fix(sync): Fix auto-sync and storage path bugs from v0.4.0

Fixed multiple bugs preventing auto-sync from working correctly:

**Bug 1: Storage path not passed to sync service**
- Sync service wasn't receiving storage path parameter
- Caused sync to use wrong path (.dex instead of configured path)
- Fixed: Pass storagePath to createGitHubSyncService()

**Bug 2: Tilde expansion not working**
- Paths like ~/.dex were used literally, creating ~/  directory
- Fixed: Added expandTilde() function to FileStorage
- Added tests: file-storage.test.ts

**Bug 3: Config path coupled to storage location**
- Project config looked in storage path instead of git root
- Global storage config prevented reading repo-local config
- Fixed: getProjectConfigPath() now always looks in git root
- Config loading no longer depends on storage location
- Added tests: config.test.ts

**Bug 4: Migration for v0.4.0 bug victims**
- Doctor detects tasks in literal ~/ directory
- Doctor --fix migrates tasks to correct location
- Startup warning alerts users to run dex doctor --fix

All tests passing (518/518).

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

Author: dcramer

.dex/config.toml

@@ -1,2 +1,5 @@
 [sync.github]
 enabled = true
+
+[sync.github.auto]
+on_change = true

src/bootstrap.ts

@@ -104,7 +104,10 @@ export function createSyncService(
   const config = loadConfig({ storagePath, configPath: cliConfigPath });
   const githubConfig = config.sync?.github ?? null;
   return {
-    syncService: createGitHubSyncService(githubConfig ?? undefined),
+    syncService: createGitHubSyncService(
+      githubConfig ?? undefined,
+      storagePath,
+    ),
     syncConfig: githubConfig,
   };
 }

src/cli/config.test.ts

@@ -2,20 +2,33 @@ import { describe, it, expect, beforeEach, afterEach, vi } from "vitest";
 import * as fs from "node:fs";
 import * as path from "node:path";
 import * as os from "node:os";
+import { execSync } from "node:child_process";
 import { configCommand } from "./config.js";
 import { captureOutput, CapturedOutput } from "./test-helpers.js";
 
 describe("config command", () => {
   let output: CapturedOutput;
   let mockExit: ReturnType<typeof vi.spyOn>;
   let tempDir: string;
-  let tempStorageDir: string;
+  let tempGitDir: string;
+  let originalCwd: string;
 
   beforeEach(() => {
+    originalCwd = process.cwd();
+
+    // Create temp dir for global config
     tempDir = fs.mkdtempSync(path.join(os.tmpdir(), "dex-config-test-"));
-    tempStorageDir = fs.mkdtempSync(
-      path.join(os.tmpdir(), "dex-config-storage-"),
-    );
+
+    // Create temp git repo for project config tests
+    tempGitDir = fs.mkdtempSync(path.join(os.tmpdir(), "dex-config-git-"));
+    execSync("git init", { cwd: tempGitDir, stdio: "ignore" });
+
+    // Create .dex directory in git repo
+    fs.mkdirSync(path.join(tempGitDir, ".dex"), { recursive: true });
+
+    // Change to git repo for tests that need it
+    process.chdir(tempGitDir);
+
     output = captureOutput();
     mockExit = vi.spyOn(process, "exit").mockImplementation((() => {
       throw new Error("process.exit called");
@@ -26,12 +39,13 @@ describe("config command", () => {
   });
 
   afterEach(() => {
+    process.chdir(originalCwd);
     output.restore();
     mockExit.mockRestore();
     delete process.env.DEX_HOME;
 
     fs.rmSync(tempDir, { recursive: true, force: true });
-    fs.rmSync(tempStorageDir, { recursive: true, force: true });
+    fs.rmSync(tempGitDir, { recursive: true, force: true });
   });
 
   describe("--help", () => {
@@ -188,24 +202,24 @@ describe("config command", () => {
         "[sync.github]\nenabled = false\n",
       );
       fs.writeFileSync(
-        path.join(tempStorageDir, "config.toml"),
+        path.join(tempGitDir, ".dex", "config.toml"),
         "[sync.github]\nenabled = true\n",
       );
 
