@epoch-ai/cli 2.2.5 → 2.2.7

package/test/storage/json-migration.test.ts

@@ -0,0 +1,791 @@
+import { describe, test, expect, beforeEach, afterEach } from "bun:test"
+import { Database } from "bun:sqlite"
+import { drizzle } from "drizzle-orm/bun-sqlite"
+import { migrate } from "drizzle-orm/bun-sqlite/migrator"
+import path from "path"
+import fs from "fs/promises"
+import { readFileSync, readdirSync } from "fs"
+import { JsonMigration } from "../../src/storage/json-migration"
+import { Global } from "../../src/global"
+import { ProjectTable } from "../../src/project/project.sql"
+import { ProjectID } from "../../src/project/schema"
+import { SessionTable, MessageTable, PartTable, TodoTable, PermissionTable } from "../../src/session/session.sql"
+import { SessionID, MessageID, PartID } from "../../src/session/schema"
+
+// Test fixtures
+const fixtures = {
+  project: {
+    id: "proj_test123abc",
+    name: "Test Project",
+    worktree: "/test/path",
+    vcs: "git" as const,
+    sandboxes: [],
+  },
+  session: {
+    id: "ses_test456def",
+    projectID: "proj_test123abc",
+    slug: "test-session",
+    directory: "/test/path",
+    title: "Test Session",
+    version: "1.0.0",
+    time: { created: 1700000000000, updated: 1700000001000 },
+  },
+  message: {
+    id: "msg_test789ghi",
+    sessionID: "ses_test456def",
+    role: "user" as const,
+    agent: "default",
+    model: { providerID: "openai", modelID: "gpt-4" },
+    time: { created: 1700000000000 },
+  },
+  part: {
+    id: "prt_testabc123",
+    messageID: "msg_test789ghi",
+    sessionID: "ses_test456def",
+    type: "text" as const,
+    text: "Hello, world!",
+  },
+}
+
+// Helper to create test storage directory structure
+async function setupStorageDir() {
+  const storageDir = path.join(Global.Path.data, "storage")
+  await fs.rm(storageDir, { recursive: true, force: true })
+  await fs.mkdir(path.join(storageDir, "project"), { recursive: true })
+  await fs.mkdir(path.join(storageDir, "session", "proj_test123abc"), { recursive: true })
+  await fs.mkdir(path.join(storageDir, "message", "ses_test456def"), { recursive: true })
+  await fs.mkdir(path.join(storageDir, "part", "msg_test789ghi"), { recursive: true })
+  await fs.mkdir(path.join(storageDir, "session_diff"), { recursive: true })
+  await fs.mkdir(path.join(storageDir, "todo"), { recursive: true })
+  await fs.mkdir(path.join(storageDir, "permission"), { recursive: true })
+  await fs.mkdir(path.join(storageDir, "session_share"), { recursive: true })
+  // Create legacy marker to indicate JSON storage exists
+  await Bun.write(path.join(storageDir, "migration"), "1")
+  return storageDir
+}
+
+async function writeProject(storageDir: string, project: Record<string, unknown>) {
+  await Bun.write(path.join(storageDir, "project", `${project.id}.json`), JSON.stringify(project))
+}
+
+async function writeSession(storageDir: string, projectID: string, session: Record<string, unknown>) {
+  await Bun.write(path.join(storageDir, "session", projectID, `${session.id}.json`), JSON.stringify(session))
+}
+
+// Helper to create in-memory test database with schema
+function createTestDb() {
+  const sqlite = new Database(":memory:")
+  sqlite.exec("PRAGMA foreign_keys = ON")
+
+  // Apply schema migrations using drizzle migrate
+  const dir = path.join(import.meta.dirname, "../../migration")
+  const entries = readdirSync(dir, { withFileTypes: true })
+  const migrations = entries
+    .filter((entry) => entry.isDirectory())
+    .map((entry) => ({
