Merge pull request #816 from paperclipai/fix/worktree-seed-and-env-quoting

fix(cli): preserve worktree seed source config and quote special env values

cli/src/__tests__/agent-jwt-env.test.ts

@@ -4,7 +4,9 @@ import path from "node:path";
 import { afterEach, beforeEach, describe, expect, it } from "vitest";
 import {
   ensureAgentJwtSecret,
+  mergePaperclipEnvEntries,
   readAgentJwtSecretFromEnv,
+  readPaperclipEnvEntries,
   resolveAgentJwtEnvFile,
 } from "../config/env.js";
 import { agentJwtSecretCheck } from "../checks/agent-jwt-secret-check.js";
@@ -58,4 +60,20 @@ describe("agent jwt env helpers", () => {
     const result = agentJwtSecretCheck(configPath);
     expect(result.status).toBe("pass");
   });
+
+  it("quotes hash-prefixed env values so dotenv round-trips them", () => {
+    const configPath = tempConfigPath();
+    const envPath = resolveAgentJwtEnvFile(configPath);
+
+    mergePaperclipEnvEntries(
+      {
+        PAPERCLIP_WORKTREE_COLOR: "#439edb",
+      },
+      envPath,
+    );
+
+    const contents = fs.readFileSync(envPath, "utf-8");
+    expect(contents).toContain('PAPERCLIP_WORKTREE_COLOR="#439edb"');
+    expect(readPaperclipEnvEntries(envPath).PAPERCLIP_WORKTREE_COLOR).toBe("#439edb");
+  });
 });

cli/src/__tests__/worktree.test.ts

@@ -7,6 +7,7 @@ import {
   copyGitHooksToWorktreeGitDir,
   copySeededSecretsKey,
   rebindWorkspaceCwd,
+  resolveSourceConfigPath,
   resolveGitWorktreeAddArgs,
   resolveWorktreeMakeTargetPath,
   worktreeInitCommand,
@@ -293,7 +294,7 @@ describe("worktree helpers", () => {
       const envContents = fs.readFileSync(envPath, "utf8");
       expect(envContents).toContain("PAPERCLIP_AGENT_JWT_SECRET=worktree-shared-secret");
       expect(envContents).toContain("PAPERCLIP_WORKTREE_NAME=repo");
-      expect(envContents).toMatch(/PAPERCLIP_WORKTREE_COLOR=#[0-9a-f]{6}/);
+      expect(envContents).toMatch(/PAPERCLIP_WORKTREE_COLOR=\"#[0-9a-f]{6}\"/);
     } finally {
       process.chdir(originalCwd);
       if (originalJwtSecret === undefined) {
@@ -305,6 +306,59 @@ describe("worktree helpers", () => {
     }
   });
 
+  it("defaults the seed source config to the current repo-local Paperclip config", () => {
+    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-source-config-"));
+    const repoRoot = path.join(tempRoot, "repo");
+    const localConfigPath = path.join(repoRoot, ".paperclip", "config.json");
+    const originalCwd = process.cwd();
+    const originalPaperclipConfig = process.env.PAPERCLIP_CONFIG;
+
+    try {
+      fs.mkdirSync(path.dirname(localConfigPath), { recursive: true });
+      fs.writeFileSync(localConfigPath, JSON.stringify(buildSourceConfig()), "utf8");
+      delete process.env.PAPERCLIP_CONFIG;
+      process.chdir(repoRoot);
+
+      expect(fs.realpathSync(resolveSourceConfigPath({}))).toBe(fs.realpathSync(localConfigPath));
+    } finally {
+      process.chdir(originalCwd);
+      if (originalPaperclipConfig === undefined) {
+        delete process.env.PAPERCLIP_CONFIG;
+      } else {
+        process.env.PAPERCLIP_CONFIG = originalPaperclipConfig;
+      }
+      fs.rmSync(tempRoot, { recursive: true, force: true });
+    }
+  });
+
+  it("preserves the source config path across worktree:make cwd changes", () => {
+    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-source-override-"));
+    const sourceConfigPath = path.join(tempRoot, "source", "config.json");
+    const targetRoot = path.join(tempRoot, "target");
+    const originalCwd = process.cwd();
+    const originalPaperclipConfig = process.env.PAPERCLIP_CONFIG;
+
+    try {
+      fs.mkdirSync(path.dirname(sourceConfigPath), { recursive: true });
+      fs.mkdirSync(targetRoot, { recursive: true });
+      fs.writeFileSync(sourceConfigPath, JSON.stringify(buildSourceConfig()), "utf8");
+      delete process.env.PAPERCLIP_CONFIG;
+      process.chdir(targetRoot);
+
+      expect(resolveSourceConfigPath({ sourceConfigPathOverride: sourceConfigPath })).toBe(
+        path.resolve(sourceConfigPath),
+      );
+    } finally {
+      process.chdir(originalCwd);
+      if (originalPaperclipConfig === undefined) {
+        delete process.env.PAPERCLIP_CONFIG;
+      } else {
+        process.env.PAPERCLIP_CONFIG = originalPaperclipConfig;
+      }
+      fs.rmSync(tempRoot, { recursive: true, force: true });
+    }
+  });
+
   it("rebinds same-repo workspace paths onto the current worktree root", () => {
     expect(
       rebindWorkspaceCwd({