-      await configCommand(["--list"], { storagePath: tempStorageDir });
+      await configCommand(["--list"], { storagePath: tempGitDir });
       const out = output.stdout.join("\n");
       expect(out).toContain("sync.github.enabled = true");
       expect(out).toContain("[local]");
     });
   });
 
   describe("--local", () => {
-    it("writes to project config file", async () => {
+    it("writes to project config file in git root", async () => {
       await configCommand(["--local", "sync.github.enabled=true"], {
-        storagePath: tempStorageDir,
+        storagePath: tempGitDir,
       });
 
-      const projectConfig = path.join(tempStorageDir, "config.toml");
+      const projectConfig = path.join(tempGitDir, ".dex", "config.toml");
       expect(fs.existsSync(projectConfig)).toBe(true);
       const content = fs.readFileSync(projectConfig, "utf-8");
       expect(content).toContain("enabled = true");
@@ -228,7 +242,7 @@ describe("config command", () => {
     it("fails when both are specified", async () => {
       await expect(
         configCommand(["--global", "--local", "sync.github.enabled=true"], {
-          storagePath: tempStorageDir,
+          storagePath: tempGitDir,
         }),
       ).rejects.toThrow("process.exit");
       const err = output.stderr.join("\n");
@@ -243,12 +257,12 @@ describe("config command", () => {
         "[sync.github]\nenabled = false\n",
       );
       fs.writeFileSync(
-        path.join(tempStorageDir, "config.toml"),
+        path.join(tempGitDir, ".dex", "config.toml"),
         "[sync.github]\nenabled = true\n",
       );
 
       await configCommand(["sync.github.enabled"], {
-        storagePath: tempStorageDir,
+        storagePath: tempGitDir,
       });
       const out = output.stdout.join("\n");
       expect(out).toBe("true");
@@ -260,12 +274,12 @@ describe("config command", () => {
         '[sync.github]\nlabel_prefix = "global-prefix"\n',
       );
       fs.writeFileSync(
-        path.join(tempStorageDir, "config.toml"),
+        path.join(tempGitDir, "config.toml"),
         "[sync.github]\nenabled = true\n",
       );
 
       await configCommand(["sync.github.label_prefix"], {
-        storagePath: tempStorageDir,
+        storagePath: tempGitDir,
       });
       const out = output.stdout.join("\n");
       expect(out).toBe("global-prefix");

src/cli/config.ts

@@ -270,7 +270,14 @@ ${colors.bold}EXAMPLES:${colors.reset}
       );
       process.exit(1);
     }
-    configPath = getProjectConfigPath(options.storagePath);
+    const projectPath = getProjectConfigPath();
+    if (!projectPath) {
+      console.error(
+        `${colors.dim}Run "dex init" to initialize a git repository or use --global${colors.reset}`,
+      );
+      process.exit(1);
+    }
+    configPath = projectPath;
     configLabel = "local";
   } else {
     // Default to global
@@ -281,9 +288,8 @@ ${colors.bold}EXAMPLES:${colors.reset}
   // Handle --list
   if (listAll) {
     const globalConfig = readConfigFile(getConfigPath());
-    const localConfig = options.storagePath
-      ? readConfigFile(getProjectConfigPath(options.storagePath))
-      : {};
+    const projectPath = getProjectConfigPath();
+    const localConfig = projectPath ? readConfigFile(projectPath) : {};
 
     console.log(`${colors.bold}Configuration:${colors.reset}`);
     console.log();
@@ -356,9 +362,8 @@ ${colors.bold}EXAMPLES:${colors.reset}
 