+      sql: readFileSync(path.join(dir, entry.name, "migration.sql"), "utf-8"),
+      timestamp: Number(entry.name.split("_")[0]),
+      name: entry.name,
+    }))
+    .sort((a, b) => a.timestamp - b.timestamp)
+  migrate(drizzle({ client: sqlite }), migrations)
+
+  return sqlite
+}
+
+describe("JSON to SQLite migration", () => {
+  let storageDir: string
+  let sqlite: Database
+
+  beforeEach(async () => {
+    storageDir = await setupStorageDir()
+    sqlite = createTestDb()
+  })
+
+  afterEach(async () => {
+    sqlite.close()
+    await fs.rm(storageDir, { recursive: true, force: true })
+  })
+
+  test("migrates project", async () => {
+    await writeProject(storageDir, {
+      id: "proj_test123abc",
+      worktree: "/test/path",
+      vcs: "git",
+      name: "Test Project",
+      time: { created: 1700000000000, updated: 1700000001000 },
+      sandboxes: ["/test/sandbox"],
+    })
+
+    const stats = await JsonMigration.run(sqlite)
+
+    expect(stats?.projects).toBe(1)
+
+    const db = drizzle({ client: sqlite })
+    const projects = db.select().from(ProjectTable).all()
+    expect(projects.length).toBe(1)
+    expect(projects[0].id).toBe(ProjectID.make("proj_test123abc"))
+    expect(projects[0].worktree).toBe("/test/path")
+    expect(projects[0].name).toBe("Test Project")
+    expect(projects[0].sandboxes).toEqual(["/test/sandbox"])
+  })
+
+  test("uses filename for project id when JSON has different value", async () => {
+    await Bun.write(
+      path.join(storageDir, "project", "proj_filename.json"),
+      JSON.stringify({
+        id: "proj_different_in_json", // Stale! Should be ignored
+        worktree: "/test/path",
+        vcs: "git",
+        name: "Test Project",
+        sandboxes: [],
+      }),
+    )
+
+    const stats = await JsonMigration.run(sqlite)
+
+    expect(stats?.projects).toBe(1)
+
+    const db = drizzle({ client: sqlite })
+    const projects = db.select().from(ProjectTable).all()
+    expect(projects.length).toBe(1)
+    expect(projects[0].id).toBe(ProjectID.make("proj_filename")) // Uses filename, not JSON id
+  })
+
+  test("migrates project with commands", async () => {
+    await writeProject(storageDir, {
+      id: "proj_with_commands",
+      worktree: "/test/path",
+      vcs: "git",
+      name: "Project With Commands",
+      time: { created: 1700000000000, updated: 1700000001000 },
+      sandboxes: ["/test/sandbox"],
+      commands: { start: "npm run dev" },
+    })
+
+    const stats = await JsonMigration.run(sqlite)
+
+    expect(stats?.projects).toBe(1)
+
+    const db = drizzle({ client: sqlite })
+    const projects = db.select().from(ProjectTable).all()
+    expect(projects.length).toBe(1)
+    expect(projects[0].id).toBe(ProjectID.make("proj_with_commands"))
+    expect(projects[0].commands).toEqual({ start: "npm run dev" })
+  })
+
+  test("migrates project without commands field", async () => {
+    await writeProject(storageDir, {
+      id: "proj_no_commands",
+      worktree: "/test/path",
+      vcs: "git",
+      name: "Project Without Commands",
+      time: { created: 1700000000000, updated: 1700000001000 },
+      sandboxes: [],
+    })
+
+    const stats = await JsonMigration.run(sqlite)
+
+    expect(stats?.projects).toBe(1)
+
+    const db = drizzle({ client: sqlite })
+    const projects = db.select().from(ProjectTable).all()
+    expect(projects.length).toBe(1)
+    expect(projects[0].id).toBe(ProjectID.make("proj_no_commands"))
+    expect(projects[0].commands).toBeNull()
+  })
+
+  test("migrates session with individual columns", async () => {