cli/src/commands/worktree.ts

@@ -56,6 +56,7 @@ type WorktreeInitOptions = {
   fromConfig?: string;
   fromDataDir?: string;
   fromInstance?: string;
+  sourceConfigPathOverride?: string;
   serverPort?: number;
   dbPort?: number;
   seed?: boolean;
@@ -426,8 +427,12 @@ async function rebindSeededProjectWorkspaces(input: {
   }
 }
 
-function resolveSourceConfigPath(opts: WorktreeInitOptions): string {
+export function resolveSourceConfigPath(opts: WorktreeInitOptions): string {
+  if (opts.sourceConfigPathOverride) return path.resolve(opts.sourceConfigPathOverride);
   if (opts.fromConfig) return path.resolve(opts.fromConfig);
+  if (!opts.fromDataDir && !opts.fromInstance) {
+    return resolveConfigPath();
+  }
   const sourceHome = path.resolve(expandHomePrefix(opts.fromDataDir ?? "~/.paperclip"));
   const sourceInstanceId = sanitizeWorktreeInstanceId(opts.fromInstance ?? "default");
   return path.resolve(sourceHome, "instances", sourceInstanceId, "config.json");
@@ -751,6 +756,7 @@ export async function worktreeMakeCommand(nameArg: string, opts: WorktreeMakeOpt
   const name = resolveWorktreeMakeName(nameArg);
   const startPoint = resolveWorktreeStartPoint(opts.startPoint);
   const sourceCwd = process.cwd();
+  const sourceConfigPath = resolveSourceConfigPath(opts);
   const targetPath = resolveWorktreeMakeTargetPath(name);
   if (existsSync(targetPath)) {
     throw new Error(`Target path already exists: ${targetPath}`);
@@ -810,6 +816,7 @@ export async function worktreeMakeCommand(nameArg: string, opts: WorktreeMakeOpt
     await runWorktreeInit({
       ...opts,
       name,
+      sourceConfigPathOverride: sourceConfigPath,
     });
   } catch (error) {
     throw error;

cli/src/config/env.ts

@@ -22,11 +22,18 @@ function parseEnvFile(contents: string) {
   }
 }
 
+function formatEnvValue(value: string): string {
+  if (/^[A-Za-z0-9_./:@-]+$/.test(value)) {
+    return value;
+  }
+  return JSON.stringify(value);
+}
+
 function renderEnvFile(entries: Record<string, string>) {
   const lines = [
     "# Paperclip environment variables",
     "# Generated by Paperclip CLI commands",
-    ...Object.entries(entries).map(([key, value]) => `${key}=${value}`),
+    ...Object.entries(entries).map(([key, value]) => `${key}=${formatEnvValue(value)}`),
     "",
   ];
   return lines.join("\n");

doc/DEVELOPING.md

@@ -142,7 +142,7 @@ This command:
 - creates an isolated instance under `~/.paperclip-worktrees/instances/<worktree-id>/`
 - when run inside a linked git worktree, mirrors the effective git hooks into that worktree's private git dir
 - picks a free app port and embedded PostgreSQL port
-- by default seeds the isolated DB in `minimal` mode from your main instance via a logical SQL snapshot
+- by default seeds the isolated DB in `minimal` mode from the current effective Paperclip instance/config (repo-local worktree config when present, otherwise the default instance) via a logical SQL snapshot
 
 Seed modes: