@epoch-ai/cli 2.2.5 → 2.2.7

package/test/config/config.test.ts

@@ -0,0 +1,2337 @@
+import { test, expect, describe, mock, afterEach, beforeEach, spyOn } from "bun:test"
+import { Effect, Layer, Option } from "effect"
+import { NodeFileSystem, NodePath } from "@effect/platform-node"
+import { Config } from "../../src/config/config"
+import { Instance } from "../../src/project/instance"
+import { Auth } from "../../src/auth"
+import { AccessToken, Account, AccountID, OrgID } from "../../src/account"
+import { AppFileSystem } from "../../src/filesystem"
+import { provideTmpdirInstance } from "../fixture/fixture"
+import { tmpdir } from "../fixture/fixture"
+import * as CrossSpawnSpawner from "../../src/effect/cross-spawn-spawner"
+
+/** Infra layer that provides FileSystem, Path, ChildProcessSpawner for test fixtures */
+const infra = CrossSpawnSpawner.defaultLayer.pipe(
+  Layer.provideMerge(Layer.mergeAll(NodeFileSystem.layer, NodePath.layer)),
+)
+import path from "path"
+import fs from "fs/promises"
+import { pathToFileURL } from "url"
+import { Global } from "../../src/global"
+import { ProjectID } from "../../src/project/schema"
+import { Filesystem } from "../../src/util/filesystem"
+import * as Network from "../../src/util/network"
+import { Npm } from "../../src/npm"
+
+const emptyAccount = Layer.mock(Account.Service)({
+  active: () => Effect.succeed(Option.none()),
+  activeOrg: () => Effect.succeed(Option.none()),
+})
+
+const emptyAuth = Layer.mock(Auth.Service)({
+  all: () => Effect.succeed({}),
+})
+
+// Get managed config directory from environment (set in preload.ts)
+const managedConfigDir = process.env.EPOCHCLI_TEST_MANAGED_CONFIG_DIR!
+
+beforeEach(async () => {
+  await Config.invalidate(true)
+})
+
+afterEach(async () => {
+  await fs.rm(managedConfigDir, { force: true, recursive: true }).catch(() => {})
+  await Config.invalidate(true)
+})
+
+async function writeManagedSettings(settings: object, filename = "epochcli.json") {
+  await fs.mkdir(managedConfigDir, { recursive: true })
+  await Filesystem.write(path.join(managedConfigDir, filename), JSON.stringify(settings))
+}
+
+async function writeConfig(dir: string, config: object, name = "epochcli.json") {
+  await Filesystem.write(path.join(dir, name), JSON.stringify(config))
+}
+
+async function check(map: (dir: string) => string) {
+  if (process.platform !== "win32") return
+  await using globalTmp = await tmpdir()
+  await using tmp = await tmpdir({ git: true, config: { snapshot: true } })
+  const prev = Global.Path.config
+  ;(Global.Path as { config: string }).config = globalTmp.path
+  await Config.invalidate()
+  try {
+    await writeConfig(globalTmp.path, {
+      $schema: "https://epochcli.ai/config.json",
+      snapshot: false,
+    })
+    await Instance.provide({
+      directory: map(tmp.path),
+      fn: async () => {
+        const cfg = await Config.get()
+        expect(cfg.snapshot).toBe(true)
+        expect(Instance.directory).toBe(Filesystem.resolve(tmp.path))
+        expect(Instance.project.id).not.toBe(ProjectID.global)
+      },
+    })
+  } finally {
+    await Instance.disposeAll()
+    ;(Global.Path as { config: string }).config = prev
+    await Config.invalidate()
+  }
+}
+
+test("loads config with defaults when no files exist", async () => {
+  await using tmp = await tmpdir()
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.username).toBeDefined()
+    },
+  })
+})
+
+test("loads JSON config file", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await writeConfig(dir, {
+        $schema: "https://epochcli.ai/config.json",
+        model: "test/model",
+        username: "testuser",
+      })
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.model).toBe("test/model")
+      expect(config.username).toBe("testuser")
+    },
+  })
+})
+
+test("loads project config from Git Bash and MSYS2 paths on Windows", async () => {
+  // Git Bash and MSYS2 both use /<drive>/... paths on Windows.
+  await check((dir) => {
+    const drive = dir[0].toLowerCase()
+    const rest = dir.slice(2).replaceAll("\\", "/")
+    return `/${drive}${rest}`
+  })
+})
+
+test("loads project config from Cygwin paths on Windows", async () => {
+  await check((dir) => {
+    const drive = dir[0].toLowerCase()
+    const rest = dir.slice(2).replaceAll("\\", "/")
+    return `/cygdrive/${drive}${rest}`
+  })
+})
+
+test("ignores legacy tui keys in epochcli config", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await writeConfig(dir, {
+        $schema: "https://epochcli.ai/config.json",
+        model: "test/model",
+        theme: "legacy",
+        tui: { scroll_speed: 4 },
+      })
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.model).toBe("test/model")
+      expect((config as Record<string, unknown>).theme).toBeUndefined()
+      expect((config as Record<string, unknown>).tui).toBeUndefined()
+    },
+  })
+})
+
+test("loads JSONC config file", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(
+        path.join(dir, "epochcli.jsonc"),
+        `{
+        // This is a comment
+        "$schema": "https://epochcli.ai/config.json",
+        "model": "test/model",
+        "username": "testuser"
+      }`,
+      )
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.model).toBe("test/model")
+      expect(config.username).toBe("testuser")
+    },
+  })
+})
+
+test("jsonc overrides json in the same directory", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await writeConfig(
+        dir,
+        {
+          $schema: "https://epochcli.ai/config.json",
+          model: "base",
+          username: "base",
+        },
+        "epochcli.jsonc",
+      )
+      await writeConfig(dir, {
+        $schema: "https://epochcli.ai/config.json",
+        model: "override",
+      })
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.model).toBe("base")
+      expect(config.username).toBe("base")
+    },
+  })
+})
+
+test("handles environment variable substitution", async () => {
+  const originalEnv = process.env["TEST_VAR"]
+  process.env["TEST_VAR"] = "test-user"
+
+  try {
+    await using tmp = await tmpdir({
+      init: async (dir) => {
+        await writeConfig(dir, {
+          $schema: "https://epochcli.ai/config.json",
+          username: "{env:TEST_VAR}",
+        })
+      },
+    })
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const config = await Config.get()
+        expect(config.username).toBe("test-user")
+      },
+    })
+  } finally {
+    if (originalEnv !== undefined) {
+      process.env["TEST_VAR"] = originalEnv
+    } else {
+      delete process.env["TEST_VAR"]
+    }
+  }
+})
+
+test("preserves env variables when adding $schema to config", async () => {
+  const originalEnv = process.env["PRESERVE_VAR"]
+  process.env["PRESERVE_VAR"] = "secret_value"
+
+  try {
+    await using tmp = await tmpdir({
+      init: async (dir) => {
+        // Config without $schema - should trigger auto-add
+        await Filesystem.write(
+          path.join(dir, "epochcli.json"),
+          JSON.stringify({
+            username: "{env:PRESERVE_VAR}",
+          }),
+        )
+      },
+    })
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const config = await Config.get()
+        expect(config.username).toBe("secret_value")
+
+        // Read the file to verify the env variable was preserved
+        const content = await Filesystem.readText(path.join(tmp.path, "epochcli.json"))
+        expect(content).toContain("{env:PRESERVE_VAR}")
+        expect(content).not.toContain("secret_value")
+        expect(content).toContain("$schema")
+      },
+    })
+  } finally {
+    if (originalEnv !== undefined) {
+      process.env["PRESERVE_VAR"] = originalEnv
+    } else {
+      delete process.env["PRESERVE_VAR"]
+    }
+  }
+})
+
+test("resolves env templates in account config with account token", async () => {
+  const originalControlToken = process.env["EPOCHCLI_CONSOLE_TOKEN"]
+
+  const fakeAccount = Layer.mock(Account.Service)({
+    active: () =>
+      Effect.succeed(
+        Option.some({
+          id: AccountID.make("account-1"),
+          email: "user@example.com",
+          url: "https://control.example.com",
+          active_org_id: OrgID.make("org-1"),
+        }),
+      ),
+    activeOrg: () =>
+      Effect.succeed(
+        Option.some({
+          account: {
+            id: AccountID.make("account-1"),
+            email: "user@example.com",
+            url: "https://control.example.com",
+            active_org_id: OrgID.make("org-1"),
+          },
+          org: {
+            id: OrgID.make("org-1"),
+            name: "Example Org",
+          },
+        }),
+      ),
+    config: () =>
+      Effect.succeed(
+        Option.some({
+          provider: { epochcli: { options: { apiKey: "{env:EPOCHCLI_CONSOLE_TOKEN}" } } },
+        }),
+      ),
+    token: () => Effect.succeed(Option.some(AccessToken.make("st_test_token"))),
+  })
+
+  const layer = Config.layer.pipe(
+    Layer.provide(AppFileSystem.defaultLayer),
+    Layer.provide(emptyAuth),
+    Layer.provide(fakeAccount),
+    Layer.provideMerge(infra),
+  )
+
+  try {
+    await provideTmpdirInstance(() =>
+      Config.Service.use((svc) =>
+        Effect.gen(function* () {
+          const config = yield* svc.get()
+          expect(config.provider?.["epochcli"]?.options?.apiKey).toBe("st_test_token")
+        }),
+      ),
+    ).pipe(Effect.scoped, Effect.provide(layer), Effect.runPromise)
+  } finally {
+    if (originalControlToken !== undefined) {
+      process.env["EPOCHCLI_CONSOLE_TOKEN"] = originalControlToken
+    } else {
+      delete process.env["EPOCHCLI_CONSOLE_TOKEN"]
+    }
+  }
+})
+
+test("handles file inclusion substitution", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(path.join(dir, "included.txt"), "test-user")
+      await writeConfig(dir, {
+        $schema: "https://epochcli.ai/config.json",
+        username: "{file:included.txt}",
+      })
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.username).toBe("test-user")
+    },
+  })
+})
+
+test("handles file inclusion with replacement tokens", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(path.join(dir, "included.md"), "const out = await Bun.$`echo hi`")
+      await writeConfig(dir, {
+        $schema: "https://epochcli.ai/config.json",
+        username: "{file:included.md}",
+      })
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.username).toBe("const out = await Bun.$`echo hi`")
+    },
+  })
+})
+
+test("validates config schema and throws on invalid fields", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await writeConfig(dir, {
+        $schema: "https://epochcli.ai/config.json",
+        invalid_field: "should cause error",
+      })
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      // Strict schema should throw an error for invalid fields
+      await expect(Config.get()).rejects.toThrow()
+    },
+  })
+})
+
+test("throws error for invalid JSON", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(path.join(dir, "epochcli.json"), "{ invalid json }")
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      await expect(Config.get()).rejects.toThrow()
+    },
+  })
+})
+
+test("handles agent configuration", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await writeConfig(dir, {
+        $schema: "https://epochcli.ai/config.json",
+        agent: {
+          test_agent: {
+            model: "test/model",
+            temperature: 0.7,
+            description: "test agent",
+          },
+        },
+      })
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.agent?.["test_agent"]).toEqual(
+        expect.objectContaining({
+          model: "test/model",
+          temperature: 0.7,
+          description: "test agent",
+        }),
+      )
+    },
+  })
+})
+
+test("treats agent variant as model-scoped setting (not provider option)", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await writeConfig(dir, {
+        $schema: "https://epochcli.ai/config.json",
+        agent: {
+          test_agent: {
+            model: "openai/gpt-5.2",
+            variant: "xhigh",
+            max_tokens: 123,
+          },
+        },
+      })
+    },
+  })
+
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      const agent = config.agent?.["test_agent"]
+
+      expect(agent?.variant).toBe("xhigh")
+      expect(agent?.options).toMatchObject({
+        max_tokens: 123,
+      })
+      expect(agent?.options).not.toHaveProperty("variant")
+    },
+  })
+})
+
+test("handles command configuration", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await writeConfig(dir, {
+        $schema: "https://epochcli.ai/config.json",
+        command: {
+          test_command: {
+            template: "test template",
+            description: "test command",
+            agent: "test_agent",
+          },
+        },
+      })
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.command?.["test_command"]).toEqual({
+        template: "test template",
+        description: "test command",
+        agent: "test_agent",
+      })
+    },
+  })
+})
+
+test("migrates mode field to agent field", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          mode: {
+            test_mode: {
+              model: "test/model",
+              temperature: 0.5,
+            },
+          },
+        }),
+      )
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.agent?.["test_mode"]).toEqual({
+        model: "test/model",
+        temperature: 0.5,
+        mode: "primary",
+        options: {},
+        permission: {},
+      })
+    },
+  })
+})
+
+test("loads config from .epochcli directory", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      const epochcliDir = path.join(dir, ".epochcli")
+      await fs.mkdir(epochcliDir, { recursive: true })
+      const agentDir = path.join(epochcliDir, "agent")
+      await fs.mkdir(agentDir, { recursive: true })
+
+      await Filesystem.write(
+        path.join(agentDir, "test.md"),
+        `---
+model: test/model
+---
+Test agent prompt`,
+      )
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.agent?.["test"]).toEqual(
+        expect.objectContaining({
+          name: "test",
+          model: "test/model",
+          prompt: "Test agent prompt",
+        }),
+      )
+    },
+  })
+})
+
+test("loads agents from .epochcli/agents (plural)", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      const epochcliDir = path.join(dir, ".epochcli")
+      await fs.mkdir(epochcliDir, { recursive: true })
+
+      const agentsDir = path.join(epochcliDir, "agents")
+      await fs.mkdir(path.join(agentsDir, "nested"), { recursive: true })
+
+      await Filesystem.write(
+        path.join(agentsDir, "helper.md"),
+        `---
+model: test/model
+mode: subagent
+---
+Helper agent prompt`,
+      )
+
+      await Filesystem.write(
+        path.join(agentsDir, "nested", "child.md"),
+        `---
+model: test/model
+mode: subagent
+---
+Nested agent prompt`,
+      )
+    },
+  })
+
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+
+      expect(config.agent?.["helper"]).toMatchObject({
+        name: "helper",
+        model: "test/model",
+        mode: "subagent",
+        prompt: "Helper agent prompt",
+      })
+
+      expect(config.agent?.["nested/child"]).toMatchObject({
+        name: "nested/child",
+        model: "test/model",
+        mode: "subagent",
+        prompt: "Nested agent prompt",
+      })
+    },
+  })
+})
+
+test("loads commands from .epochcli/command (singular)", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      const epochcliDir = path.join(dir, ".epochcli")
+      await fs.mkdir(epochcliDir, { recursive: true })
+
+      const commandDir = path.join(epochcliDir, "command")
+      await fs.mkdir(path.join(commandDir, "nested"), { recursive: true })
+
+      await Filesystem.write(
+        path.join(commandDir, "hello.md"),
+        `---
+description: Test command
+---
+Hello from singular command`,
+      )
+
+      await Filesystem.write(
+        path.join(commandDir, "nested", "child.md"),
+        `---
+description: Nested command
+---
+Nested command template`,
+      )
+    },
+  })
+
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+
+      expect(config.command?.["hello"]).toEqual({
+        description: "Test command",
+        template: "Hello from singular command",
+      })
+
+      expect(config.command?.["nested/child"]).toEqual({
+        description: "Nested command",
+        template: "Nested command template",
+      })
+    },
+  })
+})
+
+test("loads commands from .epochcli/commands (plural)", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      const epochcliDir = path.join(dir, ".epochcli")
+      await fs.mkdir(epochcliDir, { recursive: true })
+
+      const commandsDir = path.join(epochcliDir, "commands")
+      await fs.mkdir(path.join(commandsDir, "nested"), { recursive: true })
+
+      await Filesystem.write(
+        path.join(commandsDir, "hello.md"),
+        `---
+description: Test command
+---
+Hello from plural commands`,
+      )
+
+      await Filesystem.write(
+        path.join(commandsDir, "nested", "child.md"),
+        `---
+description: Nested command
+---
+Nested command template`,
+      )
+    },
+  })
+
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+
+      expect(config.command?.["hello"]).toEqual({
+        description: "Test command",
+        template: "Hello from plural commands",
+      })
+
+      expect(config.command?.["nested/child"]).toEqual({
+        description: "Nested command",
+        template: "Nested command template",
+      })
+    },
+  })
+})
+
+test("updates config and writes to file", async () => {
+  await using tmp = await tmpdir()
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const newConfig = { model: "updated/model" }
+      await Config.update(newConfig as any)
+
+      const writtenConfig = await Filesystem.readJson(path.join(tmp.path, "config.json"))
+      expect(writtenConfig.model).toBe("updated/model")
+    },
+  })
+})
+
+test("gets config directories", async () => {
+  await using tmp = await tmpdir()
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const dirs = await Config.directories()
+      expect(dirs.length).toBeGreaterThanOrEqual(1)
+    },
+  })
+})
+
+test("does not try to install dependencies in read-only EPOCHCLI_CONFIG_DIR", async () => {
+  if (process.platform === "win32") return
+
+  await using tmp = await tmpdir<string>({
+    init: async (dir) => {
+      const ro = path.join(dir, "readonly")
+      await fs.mkdir(ro, { recursive: true })
+      await fs.chmod(ro, 0o555)
+      return ro
+    },
+    dispose: async (dir) => {
+      const ro = path.join(dir, "readonly")
+      await fs.chmod(ro, 0o755).catch(() => {})
+      return ro
+    },
+  })
+
+  const prev = process.env.EPOCHCLI_CONFIG_DIR
+  process.env.EPOCHCLI_CONFIG_DIR = tmp.extra
+
+  try {
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        await Config.get()
+      },
+    })
+  } finally {
+    if (prev === undefined) delete process.env.EPOCHCLI_CONFIG_DIR
+    else process.env.EPOCHCLI_CONFIG_DIR = prev
+  }
+})
+
+test("installs dependencies in writable EPOCHCLI_CONFIG_DIR", async () => {
+  await using tmp = await tmpdir<string>({
+    init: async (dir) => {
+      const cfg = path.join(dir, "configdir")
+      await fs.mkdir(cfg, { recursive: true })
+      return cfg
+    },
+  })
+
+  const prev = process.env.EPOCHCLI_CONFIG_DIR
+  process.env.EPOCHCLI_CONFIG_DIR = tmp.extra
+  const online = spyOn(Network, "online").mockReturnValue(false)
+  const install = spyOn(Npm, "install").mockImplementation(async (dir: string) => {
+    const mod = path.join(dir, "node_modules", "@epoch-ai", "plugin")
+    await fs.mkdir(mod, { recursive: true })
+    await Filesystem.write(
+      path.join(mod, "package.json"),
+      JSON.stringify({ name: "@epoch-ai/plugin", version: "1.0.0" }),
+    )
+  })
+
+  try {
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        await Config.get()
+        await Config.waitForDependencies()
+      },
+    })
+
+    expect(await Filesystem.exists(path.join(tmp.extra, "package.json"))).toBe(true)
+    expect(await Filesystem.exists(path.join(tmp.extra, ".gitignore"))).toBe(true)
+    expect(await Filesystem.readText(path.join(tmp.extra, ".gitignore"))).toContain("package-lock.json")
+  } finally {
+    online.mockRestore()
+    install.mockRestore()
+    if (prev === undefined) delete process.env.EPOCHCLI_CONFIG_DIR
+    else process.env.EPOCHCLI_CONFIG_DIR = prev
+  }
+})
+
+test("dedupes concurrent config dependency installs for the same dir", async () => {
+  await using tmp = await tmpdir()
+  const dir = path.join(tmp.path, "a")
+  await fs.mkdir(dir, { recursive: true })
+
+  const ticks: number[] = []
+  let calls = 0
+  let start = () => {}
+  let done = () => {}
+  let blocked = () => {}
+  const ready = new Promise<void>((resolve) => {
+    start = resolve
+  })
+  const gate = new Promise<void>((resolve) => {
+    done = resolve
+  })
+  const waiting = new Promise<void>((resolve) => {
+    blocked = resolve
+  })
+  const online = spyOn(Network, "online").mockReturnValue(false)
+  const targetDir = dir
+  const run = spyOn(Npm, "install").mockImplementation(async (d: string) => {
+    const hit = path.normalize(d) === path.normalize(targetDir)
+    if (hit) {
+      calls += 1
+      start()
+      await gate
+    }
+    const mod = path.join(d, "node_modules", "@epoch-ai", "plugin")
+    await fs.mkdir(mod, { recursive: true })
+    await Filesystem.write(
+      path.join(mod, "package.json"),
+      JSON.stringify({ name: "@epoch-ai/plugin", version: "1.0.0" }),
+    )
+    if (hit) {
+      start()
+      await gate
+    }
+  })
+
+  try {
+    const first = Config.installDependencies(dir)
+    await ready
+    const second = Config.installDependencies(dir, {
+      waitTick: (tick) => {
+        ticks.push(tick.attempt)
+        blocked()
+        blocked = () => {}
+      },
+    })
+    await waiting
+    done()
+    await Promise.all([first, second])
+  } finally {
+    online.mockRestore()
+    run.mockRestore()
+  }
+
+  expect(calls).toBe(2)
+  expect(ticks.length).toBeGreaterThan(0)
+  expect(await Filesystem.exists(path.join(dir, "package.json"))).toBe(true)
+})
+
+test("serializes config dependency installs across dirs", async () => {
+  if (process.platform !== "win32") return
+
+  await using tmp = await tmpdir()
+  const a = path.join(tmp.path, "a")
+  const b = path.join(tmp.path, "b")
+  await fs.mkdir(a, { recursive: true })
+  await fs.mkdir(b, { recursive: true })
+
+  let calls = 0
+  let open = 0
+  let peak = 0
+  let start = () => {}
+  let done = () => {}
+  const ready = new Promise<void>((resolve) => {
+    start = resolve
+  })
+  const gate = new Promise<void>((resolve) => {
+    done = resolve
+  })
+
+  const online = spyOn(Network, "online").mockReturnValue(false)
+  const run = spyOn(Npm, "install").mockImplementation(async (dir: string) => {
+    const cwd = path.normalize(dir)
+    const hit = cwd === path.normalize(a) || cwd === path.normalize(b)
+    if (hit) {
+      calls += 1
+      open += 1
+      peak = Math.max(peak, open)
+      if (calls === 1) {
+        start()
+        await gate
+      }
+    }
+    const mod = path.join(cwd, "node_modules", "@epoch-ai", "plugin")
+    await fs.mkdir(mod, { recursive: true })
+    await Filesystem.write(
+      path.join(mod, "package.json"),
+      JSON.stringify({ name: "@epoch-ai/plugin", version: "1.0.0" }),
+    )
+    if (hit) {
+      open -= 1
+    }
+  })
+
+  try {
+    const first = Config.installDependencies(a)
+    await ready
+    const second = Config.installDependencies(b)
+    done()
+    await Promise.all([first, second])
+  } finally {
+    online.mockRestore()
+    run.mockRestore()
+  }
+
+  expect(calls).toBe(2)
+  expect(peak).toBe(1)
+})
+
+test("resolves scoped npm plugins in config", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      const pluginDir = path.join(dir, "node_modules", "@scope", "plugin")
+      await fs.mkdir(pluginDir, { recursive: true })
+
+      await Filesystem.write(
+        path.join(dir, "package.json"),
+        JSON.stringify({ name: "config-fixture", version: "1.0.0", type: "module" }, null, 2),
+      )
+
+      await Filesystem.write(
+        path.join(pluginDir, "package.json"),
+        JSON.stringify(
+          {
+            name: "@scope/plugin",
+            version: "1.0.0",
+            type: "module",
+            main: "./index.js",
+          },
+          null,
+          2,
+        ),
+      )
+
+      await Filesystem.write(path.join(pluginDir, "index.js"), "export default {}\n")
+
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({ $schema: "https://epochcli.ai/config.json", plugin: ["@scope/plugin"] }, null, 2),
+      )
+    },
+  })
+
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      const pluginEntries = config.plugin ?? []
+      expect(pluginEntries).toContain("@scope/plugin")
+    },
+  })
+})
+
+test("merges plugin arrays from global and local configs", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      // Create a nested project structure with local .epochcli config
+      const projectDir = path.join(dir, "project")
+      const epochcliDir = path.join(projectDir, ".epochcli")
+      await fs.mkdir(epochcliDir, { recursive: true })
+
+      // Global config with plugins
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          plugin: ["global-plugin-1", "global-plugin-2"],
+        }),
+      )
+
+      // Local .epochcli config with different plugins
+      await Filesystem.write(
+        path.join(epochcliDir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          plugin: ["local-plugin-1"],
+        }),
+      )
+    },
+  })
+
+  await Instance.provide({
+    directory: path.join(tmp.path, "project"),
+    fn: async () => {
+      const config = await Config.get()
+      const plugins = config.plugin ?? []
+
+      // Should contain both global and local plugins
+      expect(plugins.some((p) => p.includes("global-plugin-1"))).toBe(true)
+      expect(plugins.some((p) => p.includes("global-plugin-2"))).toBe(true)
+      expect(plugins.some((p) => p.includes("local-plugin-1"))).toBe(true)
+
+      // Should have all 3 plugins (not replaced, but merged)
+      const pluginNames = plugins.filter((p) => p.includes("global-plugin") || p.includes("local-plugin"))
+      expect(pluginNames.length).toBeGreaterThanOrEqual(3)
+    },
+  })
+})
+
+test("does not error when only custom agent is a subagent", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      const epochcliDir = path.join(dir, ".epochcli")
+      await fs.mkdir(epochcliDir, { recursive: true })
+      const agentDir = path.join(epochcliDir, "agent")
+      await fs.mkdir(agentDir, { recursive: true })
+
+      await Filesystem.write(
+        path.join(agentDir, "helper.md"),
+        `---
+model: test/model
+mode: subagent
+---
+Helper subagent prompt`,
+      )
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.agent?.["helper"]).toMatchObject({
+        name: "helper",
+        model: "test/model",
+        mode: "subagent",
+        prompt: "Helper subagent prompt",
+      })
+    },
+  })
+})
+
+test("merges instructions arrays from global and local configs", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      const projectDir = path.join(dir, "project")
+      const epochcliDir = path.join(projectDir, ".epochcli")
+      await fs.mkdir(epochcliDir, { recursive: true })
+
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          instructions: ["global-instructions.md", "shared-rules.md"],
+        }),
+      )
+
+      await Filesystem.write(
+        path.join(epochcliDir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          instructions: ["local-instructions.md"],
+        }),
+      )
+    },
+  })
+
+  await Instance.provide({
+    directory: path.join(tmp.path, "project"),
+    fn: async () => {
+      const config = await Config.get()
+      const instructions = config.instructions ?? []
+
+      expect(instructions).toContain("global-instructions.md")
+      expect(instructions).toContain("shared-rules.md")
+      expect(instructions).toContain("local-instructions.md")
+      expect(instructions.length).toBe(3)
+    },
+  })
+})
+
+test("deduplicates duplicate instructions from global and local configs", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      const projectDir = path.join(dir, "project")
+      const epochcliDir = path.join(projectDir, ".epochcli")
+      await fs.mkdir(epochcliDir, { recursive: true })
+
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          instructions: ["duplicate.md", "global-only.md"],
+        }),
+      )
+
+      await Filesystem.write(
+        path.join(epochcliDir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          instructions: ["duplicate.md", "local-only.md"],
+        }),
+      )
+    },
+  })
+
+  await Instance.provide({
+    directory: path.join(tmp.path, "project"),
+    fn: async () => {
+      const config = await Config.get()
+      const instructions = config.instructions ?? []
+
+      expect(instructions).toContain("global-only.md")
+      expect(instructions).toContain("local-only.md")
+      expect(instructions).toContain("duplicate.md")
+
+      const duplicates = instructions.filter((i) => i === "duplicate.md")
+      expect(duplicates.length).toBe(1)
+      expect(instructions.length).toBe(3)
+    },
+  })
+})
+
+test("deduplicates duplicate plugins from global and local configs", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      // Create a nested project structure with local .epochcli config
+      const projectDir = path.join(dir, "project")
+      const epochcliDir = path.join(projectDir, ".epochcli")
+      await fs.mkdir(epochcliDir, { recursive: true })
+
+      // Global config with plugins
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          plugin: ["duplicate-plugin", "global-plugin-1"],
+        }),
+      )
+
+      // Local .epochcli config with some overlapping plugins
+      await Filesystem.write(
+        path.join(epochcliDir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          plugin: ["duplicate-plugin", "local-plugin-1"],
+        }),
+      )
+    },
+  })
+
+  await Instance.provide({
+    directory: path.join(tmp.path, "project"),
+    fn: async () => {
+      const config = await Config.get()
+      const plugins = config.plugin ?? []
+
+      // Should contain all unique plugins
+      expect(plugins.some((p) => p.includes("global-plugin-1"))).toBe(true)
+      expect(plugins.some((p) => p.includes("local-plugin-1"))).toBe(true)
+      expect(plugins.some((p) => p.includes("duplicate-plugin"))).toBe(true)
+
+      // Should deduplicate the duplicate plugin
+      const duplicatePlugins = plugins.filter((p) => p.includes("duplicate-plugin"))
+      expect(duplicatePlugins.length).toBe(1)
+
+      // Should have exactly 3 unique plugins
+      const pluginNames = plugins.filter(
+        (p) => p.includes("global-plugin") || p.includes("local-plugin") || p.includes("duplicate-plugin"),
+      )
+      expect(pluginNames.length).toBe(3)
+    },
+  })
+})
+
+test("keeps plugin origins aligned with merged plugin list", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      const project = path.join(dir, "project")
+      const local = path.join(project, ".epochcli")
+      await fs.mkdir(local, { recursive: true })
+
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          plugin: [["shared-plugin@1.0.0", { source: "global" }], "global-only@1.0.0"],
+        }),
+      )
+
+      await Filesystem.write(
+        path.join(local, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          plugin: [["shared-plugin@2.0.0", { source: "local" }], "local-only@1.0.0"],
+        }),
+      )
+    },
+  })
+
+  await Instance.provide({
+    directory: path.join(tmp.path, "project"),
+    fn: async () => {
+      const cfg = await Config.get()
+      const plugins = cfg.plugin ?? []
+      const origins = cfg.plugin_origins ?? []
+      const names = plugins.map((item) => Config.pluginSpecifier(item))
+
+      expect(names).toContain("shared-plugin@2.0.0")
+      expect(names).not.toContain("shared-plugin@1.0.0")
+      expect(names).toContain("global-only@1.0.0")
+      expect(names).toContain("local-only@1.0.0")
+
+      expect(origins.map((item) => item.spec)).toEqual(plugins)
+      const hit = origins.find((item) => Config.pluginSpecifier(item.spec) === "shared-plugin@2.0.0")
+      expect(hit?.scope).toBe("local")
+    },
+  })
+})
+
+// Legacy tools migration tests
+
+test("migrates legacy tools config to permissions - allow", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          agent: {
+            test: {
+              tools: {
+                bash: true,
+                read: true,
+              },
+            },
+          },
+        }),
+      )
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.agent?.["test"]?.permission).toEqual({
+        bash: "allow",
+        read: "allow",
+      })
+    },
+  })
+})
+
+test("migrates legacy tools config to permissions - deny", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          agent: {
+            test: {
+              tools: {
+                bash: false,
+                webfetch: false,
+              },
+            },
+          },
+        }),
+      )
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.agent?.["test"]?.permission).toEqual({
+        bash: "deny",
+        webfetch: "deny",
+      })
+    },
+  })
+})
+
+test("migrates legacy write tool to edit permission", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          agent: {
+            test: {
+              tools: {
+                write: true,
+              },
+            },
+          },
+        }),
+      )
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.agent?.["test"]?.permission).toEqual({
+        edit: "allow",
+      })
+    },
+  })
+})
+
+// Managed settings tests
+// Note: preload.ts sets EPOCHCLI_TEST_MANAGED_CONFIG which Global.Path.managedConfig uses
+
+test("managed settings override user settings", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await writeConfig(dir, {
+        $schema: "https://epochcli.ai/config.json",
+        model: "user/model",
+        username: "testuser",
+      })
+    },
+  })
+
+  await writeManagedSettings({
+    $schema: "https://epochcli.ai/config.json",
+    model: "managed/model",
+  })
+
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.model).toBe("managed/model")
+      expect(config.username).toBe("testuser")
+    },
+  })
+})
+
+test("managed settings override project settings", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await writeConfig(dir, {
+        $schema: "https://epochcli.ai/config.json",
+        autoupdate: true,
+        disabled_providers: [],
+      })
+    },
+  })
+
+  await writeManagedSettings({
+    $schema: "https://epochcli.ai/config.json",
+    autoupdate: false,
+    disabled_providers: ["openai"],
+  })
+
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.autoupdate).toBe(false)
+      expect(config.disabled_providers).toEqual(["openai"])
+    },
+  })
+})
+
+test("missing managed settings file is not an error", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await writeConfig(dir, {
+        $schema: "https://epochcli.ai/config.json",
+        model: "user/model",
+      })
+    },
+  })
+
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.model).toBe("user/model")
+    },
+  })
+})
+
+test("migrates legacy edit tool to edit permission", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          agent: {
+            test: {
+              tools: {
+                edit: false,
+              },
+            },
+          },
+        }),
+      )
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.agent?.["test"]?.permission).toEqual({
+        edit: "deny",
+      })
+    },
+  })
+})
+
+test("migrates legacy patch tool to edit permission", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          agent: {
+            test: {
+              tools: {
+                patch: true,
+              },
+            },
+          },
+        }),
+      )
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.agent?.["test"]?.permission).toEqual({
+        edit: "allow",
+      })
+    },
+  })
+})
+
+test("migrates legacy multiedit tool to edit permission", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          agent: {
+            test: {
+              tools: {
+                multiedit: false,
+              },
+            },
+          },
+        }),
+      )
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.agent?.["test"]?.permission).toEqual({
+        edit: "deny",
+      })
+    },
+  })
+})
+
+test("migrates mixed legacy tools config", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          agent: {
+            test: {
+              tools: {
+                bash: true,
+                write: true,
+                read: false,
+                webfetch: true,
+              },
+            },
+          },
+        }),
+      )
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.agent?.["test"]?.permission).toEqual({
+        bash: "allow",
+        edit: "allow",
+        read: "deny",
+        webfetch: "allow",
+      })
+    },
+  })
+})
+
+test("merges legacy tools with existing permission config", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          agent: {
+            test: {
+              permission: {
+                glob: "allow",
+              },
+              tools: {
+                bash: true,
+              },
+            },
+          },
+        }),
+      )
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.agent?.["test"]?.permission).toEqual({
+        glob: "allow",
+        bash: "allow",
+      })
+    },
+  })
+})
+
+test("permission config preserves key order", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          permission: {
+            "*": "deny",
+            edit: "ask",
+            write: "ask",
+            external_directory: "ask",
+            read: "allow",
+            todowrite: "allow",
+            "thoughts_*": "allow",
+            "reasoning_model_*": "allow",
+            "tools_*": "allow",
+            "pr_comments_*": "allow",
+          },
+        }),
+      )
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(Object.keys(config.permission!)).toEqual([
+        "*",
+        "edit",
+        "write",
+        "external_directory",
+        "read",
+        "todowrite",
+        "thoughts_*",
+        "reasoning_model_*",
+        "tools_*",
+        "pr_comments_*",
+      ])
+    },
+  })
+})
+
+// MCP config merging tests
+
+test("project config can override MCP server enabled status", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      // Simulates a base config (like from remote .well-known) with disabled MCP
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          mcp: {
+            jira: {
+              type: "remote",
+              url: "https://jira.example.com/mcp",
+              enabled: false,
+            },
+            wiki: {
+              type: "remote",
+              url: "https://wiki.example.com/mcp",
+              enabled: false,
+            },
+          },
+        }),
+      )
+      // Project config enables just jira
+      await Filesystem.write(
+        path.join(dir, "epochcli.jsonc"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          mcp: {
+            jira: {
+              type: "remote",
+              url: "https://jira.example.com/mcp",
+              enabled: true,
+            },
+          },
+        }),
+      )
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      // jira should be enabled (overridden by project config)
+      expect(config.mcp?.jira).toEqual({
+        type: "remote",
+        url: "https://jira.example.com/mcp",
+        enabled: true,
+      })
+      // wiki should still be disabled (not overridden)
+      expect(config.mcp?.wiki).toEqual({
+        type: "remote",
+        url: "https://wiki.example.com/mcp",
+        enabled: false,
+      })
+    },
+  })
+})
+
+test("MCP config deep merges preserving base config properties", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      // Base config with full MCP definition
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          mcp: {
+            myserver: {
+              type: "remote",
+              url: "https://myserver.example.com/mcp",
+              enabled: false,
+              headers: {
+                "X-Custom-Header": "value",
+              },
+            },
+          },
+        }),
+      )
+      // Override just enables it, should preserve other properties
+      await Filesystem.write(
+        path.join(dir, "epochcli.jsonc"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          mcp: {
+            myserver: {
+              type: "remote",
+              url: "https://myserver.example.com/mcp",
+              enabled: true,
+            },
+          },
+        }),
+      )
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.mcp?.myserver).toEqual({
+        type: "remote",
+        url: "https://myserver.example.com/mcp",
+        enabled: true,
+        headers: {
+          "X-Custom-Header": "value",
+        },
+      })
+    },
+  })
+})
+
+test("local .epochcli config can override MCP from project config", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      // Project config with disabled MCP
+      await Filesystem.write(
+        path.join(dir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          mcp: {
+            docs: {
+              type: "remote",
+              url: "https://docs.example.com/mcp",
+              enabled: false,
+            },
+          },
+        }),
+      )
+      // Local .epochcli directory config enables it
+      const epochcliDir = path.join(dir, ".epochcli")
+      await fs.mkdir(epochcliDir, { recursive: true })
+      await Filesystem.write(
+        path.join(epochcliDir, "epochcli.json"),
+        JSON.stringify({
+          $schema: "https://epochcli.ai/config.json",
+          mcp: {
+            docs: {
+              type: "remote",
+              url: "https://docs.example.com/mcp",
+              enabled: true,
+            },
+          },
+        }),
+      )
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await Config.get()
+      expect(config.mcp?.docs?.enabled).toBe(true)
+    },
+  })
+})
+
+test("project config overrides remote well-known config", async () => {
+  const originalFetch = globalThis.fetch
+  let fetchedUrl: string | undefined
+  globalThis.fetch = mock((url: string | URL | Request) => {
+    const urlStr = url.toString()
+    if (urlStr.includes(".well-known/epochcli")) {
+      fetchedUrl = urlStr
+      return Promise.resolve(
+        new Response(
+          JSON.stringify({
+            config: {
+              mcp: { jira: { type: "remote", url: "https://jira.example.com/mcp", enabled: false } },
+            },
+          }),
+          { status: 200 },
+        ),
+      )
+    }
+    return originalFetch(url)
+  }) as unknown as typeof fetch
+
+  const fakeAuth = Layer.mock(Auth.Service)({
+    all: () =>
+      Effect.succeed({
+        "https://example.com": new Auth.WellKnown({ type: "wellknown", key: "TEST_TOKEN", token: "test-token" }),
+      }),
+  })
+
+  const layer = Config.layer.pipe(
+    Layer.provide(AppFileSystem.defaultLayer),
+    Layer.provide(fakeAuth),
+    Layer.provide(emptyAccount),
+    Layer.provideMerge(infra),
+  )
+
+  try {
+    await provideTmpdirInstance(
+      () =>
+        Config.Service.use((svc) =>
+          Effect.gen(function* () {
+            const config = yield* svc.get()
+            expect(fetchedUrl).toBe("https://example.com/.well-known/epochcli")
+            expect(config.mcp?.jira?.enabled).toBe(true)
+          }),
+        ),
+      {
+        git: true,
+        config: { mcp: { jira: { type: "remote", url: "https://jira.example.com/mcp", enabled: true } } },
+      },
+    ).pipe(Effect.scoped, Effect.provide(layer), Effect.runPromise)
+  } finally {
+    globalThis.fetch = originalFetch
+  }
+})
+
+test("wellknown URL with trailing slash is normalized", async () => {
+  const originalFetch = globalThis.fetch
+  let fetchedUrl: string | undefined
+  globalThis.fetch = mock((url: string | URL | Request) => {
+    const urlStr = url.toString()
+    if (urlStr.includes(".well-known/epochcli")) {
+      fetchedUrl = urlStr
+      return Promise.resolve(
+        new Response(
+          JSON.stringify({
+            config: {
+              mcp: { slack: { type: "remote", url: "https://slack.example.com/mcp", enabled: true } },
+            },
+          }),
+          { status: 200 },
+        ),
+      )
+    }
+    return originalFetch(url)
+  }) as unknown as typeof fetch
+
+  const fakeAuth = Layer.mock(Auth.Service)({
+    all: () =>
+      Effect.succeed({
+        "https://example.com/": new Auth.WellKnown({ type: "wellknown", key: "TEST_TOKEN", token: "test-token" }),
+      }),
+  })
+
+  const layer = Config.layer.pipe(
+    Layer.provide(AppFileSystem.defaultLayer),
+    Layer.provide(fakeAuth),
+    Layer.provide(emptyAccount),
+    Layer.provideMerge(infra),
+  )
+
+  try {
+    await provideTmpdirInstance(
+      () =>
+        Config.Service.use((svc) =>
+          Effect.gen(function* () {
+            yield* svc.get()
+            expect(fetchedUrl).toBe("https://example.com/.well-known/epochcli")
+          }),
+        ),
+      { git: true },
+    ).pipe(Effect.scoped, Effect.provide(layer), Effect.runPromise)
+  } finally {
+    globalThis.fetch = originalFetch
+  }
+})
+
+describe("resolvePluginSpec", () => {
+  test("keeps package specs unchanged", async () => {
+    await using tmp = await tmpdir()
+    const file = path.join(tmp.path, "epochcli.json")
+    expect(await Config.resolvePluginSpec("oh-my-epochcli@2.4.3", file)).toBe("oh-my-epochcli@2.4.3")
+    expect(await Config.resolvePluginSpec("@scope/pkg", file)).toBe("@scope/pkg")
+  })
+
+  test("resolves windows-style relative plugin directory specs", async () => {
+    if (process.platform !== "win32") return
+
+    await using tmp = await tmpdir({
+      init: async (dir) => {
+        const plugin = path.join(dir, "plugin")
+        await fs.mkdir(plugin, { recursive: true })
+        await Filesystem.write(path.join(plugin, "index.ts"), "export default {}")
+      },
+    })
+
+    const file = path.join(tmp.path, "epochcli.json")
+    const hit = await Config.resolvePluginSpec(".\\plugin", file)
+    expect(Config.pluginSpecifier(hit)).toBe(pathToFileURL(path.join(tmp.path, "plugin", "index.ts")).href)
+  })
+
+  test("resolves relative file plugin paths to file urls", async () => {
+    await using tmp = await tmpdir({
+      init: async (dir) => {
+        await Filesystem.write(path.join(dir, "plugin.ts"), "export default {}")
+      },
+    })
+
+    const file = path.join(tmp.path, "epochcli.json")
+    const hit = await Config.resolvePluginSpec("./plugin.ts", file)
+    expect(Config.pluginSpecifier(hit)).toBe(pathToFileURL(path.join(tmp.path, "plugin.ts")).href)
+  })
+
+  test("resolves plugin directory paths to directory urls", async () => {
+    await using tmp = await tmpdir({
+      init: async (dir) => {
+        const plugin = path.join(dir, "plugin")
+        await fs.mkdir(plugin, { recursive: true })
+        await Filesystem.writeJson(path.join(plugin, "package.json"), {
+          name: "demo-plugin",
+          type: "module",
+          main: "./index.ts",
+        })
+        await Filesystem.write(path.join(plugin, "index.ts"), "export default {}")
+      },
+    })
+
+    const file = path.join(tmp.path, "epochcli.json")
+    const hit = await Config.resolvePluginSpec("./plugin", file)
+    expect(Config.pluginSpecifier(hit)).toBe(pathToFileURL(path.join(tmp.path, "plugin")).href)
+  })
+
+  test("resolves plugin directories without package.json to index.ts", async () => {
+    await using tmp = await tmpdir({
+      init: async (dir) => {
+        const plugin = path.join(dir, "plugin")
+        await fs.mkdir(plugin, { recursive: true })
+        await Filesystem.write(path.join(plugin, "index.ts"), "export default {}")
+      },
+    })
+
+    const file = path.join(tmp.path, "epochcli.json")
+    const hit = await Config.resolvePluginSpec("./plugin", file)
+    expect(Config.pluginSpecifier(hit)).toBe(pathToFileURL(path.join(tmp.path, "plugin", "index.ts")).href)
+  })
+})
+
+describe("deduplicatePluginOrigins", () => {
+  const dedupe = (plugins: Config.PluginSpec[]) =>
+    Config.deduplicatePluginOrigins(
+      plugins.map((spec) => ({
+        spec,
+        source: "",
+        scope: "global" as const,
+      })),
+    ).map((item) => item.spec)
+
+  test("removes duplicates keeping higher priority (later entries)", () => {
+    const plugins = ["global-plugin@1.0.0", "shared-plugin@1.0.0", "local-plugin@2.0.0", "shared-plugin@2.0.0"]
+
+    const result = dedupe(plugins)
+
+    expect(result).toContain("global-plugin@1.0.0")
+    expect(result).toContain("local-plugin@2.0.0")
+    expect(result).toContain("shared-plugin@2.0.0")
+    expect(result).not.toContain("shared-plugin@1.0.0")
+    expect(result.length).toBe(3)
+  })
+
+  test("keeps path plugins separate from package plugins", () => {
+    const plugins = ["oh-my-epochcli@2.4.3", "file:///project/.epochcli/plugin/oh-my-epochcli.js"]
+
+    const result = dedupe(plugins)
+
+    expect(result).toEqual(plugins)
+  })
+
+  test("deduplicates direct path plugins by exact spec", () => {
+    const plugins = ["file:///project/.epochcli/plugin/demo.ts", "file:///project/.epochcli/plugin/demo.ts"]
+
+    const result = dedupe(plugins)
+
+    expect(result).toEqual(["file:///project/.epochcli/plugin/demo.ts"])
+  })
+
+  test("preserves order of remaining plugins", () => {
+    const plugins = ["a-plugin@1.0.0", "b-plugin@1.0.0", "c-plugin@1.0.0"]
+
+    const result = dedupe(plugins)
+
+    expect(result).toEqual(["a-plugin@1.0.0", "b-plugin@1.0.0", "c-plugin@1.0.0"])
+  })
+
+  test("loads auto-discovered local plugins as file urls", async () => {
+    await using tmp = await tmpdir({
+      init: async (dir) => {
+        const projectDir = path.join(dir, "project")
+        const epochcliDir = path.join(projectDir, ".epochcli")
+        const pluginDir = path.join(epochcliDir, "plugin")
+        await fs.mkdir(pluginDir, { recursive: true })
+
+        await Filesystem.write(
+          path.join(dir, "epochcli.json"),
+          JSON.stringify({
+            $schema: "https://epochcli.ai/config.json",
+            plugin: ["my-plugin@1.0.0"],
+          }),
+        )
+
+        await Filesystem.write(path.join(pluginDir, "my-plugin.js"), "export default {}")
+      },
+    })
+
+    await Instance.provide({
+      directory: path.join(tmp.path, "project"),
+      fn: async () => {
+        const config = await Config.get()
+        const plugins = config.plugin ?? []
+
+        expect(plugins.some((p) => Config.pluginSpecifier(p) === "my-plugin@1.0.0")).toBe(true)
+        expect(plugins.some((p) => Config.pluginSpecifier(p).startsWith("file://"))).toBe(true)
+      },
+    })
+  })
+})
+
+describe("EPOCHCLI_DISABLE_PROJECT_CONFIG", () => {
+  test("skips project config files when flag is set", async () => {
+    const originalEnv = process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"]
+    process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"] = "true"
+
+    try {
+      await using tmp = await tmpdir({
+        init: async (dir) => {
+          // Create a project config that would normally be loaded
+          await Filesystem.write(
+            path.join(dir, "epochcli.json"),
+            JSON.stringify({
+              $schema: "https://epochcli.ai/config.json",
+              model: "project/model",
+              username: "project-user",
+            }),
+          )
+        },
+      })
+      await Instance.provide({
+        directory: tmp.path,
+        fn: async () => {
+          const config = await Config.get()
+          // Project config should NOT be loaded - model should be default, not "project/model"
+          expect(config.model).not.toBe("project/model")
+          expect(config.username).not.toBe("project-user")
+        },
+      })
+    } finally {
+      if (originalEnv === undefined) {
+        delete process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"]
+      } else {
+        process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"] = originalEnv
+      }
+    }
+  })
+
+  test("skips project .epochcli/ directories when flag is set", async () => {
+    const originalEnv = process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"]
+    process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"] = "true"
+
+    try {
+      await using tmp = await tmpdir({
+        init: async (dir) => {
+          // Create a .epochcli directory with a command
+          const epochcliDir = path.join(dir, ".epochcli", "command")
+          await fs.mkdir(epochcliDir, { recursive: true })
+          await Filesystem.write(path.join(epochcliDir, "test-cmd.md"), "# Test Command\nThis is a test command.")
+        },
+      })
+      await Instance.provide({
+        directory: tmp.path,
+        fn: async () => {
+          const directories = await Config.directories()
+          // Project .epochcli should NOT be in directories list
+          const hasProjectEpoch = directories.some((d) => d.startsWith(tmp.path))
+          expect(hasProjectEpoch).toBe(false)
+        },
+      })
+    } finally {
+      if (originalEnv === undefined) {
+        delete process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"]
+      } else {
+        process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"] = originalEnv
+      }
+    }
+  })
+
+  test("still loads global config when flag is set", async () => {
+    const originalEnv = process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"]
+    process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"] = "true"
+
+    try {
+      await using tmp = await tmpdir()
+      await Instance.provide({
+        directory: tmp.path,
+        fn: async () => {
+          // Should still get default config (from global or defaults)
+          const config = await Config.get()
+          expect(config).toBeDefined()
+          expect(config.username).toBeDefined()
+        },
+      })
+    } finally {
+      if (originalEnv === undefined) {
+        delete process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"]
+      } else {
+        process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"] = originalEnv
+      }
+    }
+  })
+
+  test("skips relative instructions with warning when flag is set but no config dir", async () => {
+    const originalDisable = process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"]
+    const originalConfigDir = process.env["EPOCHCLI_CONFIG_DIR"]
+
+    try {
+      // Ensure no config dir is set
+      delete process.env["EPOCHCLI_CONFIG_DIR"]
+      process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"] = "true"
+
+      await using tmp = await tmpdir({
+        init: async (dir) => {
+          // Create a config with relative instruction path
+          await Filesystem.write(
+            path.join(dir, "epochcli.json"),
+            JSON.stringify({
+              $schema: "https://epochcli.ai/config.json",
+              instructions: ["./CUSTOM.md"],
+            }),
+          )
+          // Create the instruction file (should be skipped)
+          await Filesystem.write(path.join(dir, "CUSTOM.md"), "# Custom Instructions")
+        },
+      })
+
+      await Instance.provide({
+        directory: tmp.path,
+        fn: async () => {
+          // The relative instruction should be skipped without error
+          // We're mainly verifying this doesn't throw and the config loads
+          const config = await Config.get()
+          expect(config).toBeDefined()
+          // The instruction should have been skipped (warning logged)
+          // We can't easily test the warning was logged, but we verify
+          // the relative path didn't cause an error
+        },
+      })
+    } finally {
+      if (originalDisable === undefined) {
+        delete process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"]
+      } else {
+        process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"] = originalDisable
+      }
+      if (originalConfigDir === undefined) {
+        delete process.env["EPOCHCLI_CONFIG_DIR"]
+      } else {
+        process.env["EPOCHCLI_CONFIG_DIR"] = originalConfigDir
+      }
+    }
+  })
+
+  test("EPOCHCLI_CONFIG_DIR still works when flag is set", async () => {
+    const originalDisable = process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"]
+    const originalConfigDir = process.env["EPOCHCLI_CONFIG_DIR"]
+
+    try {
+      await using configDirTmp = await tmpdir({
+        init: async (dir) => {
+          // Create config in the custom config dir
+          await Filesystem.write(
+            path.join(dir, "epochcli.json"),
+            JSON.stringify({
+              $schema: "https://epochcli.ai/config.json",
+              model: "configdir/model",
+            }),
+          )
+        },
+      })
+
+      await using projectTmp = await tmpdir({
+        init: async (dir) => {
+          // Create config in project (should be ignored)
+          await Filesystem.write(
+            path.join(dir, "epochcli.json"),
+            JSON.stringify({
+              $schema: "https://epochcli.ai/config.json",
+              model: "project/model",
+            }),
+          )
+        },
+      })
+
+      process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"] = "true"
+      process.env["EPOCHCLI_CONFIG_DIR"] = configDirTmp.path
+
+      await Instance.provide({
+        directory: projectTmp.path,
+        fn: async () => {
+          const config = await Config.get()
+          // Should load from EPOCHCLI_CONFIG_DIR, not project
+          expect(config.model).toBe("configdir/model")
+        },
+      })
+    } finally {
+      if (originalDisable === undefined) {
+        delete process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"]
+      } else {
+        process.env["EPOCHCLI_DISABLE_PROJECT_CONFIG"] = originalDisable
+      }
+      if (originalConfigDir === undefined) {
+        delete process.env["EPOCHCLI_CONFIG_DIR"]
+      } else {
+        process.env["EPOCHCLI_CONFIG_DIR"] = originalConfigDir
+      }
+    }
+  })
+})
+
+describe("EPOCHCLI_CONFIG_CONTENT token substitution", () => {
+  test("substitutes {env:} tokens in EPOCHCLI_CONFIG_CONTENT", async () => {
+    const originalEnv = process.env["EPOCHCLI_CONFIG_CONTENT"]
+    const originalTestVar = process.env["TEST_CONFIG_VAR"]
+    process.env["TEST_CONFIG_VAR"] = "test_api_key_12345"
+    process.env["EPOCHCLI_CONFIG_CONTENT"] = JSON.stringify({
+      $schema: "https://epochcli.ai/config.json",
+      username: "{env:TEST_CONFIG_VAR}",
+    })
+
+    try {
+      await using tmp = await tmpdir()
+      await Instance.provide({
+        directory: tmp.path,
+        fn: async () => {
+          const config = await Config.get()
+          expect(config.username).toBe("test_api_key_12345")
+        },
+      })
+    } finally {
+      if (originalEnv !== undefined) {
+        process.env["EPOCHCLI_CONFIG_CONTENT"] = originalEnv
+      } else {
+        delete process.env["EPOCHCLI_CONFIG_CONTENT"]
+      }
+      if (originalTestVar !== undefined) {
+        process.env["TEST_CONFIG_VAR"] = originalTestVar
+      } else {
+        delete process.env["TEST_CONFIG_VAR"]
+      }
+    }
+  })
+
+  test("substitutes {file:} tokens in EPOCHCLI_CONFIG_CONTENT", async () => {
+    const originalEnv = process.env["EPOCHCLI_CONFIG_CONTENT"]
+
+    try {
+      await using tmp = await tmpdir({
+        init: async (dir) => {
+          await Filesystem.write(path.join(dir, "api_key.txt"), "secret_key_from_file")
+          process.env["EPOCHCLI_CONFIG_CONTENT"] = JSON.stringify({
+            $schema: "https://epochcli.ai/config.json",
+            username: "{file:./api_key.txt}",
+          })
+        },
+      })
+      await Instance.provide({
+        directory: tmp.path,
+        fn: async () => {
+          const config = await Config.get()
+          expect(config.username).toBe("secret_key_from_file")
+        },
+      })
+    } finally {
+      if (originalEnv !== undefined) {
+        process.env["EPOCHCLI_CONFIG_CONTENT"] = originalEnv
+      } else {
+        delete process.env["EPOCHCLI_CONFIG_CONTENT"]
+      }
+    }
+  })
+})
+
+// parseManagedPlist unit tests — pure function, no OS interaction
+
+test("parseManagedPlist strips MDM metadata keys", async () => {
+  const config = await Config.parseManagedPlist(
+    JSON.stringify({
+      PayloadDisplayName: "Epoch CLI Managed",
+      PayloadIdentifier: "ai.epochcli.managed.test",
+      PayloadType: "ai.epochcli.managed",
+      PayloadUUID: "AAAA-BBBB-CCCC",
+      PayloadVersion: 1,
+      _manualProfile: true,
+      model: "mdm/model",
+    }),
+    "test:mobileconfig",
+  )
+  expect(config.model).toBe("mdm/model")
+  // MDM keys must not leak into the parsed config
+  expect((config as any).PayloadUUID).toBeUndefined()
+  expect((config as any).PayloadType).toBeUndefined()
+  expect((config as any)._manualProfile).toBeUndefined()
+})
+
+test("parseManagedPlist parses server settings", async () => {
+  const config = await Config.parseManagedPlist(
+    JSON.stringify({
+      $schema: "https://epochcli.ai/config.json",
+      server: { hostname: "127.0.0.1", mdns: false },
+      autoupdate: true,
+    }),
+    "test:mobileconfig",
+  )
+  expect(config.server?.hostname).toBe("127.0.0.1")
+  expect(config.server?.mdns).toBe(false)
+  expect(config.autoupdate).toBe(true)
+})
+
+test("parseManagedPlist parses permission rules", async () => {
+  const config = await Config.parseManagedPlist(
+    JSON.stringify({
+      $schema: "https://epochcli.ai/config.json",
+      permission: {
+        "*": "ask",
+        bash: { "*": "ask", "rm -rf *": "deny", "curl *": "deny" },
+        grep: "allow",
+        glob: "allow",
+        webfetch: "ask",
+        "~/.ssh/*": "deny",
+      },
+    }),
+    "test:mobileconfig",
+  )
+  expect(config.permission?.["*"]).toBe("ask")
+  expect(config.permission?.grep).toBe("allow")
+  expect(config.permission?.webfetch).toBe("ask")
+  expect(config.permission?.["~/.ssh/*"]).toBe("deny")
+  const bash = config.permission?.bash as Record<string, string>
+  expect(bash?.["rm -rf *"]).toBe("deny")
+  expect(bash?.["curl *"]).toBe("deny")
+})
+
+test("parseManagedPlist parses enabled_providers", async () => {
+  const config = await Config.parseManagedPlist(
+    JSON.stringify({
+      $schema: "https://epochcli.ai/config.json",
+      enabled_providers: ["anthropic", "google"],
+    }),
+    "test:mobileconfig",
+  )
+  expect(config.enabled_providers).toEqual(["anthropic", "google"])
+})
+
+test("parseManagedPlist handles empty config", async () => {
+  const config = await Config.parseManagedPlist(
+    JSON.stringify({ $schema: "https://epochcli.ai/config.json" }),
+    "test:mobileconfig",
+  )
+  expect(config.$schema).toBe("https://epochcli.ai/config.json")
+})