+    await writeProject(storageDir, {
+      id: "proj_test123abc",
+      worktree: "/test/path",
+      time: { created: Date.now(), updated: Date.now() },
+      sandboxes: [],
+    })
+
+    await writeSession(storageDir, "proj_test123abc", {
+      id: "ses_test456def",
+      projectID: "proj_test123abc",
+      slug: "test-session",
+      directory: "/test/dir",
+      title: "Test Session Title",
+      version: "1.0.0",
+      time: { created: 1700000000000, updated: 1700000001000 },
+      summary: { additions: 10, deletions: 5, files: 3 },
+      share: { url: "https://example.com/share" },
+    })
+
+    await JsonMigration.run(sqlite)
+
+    const db = drizzle({ client: sqlite })
+    const sessions = db.select().from(SessionTable).all()
+    expect(sessions.length).toBe(1)
+    expect(sessions[0].id).toBe(SessionID.make("ses_test456def"))
+    expect(sessions[0].project_id).toBe(ProjectID.make("proj_test123abc"))
+    expect(sessions[0].slug).toBe("test-session")
+    expect(sessions[0].title).toBe("Test Session Title")
+    expect(sessions[0].summary_additions).toBe(10)
+    expect(sessions[0].summary_deletions).toBe(5)
+  })
+
+  test("migrates messages and parts", async () => {
+    await writeProject(storageDir, {
+      id: "proj_test123abc",
+      worktree: "/",
+      time: { created: Date.now(), updated: Date.now() },
+      sandboxes: [],
+    })
+    await writeSession(storageDir, "proj_test123abc", { ...fixtures.session })
+    await Bun.write(
+      path.join(storageDir, "message", "ses_test456def", "msg_test789ghi.json"),
+      JSON.stringify({ ...fixtures.message }),
+    )
+    await Bun.write(
+      path.join(storageDir, "part", "msg_test789ghi", "prt_testabc123.json"),
+      JSON.stringify({ ...fixtures.part }),
+    )
+
+    const stats = await JsonMigration.run(sqlite)
+
+    expect(stats?.messages).toBe(1)
+    expect(stats?.parts).toBe(1)
+
+    const db = drizzle({ client: sqlite })
+    const messages = db.select().from(MessageTable).all()
+    expect(messages.length).toBe(1)
+    expect(messages[0].id).toBe(MessageID.make("msg_test789ghi"))
+
+    const parts = db.select().from(PartTable).all()
+    expect(parts.length).toBe(1)
+    expect(parts[0].id).toBe(PartID.make("prt_testabc123"))
+  })
+
+  test("migrates legacy parts without ids in body", async () => {
+    await writeProject(storageDir, {
+      id: "proj_test123abc",
+      worktree: "/",
+      time: { created: Date.now(), updated: Date.now() },
+      sandboxes: [],
+    })
+    await writeSession(storageDir, "proj_test123abc", { ...fixtures.session })
+    await Bun.write(
+      path.join(storageDir, "message", "ses_test456def", "msg_test789ghi.json"),
+      JSON.stringify({
+        role: "user",
+        agent: "default",
+        model: { providerID: "openai", modelID: "gpt-4" },
+        time: { created: 1700000000000 },
+      }),
+    )
+    await Bun.write(
+      path.join(storageDir, "part", "msg_test789ghi", "prt_testabc123.json"),
+      JSON.stringify({
+        type: "text",
+        text: "Hello, world!",
+      }),
+    )
+
+    const stats = await JsonMigration.run(sqlite)
+
+    expect(stats?.messages).toBe(1)
+    expect(stats?.parts).toBe(1)
+
+    const db = drizzle({ client: sqlite })
+    const messages = db.select().from(MessageTable).all()
+    expect(messages.length).toBe(1)
+    expect(messages[0].id).toBe(MessageID.make("msg_test789ghi"))
+    expect(messages[0].session_id).toBe(SessionID.make("ses_test456def"))
+    expect(messages[0].data).not.toHaveProperty("id")