     // Read from both configs and show effective value
     const globalConfig = readConfigFile(getConfigPath());
-    const localConfig = options.storagePath
-      ? readConfigFile(getProjectConfigPath(options.storagePath))
-      : {};
+    const projectPath = getProjectConfigPath();
+    const localConfig = projectPath ? readConfigFile(projectPath) : {};
 
     const globalValue = getNestedValue(globalConfig, input);
     const localValue = getNestedValue(localConfig, input);

src/cli/doctor.test.ts

@@ -3,17 +3,23 @@ import * as fs from "node:fs";
 import * as path from "node:path";
 import { FileStorage } from "../core/storage/index.js";
 import { runCli } from "./index.js";
-import { captureOutput, createTempStorage, CapturedOutput } from "./test-helpers.js";
+import {
+  captureOutput,
+  createTempGitStorage,
+  CapturedOutput,
+} from "./test-helpers.js";
 
 describe("doctor command", () => {
   let storage: FileStorage;
+  let gitRoot: string;
   let cleanup: () => void;
   let output: CapturedOutput;
   let mockExit: ReturnType<typeof vi.spyOn>;
 
   beforeEach(() => {
-    const temp = createTempStorage();
+    const temp = createTempGitStorage();
     storage = temp.storage;
+    gitRoot = temp.gitRoot;
     cleanup = temp.cleanup;
     output = captureOutput();
     mockExit = vi.spyOn(process, "exit").mockImplementation((() => {
@@ -53,21 +59,24 @@ describe("doctor command", () => {
     const taskPath = path.join(storagePath, "tasks", `${taskId}.json`);
 
     fs.mkdirSync(path.dirname(taskPath), { recursive: true });
-    fs.writeFileSync(taskPath, JSON.stringify({
-      id: taskId,
-      parent_id: "nonexistent",
-      description: "Test task",
-      context: "ctx",
-      priority: 1,
-      completed: false,
-      result: null,
-      blockedBy: [],
-      blocks: [],
-      children: [],
-      created_at: new Date().toISOString(),
-      updated_at: new Date().toISOString(),
-      completed_at: null,
-    }));
+    fs.writeFileSync(
+      taskPath,
+      JSON.stringify({
+        id: taskId,
+        parent_id: "nonexistent",
+        description: "Test task",
+        context: "ctx",
+        priority: 1,
+        completed: false,
+        result: null,
+        blockedBy: [],
+        blocks: [],
+        children: [],
+        created_at: new Date().toISOString(),
+        updated_at: new Date().toISOString(),
+        completed_at: null,
+      }),
+    );
 
     await runCli(["doctor"], { storage });
 
@@ -78,12 +87,14 @@ describe("doctor command", () => {
 
   it("detects missing auto-sync config when github sync is enabled", async () => {
     // Create a config file with github sync enabled but no auto section
-    const storagePath = storage.getIdentifier();
-    const configPath = path.join(storagePath, "config.toml");
+    const configPath = path.join(gitRoot, ".dex", "config.toml");
 
-    fs.writeFileSync(configPath, `[sync.github]
+    fs.writeFileSync(
+      configPath,
+      `[sync.github]
 enabled = true
-`);
+`,
+    );
 
     await runCli(["doctor"], { storage });
 
@@ -94,12 +105,14 @@ enabled = true
 
   it("fixes missing auto-sync config with --fix", async () => {
     // Create a config file with github sync enabled but no auto section
-    const storagePath = storage.getIdentifier();
-    const configPath = path.join(storagePath, "config.toml");
+    const configPath = path.join(gitRoot, ".dex", "config.toml");
 
-    fs.writeFileSync(configPath, `[sync.github]
+    fs.writeFileSync(
+      configPath,
+      `[sync.github]
 enabled = true
-`);
+`,
+    );
 
     await runCli(["doctor", "--fix"], { storage });
 
@@ -114,15 +127,17 @@ enabled = true
 
   it("does not warn about auto-sync when it's already present", async () => {
     // Create a config file with github sync and auto section
-    const storagePath = storage.getIdentifier();
-    const configPath = path.join(storagePath, "config.toml");
+    const configPath = path.join(gitRoot, ".dex", "config.toml");
 
-    fs.writeFileSync(configPath, `[sync.github]
+    fs.writeFileSync(
+      configPath,
+      `[sync.github]
 enabled = true
 
 [sync.github.auto]
 on_change = false
-`);
+`,
+    );
 
     await runCli(["doctor"], { storage });