "inner.js"), "module.exports = 3;"),
+  ]);
+
+  await runBunInstall(bunEnv, packageDir);
+
+  const installedDep = join(packageDir, "node_modules", "folder-dep");
+  expect(await file(join(installedDep, "extra.js")).exists()).toBe(true);
+  expect(await file(join(installedDep, "nested", "inner.js")).exists()).toBe(true);
+
+  // The store entry rebuilds from the source folder on every install, so a
+  // file or directory deleted from the source must not survive the rebuild.
+  await Promise.all([
+    rm(join(packageDir, "pkg-1", "extra.js")),
+    rm(join(packageDir, "pkg-1", "nested"), { recursive: true }),
+    write(join(packageDir, "pkg-1", "index.js"), "module.exports = 'updated';"),
+  ]);
+
+  await runBunInstall(bunEnv, packageDir, { savesLockfile: false });
+
+  expect(await file(join(installedDep, "extra.js")).exists()).toBe(false);
+  expect(existsSync(join(installedDep, "nested"))).toBe(false);
+  expect(await file(join(installedDep, "index.js")).text()).toBe("module.exports = 'updated';");
+
+  // The rebuild replaces only the package dir inside the store entry; the
+  // entry's dependency symlinks still resolve.
+  expect(readlinkSync(join(packageDir, "node_modules", "folder-dep"))).toBe(
+    join(".bun", "folder-dep@file+pkg-1", "node_modules", "folder-dep"),
+  );
+  expect(
+    await file(
+      join(packageDir, "node_modules", ".bun", "folder-dep@file+pkg-1", "node_modules", "no-deps", "package.json"),
+    ).json(),
+  ).toMatchObject({ name: "no-deps", version: "1.0.0" });
+});
+
 test("can install folder dependencies on root package", async () => {
   const { packageDir, packageJson } = await registry.createTestDir({ bunfigOpts: { linker: "isolated" } });