+    expect(messages[0].data).not.toHaveProperty("sessionID")
+
+    const parts = db.select().from(PartTable).all()
+    expect(parts.length).toBe(1)
+    expect(parts[0].id).toBe(PartID.make("prt_testabc123"))
+    expect(parts[0].message_id).toBe(MessageID.make("msg_test789ghi"))
+    expect(parts[0].session_id).toBe(SessionID.make("ses_test456def"))
+    expect(parts[0].data).not.toHaveProperty("id")
+    expect(parts[0].data).not.toHaveProperty("messageID")
+    expect(parts[0].data).not.toHaveProperty("sessionID")
+  })
+
+  test("uses filename for message id when JSON has different value", async () => {
+    await writeProject(storageDir, {
+      id: "proj_test123abc",
+      worktree: "/",
+      time: { created: Date.now(), updated: Date.now() },
+      sandboxes: [],
+    })
+    await writeSession(storageDir, "proj_test123abc", { ...fixtures.session })
+    await Bun.write(
+      path.join(storageDir, "message", "ses_test456def", "msg_from_filename.json"),
+      JSON.stringify({
+        id: "msg_different_in_json", // Stale! Should be ignored
+        sessionID: "ses_test456def",
+        role: "user",
+        agent: "default",
+        time: { created: 1700000000000 },
+      }),
+    )
+
+    const stats = await JsonMigration.run(sqlite)
+
+    expect(stats?.messages).toBe(1)
+
+    const db = drizzle({ client: sqlite })
+    const messages = db.select().from(MessageTable).all()
+    expect(messages.length).toBe(1)
+    expect(messages[0].id).toBe(MessageID.make("msg_from_filename")) // Uses filename, not JSON id
+    expect(messages[0].session_id).toBe(SessionID.make("ses_test456def"))
+  })
+
+  test("uses paths for part id and messageID when JSON has different values", async () => {
+    await writeProject(storageDir, {
+      id: "proj_test123abc",
+      worktree: "/",
+      time: { created: Date.now(), updated: Date.now() },
+      sandboxes: [],
+    })
+    await writeSession(storageDir, "proj_test123abc", { ...fixtures.session })
+    await Bun.write(
+      path.join(storageDir, "message", "ses_test456def", "msg_realmsgid.json"),
+      JSON.stringify({
+        role: "user",
+        agent: "default",
+        time: { created: 1700000000000 },
+      }),
+    )
+    await Bun.write(
+      path.join(storageDir, "part", "msg_realmsgid", "prt_from_filename.json"),
+      JSON.stringify({
+        id: "prt_different_in_json", // Stale! Should be ignored
+        messageID: "msg_different_in_json", // Stale! Should be ignored
+        sessionID: "ses_test456def",
+        type: "text",
+        text: "Hello",
+      }),
+    )
+
+    const stats = await JsonMigration.run(sqlite)
+
+    expect(stats?.parts).toBe(1)
+
+    const db = drizzle({ client: sqlite })
+    const parts = db.select().from(PartTable).all()
+    expect(parts.length).toBe(1)
+    expect(parts[0].id).toBe(PartID.make("prt_from_filename")) // Uses filename, not JSON id
+    expect(parts[0].message_id).toBe(MessageID.make("msg_realmsgid")) // Uses parent dir, not JSON messageID
+  })
+
+  test("skips orphaned sessions (no parent project)", async () => {
+    await Bun.write(
+      path.join(storageDir, "session", "proj_test123abc", "ses_orphan.json"),
+      JSON.stringify({
+        id: "ses_orphan",
+        projectID: "proj_nonexistent",
+        slug: "orphan",
+        directory: "/",
+        title: "Orphan",
+        version: "1.0.0",
+        time: { created: Date.now(), updated: Date.now() },
+      }),
+    )
+
+    const stats = await JsonMigration.run(sqlite)
+
+    expect(stats?.sessions).toBe(0)
