From 22af797ca3faa65e4713d57d5b074d3efefa4cb7 Mon Sep 17 00:00:00 2001
From: dotta <dotta@example.com>
Date: Sat, 28 Mar 2026 11:40:48 -0500
Subject: [PATCH] Provision local node_modules in issue worktrees

Co-Authored-By: Paperclip <noreply@paperclip.ing>
---
 scripts/provision-worktree.sh                 |  38 +++++++
 .../src/__tests__/workspace-runtime.test.ts   | 105 ++++++++++++++++++
 2 files changed, 143 insertions(+)

diff --git a/scripts/provision-worktree.sh b/scripts/provision-worktree.sh
index 09cfc36b..14acc040 100644
--- a/scripts/provision-worktree.sh
+++ b/scripts/provision-worktree.sh
@@ -335,6 +335,44 @@ disable_seeded_routines() {
 
 disable_seeded_routines
 
+if [[ -f "$worktree_cwd/package.json" && -f "$worktree_cwd/pnpm-lock.yaml" ]]; then
+  needs_install=0
+
+  while IFS= read -r relative_path; do
+    [[ -n "$relative_path" ]] || continue
+    target_path="$worktree_cwd/$relative_path"
+
+    if [[ -L "$target_path" ]]; then
+      rm "$target_path"
+      needs_install=1
+      continue
+    fi
+
+    if [[ ! -e "$target_path" ]]; then
+      needs_install=1
+    fi
+  done < <(
+    cd "$base_cwd" &&
+      find . \
+        -mindepth 1 \
+        -maxdepth 3 \
+        -type d \
+        -name node_modules \
+        ! -path './.git/*' \
+        ! -path './.paperclip/*' \
+        | sed 's#^\./##'
+  )
+
+  if [[ "$needs_install" -eq 1 ]]; then
+    (
+      cd "$worktree_cwd"
+      pnpm install --frozen-lockfile
+    )
+  fi
+
+  exit 0
+fi
+
 while IFS= read -r relative_path; do
   [[ -n "$relative_path" ]] || continue
   source_path="$base_cwd/$relative_path"
diff --git a/server/src/__tests__/workspace-runtime.test.ts b/server/src/__tests__/workspace-runtime.test.ts
index 472f58b0..a04e5302 100644
--- a/server/src/__tests__/workspace-runtime.test.ts
+++ b/server/src/__tests__/workspace-runtime.test.ts
@@ -50,11 +50,16 @@ if (!embeddedPostgresSupport.supported) {
     `Skipping embedded Postgres workspace-runtime tests on this host: ${embeddedPostgresSupport.reason ?? "unsupported environment"}`,
   );
 }
+const provisionWorktreeScriptPath = new URL("../../../scripts/provision-worktree.sh", import.meta.url);
 
 async function runGit(cwd: string, args: string[]) {
   await execFileAsync("git", args, { cwd });
 }
 
+async function runPnpm(cwd: string, args: string[]) {
+  await execFileAsync("pnpm", args, { cwd });
+}
+
 async function createTempRepo(defaultBranch = "main") {
   const repoRoot = await fs.mkdtemp(path.join(os.tmpdir(), "paperclip-worktree-repo-"));
   await runGit(repoRoot, ["init"]);
@@ -557,6 +562,106 @@ describe("realizeExecutionWorkspace", () => {
     }
   }, 15_000);
 
+  it("provisions worktree-local pnpm node_modules instead of reusing base-repo links", async () => {
+    const repoRoot = await createTempRepo();
+    await fs.mkdir(path.join(repoRoot, "scripts"), { recursive: true });
+    await fs.mkdir(path.join(repoRoot, "packages", "shared"), { recursive: true });
+    await fs.mkdir(path.join(repoRoot, "server"), { recursive: true });
+    await fs.writeFile(
+      path.join(repoRoot, "package.json"),
+      JSON.stringify(
+        {
+          name: "workspace-root",
+          private: true,
+          packageManager: "pnpm@9.15.4",
+        },
+        null,
+        2,
+      ),
+      "utf8",
+    );
+    await fs.writeFile(
+      path.join(repoRoot, "pnpm-workspace.yaml"),
+      ["packages:", "  - packages/*", "  - server", ""].join("\n"),
+      "utf8",
+    );
+    await fs.writeFile(
+      path.join(repoRoot, "packages", "shared", "package.json"),
+      JSON.stringify(
+        {
+          name: "@repo/shared",
+          version: "1.0.0",
+          private: true,
+          type: "module",
+          exports: "./index.js",
+        },
+        null,
+        2,
+      ),
+      "utf8",
+    );
+    await fs.writeFile(path.join(repoRoot, "packages", "shared", "index.js"), "export const value = 'shared';\n", "utf8");
+    await fs.writeFile(
+      path.join(repoRoot, "server", "package.json"),
+      JSON.stringify(
+        {
+          name: "server",
+          private: true,
+          type: "module",
+          dependencies: {
+            "@repo/shared": "workspace:*",
+          },
+        },
+        null,
+        2,
+      ),
+      "utf8",
+    );
+    await fs.writeFile(path.join(repoRoot, "server", "index.js"), "export {};\n", "utf8");
+    await fs.copyFile(provisionWorktreeScriptPath, path.join(repoRoot, "scripts", "provision-worktree.sh"));
+    await fs.chmod(path.join(repoRoot, "scripts", "provision-worktree.sh"), 0o755);
+    await runPnpm(repoRoot, ["install"]);
+    await runGit(repoRoot, ["add", "."]);
+    await runGit(repoRoot, ["commit", "-m", "Add pnpm workspace fixture"]);
+
+    const workspace = await realizeExecutionWorkspace({
+      base: {
+        baseCwd: repoRoot,
+        source: "project_primary",
+        projectId: "project-1",
+        workspaceId: "workspace-1",
+        repoUrl: null,
+        repoRef: "HEAD",
+      },
+      config: {
+        workspaceStrategy: {
+          type: "git_worktree",
+          branchTemplate: "{{issue.identifier}}-{{slug}}",
+          provisionCommand: "bash ./scripts/provision-worktree.sh",
+        },
+      },
+      issue: {
+        id: "issue-1",
+        identifier: "PAP-551",
+        title: "Provision local workspace dependencies",
+      },
+      agent: {
+        id: "agent-1",
+        name: "Codex Coder",
+        companyId: "company-1",
+      },
+    });
+
+    expect((await fs.lstat(path.join(workspace.cwd, "node_modules"))).isSymbolicLink()).toBe(false);
+    expect((await fs.lstat(path.join(workspace.cwd, "server", "node_modules"))).isSymbolicLink()).toBe(false);
+    await expect(fs.realpath(path.join(workspace.cwd, "server", "node_modules", "@repo", "shared"))).resolves.toBe(
+      await fs.realpath(path.join(workspace.cwd, "packages", "shared")),
+    );
+    await expect(fs.realpath(path.join(repoRoot, "server", "node_modules", "@repo", "shared"))).resolves.toBe(
+      await fs.realpath(path.join(repoRoot, "packages", "shared")),
+    );
+  });
+
   it("records worktree setup and provision operations when a recorder is provided", async () => {
     const repoRoot = await createTempRepo();
     const { recorder, operations } = createWorkspaceOperationRecorderDouble();