+  })
+
+  test("uses directory path for projectID when JSON has stale value", async () => {
+    // Simulates the scenario where earlier migration moved sessions to new
+    // git-based project directories but didn't update the projectID field
+    const gitBasedProjectID = "abc123gitcommit"
+    await writeProject(storageDir, {
+      id: gitBasedProjectID,
+      worktree: "/test/path",
+      vcs: "git",
+      time: { created: Date.now(), updated: Date.now() },
+      sandboxes: [],
+    })
+
+    // Session is in the git-based directory but JSON still has old projectID
+    await writeSession(storageDir, gitBasedProjectID, {
+      id: "ses_migrated",
+      projectID: "old-project-name", // Stale! Should be ignored
+      slug: "migrated-session",
+      directory: "/test/path",
+      title: "Migrated Session",
+      version: "1.0.0",
+      time: { created: 1700000000000, updated: 1700000001000 },
+    })
+
+    const stats = await JsonMigration.run(sqlite)
+
+    expect(stats?.sessions).toBe(1)
+
+    const db = drizzle({ client: sqlite })
+    const sessions = db.select().from(SessionTable).all()
+    expect(sessions.length).toBe(1)
+    expect(sessions[0].id).toBe(SessionID.make("ses_migrated"))
+    expect(sessions[0].project_id).toBe(ProjectID.make(gitBasedProjectID)) // Uses directory, not stale JSON
+  })
+
+  test("uses filename for session id when JSON has different value", async () => {
+    await writeProject(storageDir, {
+      id: "proj_test123abc",
+      worktree: "/test/path",
+      time: { created: Date.now(), updated: Date.now() },
+      sandboxes: [],
+    })
+
+    await Bun.write(
+      path.join(storageDir, "session", "proj_test123abc", "ses_from_filename.json"),
+      JSON.stringify({
+        id: "ses_different_in_json", // Stale! Should be ignored
+        projectID: "proj_test123abc",
+        slug: "test-session",
+        directory: "/test/path",
+        title: "Test Session",
+        version: "1.0.0",
+        time: { created: 1700000000000, updated: 1700000001000 },
+      }),
+    )
+
+    const stats = await JsonMigration.run(sqlite)
+
+    expect(stats?.sessions).toBe(1)
+
+    const db = drizzle({ client: sqlite })
+    const sessions = db.select().from(SessionTable).all()
+    expect(sessions.length).toBe(1)
+    expect(sessions[0].id).toBe(SessionID.make("ses_from_filename")) // Uses filename, not JSON id
+    expect(sessions[0].project_id).toBe(ProjectID.make("proj_test123abc"))
+  })
+
+  test("is idempotent (running twice doesn't duplicate)", async () => {
+    await writeProject(storageDir, {
+      id: "proj_test123abc",
+      worktree: "/",
+      time: { created: Date.now(), updated: Date.now() },
+      sandboxes: [],
+    })
+
+    await JsonMigration.run(sqlite)
+    await JsonMigration.run(sqlite)
+
+    const db = drizzle({ client: sqlite })
+    const projects = db.select().from(ProjectTable).all()
+    expect(projects.length).toBe(1) // Still only 1 due to onConflictDoNothing
+  })
+
+  test("migrates todos", async () => {
+    await writeProject(storageDir, {
+      id: "proj_test123abc",
+      worktree: "/",
+      time: { created: Date.now(), updated: Date.now() },
+      sandboxes: [],
+    })
+    await writeSession(storageDir, "proj_test123abc", { ...fixtures.session })
+
+    // Create todo file (named by sessionID, contains array of todos)
+    await Bun.write(
+      path.join(storageDir, "todo", "ses_test456def.json"),
+      JSON.stringify([
+        {
+          id: "todo_1",
+          content: "First todo",
+          status: "pending",
+          priority: "high",
+        },
+        {
+          id: "todo_2",
+          content: "Second todo",
+          status: "completed",
+          priority: "medium",
+        },
+      ]),
+    )
+
+    const stats = await JsonMigration.run(sqlite)
+
+    expect(stats?.todos).toBe(2)
+
+    const db = drizzle({ client: sqlite })
+    const todos = db.select().from(TodoTable).orderBy(TodoTable.position).all()
+    expect(todos.length).toBe(2)
+    expect(todos[0].content).toBe("First todo")
+    expect(todos[0].status).toBe("pending")
+    expect(todos[0].priority).toBe("high")
+    expect(todos[0].position).toBe(0)
+    expect(todos[1].content).toBe("Second todo")
+    expect(todos[1].position).toBe(1)
+  })
+
+  test("todos are ordered by position", async () => {
+    await writeProject(storageDir, {
+      id: "proj_test123abc",
+      worktree: "/",
+      time: { created: Date.now(), updated: Date.now() },
+      sandboxes: [],
+    })
+    await writeSession(storageDir, "proj_test123abc", { ...fixtures.session })
+
+    await Bun.write(
+      path.join(storageDir, "todo", "ses_test456def.json"),
+      JSON.stringify([
+        { content: "Third", status: "pending", priority: "low" },
+        { content: "First", status: "pending", priority: "high" },
+        { content: "Second", status: "in_progress", priority: "medium" },
+      ]),
+    )
+
+    await JsonMigration.run(sqlite)
+
+    const db = drizzle({ client: sqlite })
+    const todos = db.select().from(TodoTable).orderBy(TodoTable.position).all()
+
+    expect(todos.length).toBe(3)
+    expect(todos[0].content).toBe("Third")
+    expect(todos[0].position).toBe(0)
+    expect(todos[1].content).toBe("First")
+    expect(todos[1].position).toBe(1)
+    expect(todos[2].content).toBe("Second")
+    expect(todos[2].position).toBe(2)
+  })
+
+  test("migrates permissions", async () => {
+    await writeProject(storageDir, {
+      id: "proj_test123abc",
+      worktree: "/",
+      time: { created: Date.now(), updated: Date.now() },
+      sandboxes: [],
+    })
+
+    // Create permission file (named by projectID, contains array of rules)
+    const permissionData = [
+      { permission: "file.read", pattern: "/test/file1.ts", action: "allow" as const },
+      { permission: "file.write", pattern: "/test/file2.ts", action: "ask" as const },
+      { permission: "command.run", pattern: "npm install", action: "deny" as const },
+    ]
+    await Bun.write(path.join(storageDir, "permission", "proj_test123abc.json"), JSON.stringify(permissionData))
+
+    const stats = await JsonMigration.run(sqlite)
+
+    expect(stats?.permissions).toBe(1)
+
+    const db = drizzle({ client: sqlite })
+    const permissions = db.select().from(PermissionTable).all()
+    expect(permissions.length).toBe(1)
+    expect(permissions[0].project_id).toBe("proj_test123abc")
+    expect(permissions[0].data).toEqual(permissionData)
+  })
+
+  test("returns empty stats when storage directory does not exist", async () => {
+    await fs.rm(storageDir, { recursive: true, force: true })
+
+    const stats = await JsonMigration.run(sqlite)
+
+    expect(stats.projects).toBe(0)
+    expect(stats.sessions).toBe(0)
+    expect(stats.messages).toBe(0)
+    expect(stats.parts).toBe(0)
+    expect(stats.todos).toBe(0)
+    expect(stats.permissions).toBe(0)
+    expect(stats.errors).toEqual([])
+  })
+
+  test("continues when a JSON file is unreadable and records an error", async () => {
+    await writeProject(storageDir, {
+      id: "proj_test123abc",
+      worktree: "/",
+      time: { created: Date.now(), updated: Date.now() },
+      sandboxes: [],
+    })
+    await Bun.write(path.join(storageDir, "project", "broken.json"), "{ invalid json")
+
+    const stats = await JsonMigration.run(sqlite)
+
+    expect(stats.projects).toBe(1)
+    expect(stats.errors.some((x) => x.includes("failed to read") && x.includes("broken.json"))).toBe(true)
+
+    const db = drizzle({ client: sqlite })
+    const projects = db.select().from(ProjectTable).all()
+    expect(projects.length).toBe(1)
+    expect(projects[0].id).toBe(ProjectID.make("proj_test123abc"))
+  })
+
+  test("skips invalid todo entries while preserving source positions", async () => {
+    await writeProject(storageDir, {
+      id: "proj_test123abc",
+      worktree: "/",
+      time: { created: Date.now(), updated: Date.now() },
+      sandboxes: [],
+    })
+    await writeSession(storageDir, "proj_test123abc", { ...fixtures.session })
+
+    await Bun.write(
+      path.join(storageDir, "todo", "ses_test456def.json"),
+      JSON.stringify([
+        { content: "keep-0", status: "pending", priority: "high" },
+        { content: "drop-1", priority: "low" },
+        { content: "keep-2", status: "completed", priority: "medium" },
+      ]),
+    )
+
+    const stats = await JsonMigration.run(sqlite)
+    expect(stats.todos).toBe(2)
+
+    const db = drizzle({ client: sqlite })
+    const todos = db.select().from(TodoTable).orderBy(TodoTable.position).all()
+    expect(todos.length).toBe(2)
+    expect(todos[0].content).toBe("keep-0")
+    expect(todos[0].position).toBe(0)
+    expect(todos[1].content).toBe("keep-2")
+    expect(todos[1].position).toBe(2)
+  })
+
+  test("skips orphaned todos and permissions", async () => {
+    await writeProject(storageDir, {
+      id: "proj_test123abc",
+      worktree: "/",
+      time: { created: Date.now(), updated: Date.now() },
+      sandboxes: [],
+    })
+    await writeSession(storageDir, "proj_test123abc", { ...fixtures.session })
+
+    await Bun.write(
+      path.join(storageDir, "todo", "ses_test456def.json"),
+      JSON.stringify([{ content: "valid", status: "pending", priority: "high" }]),
+    )
+    await Bun.write(
+      path.join(storageDir, "todo", "ses_missing.json"),
+      JSON.stringify([{ content: "orphan", status: "pending", priority: "high" }]),
+    )
+
+    await Bun.write(
+      path.join(storageDir, "permission", "proj_test123abc.json"),
+      JSON.stringify([{ permission: "file.read" }]),
+    )
+    await Bun.write(
+      path.join(storageDir, "permission", "proj_missing.json"),
+      JSON.stringify([{ permission: "file.write" }]),
+    )
+
+    const stats = await JsonMigration.run(sqlite)
+
+    expect(stats.todos).toBe(1)
+    expect(stats.permissions).toBe(1)
+
+    const db = drizzle({ client: sqlite })
+    expect(db.select().from(TodoTable).all().length).toBe(1)
+    expect(db.select().from(PermissionTable).all().length).toBe(1)
+  })
+
+  test("handles mixed corruption and partial validity in one migration run", async () => {
+    await writeProject(storageDir, {
+      id: "proj_test123abc",
+      worktree: "/ok",
+      time: { created: 1700000000000, updated: 1700000001000 },
+      sandboxes: [],
+    })
+    await Bun.write(
+      path.join(storageDir, "project", "proj_missing_id.json"),
+      JSON.stringify({ worktree: "/bad", sandboxes: [] }),
+    )
+    await Bun.write(path.join(storageDir, "project", "proj_broken.json"), "{ nope")
+
+    await writeSession(storageDir, "proj_test123abc", {
+      id: "ses_test456def",
+      projectID: "proj_test123abc",
+      slug: "ok",
+      directory: "/ok",
+      title: "Ok",
+      version: "1",
+      time: { created: 1700000000000, updated: 1700000001000 },
+    })
+    await Bun.write(
+      path.join(storageDir, "session", "proj_test123abc", "ses_missing_project.json"),
+      JSON.stringify({
+        id: "ses_missing_project",
+        slug: "bad",
+        directory: "/bad",
+        title: "Bad",
+        version: "1",
+      }),
+    )
+    await Bun.write(
+      path.join(storageDir, "session", "proj_test123abc", "ses_orphan.json"),
+      JSON.stringify({
+        id: "ses_orphan",
+        projectID: "proj_missing",
+        slug: "orphan",
+        directory: "/bad",
+        title: "Orphan",
+        version: "1",
+      }),
+    )
+
+    await Bun.write(
+      path.join(storageDir, "message", "ses_test456def", "msg_ok.json"),
+      JSON.stringify({ role: "user", time: { created: 1700000000000 } }),
+    )
+    await Bun.write(path.join(storageDir, "message", "ses_test456def", "msg_broken.json"), "{ nope")
+    await Bun.write(
+      path.join(storageDir, "message", "ses_missing", "msg_orphan.json"),
+      JSON.stringify({ role: "user", time: { created: 1700000000000 } }),
+    )
+
+    await Bun.write(
+      path.join(storageDir, "part", "msg_ok", "part_ok.json"),
+      JSON.stringify({ type: "text", text: "ok" }),
+    )
+    await Bun.write(
+      path.join(storageDir, "part", "msg_missing", "part_missing_message.json"),
+      JSON.stringify({ type: "text", text: "bad" }),
+    )
+    await Bun.write(path.join(storageDir, "part", "msg_ok", "part_broken.json"), "{ nope")
+
+    await Bun.write(
+      path.join(storageDir, "todo", "ses_test456def.json"),
+      JSON.stringify([
+        { content: "ok", status: "pending", priority: "high" },
+        { content: "skip", status: "pending" },
+      ]),
+    )
+    await Bun.write(
+      path.join(storageDir, "todo", "ses_missing.json"),
+      JSON.stringify([{ content: "orphan", status: "pending", priority: "high" }]),
+    )
+    await Bun.write(path.join(storageDir, "todo", "ses_broken.json"), "{ nope")
+
+    await Bun.write(
+      path.join(storageDir, "permission", "proj_test123abc.json"),
+      JSON.stringify([{ permission: "file.read" }]),
+    )
+    await Bun.write(
+      path.join(storageDir, "permission", "proj_missing.json"),
+      JSON.stringify([{ permission: "file.write" }]),
+    )
+    await Bun.write(path.join(storageDir, "permission", "proj_broken.json"), "{ nope")
+
+    const stats = await JsonMigration.run(sqlite)
+
+    // Projects: proj_test123abc (valid), proj_missing_id (now derives id from filename)
+    // Sessions: ses_test456def (valid), ses_missing_project (now uses dir path),
+    // ses_orphan (now uses dir path, ignores stale projectID)
+    expect(stats.projects).toBe(2)
+    expect(stats.sessions).toBe(3)
+    expect(stats.messages).toBe(1)
+    expect(stats.parts).toBe(1)
+    expect(stats.todos).toBe(1)
+    expect(stats.permissions).toBe(1)
+    expect(stats.errors.length).toBeGreaterThanOrEqual(3)
+
+    const db = drizzle({ client: sqlite })
+    expect(db.select().from(ProjectTable).all().length).toBe(2)
+    expect(db.select().from(SessionTable).all().length).toBe(3)
+    expect(db.select().from(MessageTable).all().length).toBe(1)
+    expect(db.select().from(PartTable).all().length).toBe(1)
+    expect(db.select().from(TodoTable).all().length).toBe(1)
+    expect(db.select().from(PermissionTable).all().length).toBe(1)
+  })
+})