@snappedly-tools/shipyard 0.4.2 → 0.4.4-staging.35704989542

package/README.md

@@ -34,10 +34,28 @@ cp .shipyard/.env.example .shipyard/.env
 ```
 
 `init` asks which agent, sandbox provider, and starter template to use. Its
-issue-based templates use GitHub Issues. When you select Codex, it also asks
-whether to sign in with ChatGPT or use an API key. Start with the `blank`
-template. Put any requested credentials in `.shipyard/.env`, then write one
-concrete task in `.shipyard/prompt.md`.
+issue-based templates use GitHub Issues. Init always attempts to create or
+update the lowercase `shipyard` label, and built-in issue workflows select only
+open issues carrying that label. When you select Codex, init also asks whether
+to sign in with ChatGPT or use an API key. Start with the `blank` template. Put
+any requested credentials in `.shipyard/.env`, then write one concrete task in
+`.shipyard/prompt.md`.
+
+Use a subscription first when the selected agent supports it. If subscription
+authentication does not work in your environment, use the API-key fallback:
+
+- Codex subscription authentication: choose **Sign in with ChatGPT** during
+  interactive init and complete the browser login. The generated configuration
+  mounts `~/.codex/auth.json` read-only. For non-interactive init, run
+  `codex login` on the host, then pass `--codex-auth chatgpt`.
+- Codex API authentication: choose **OpenAI API key** during interactive init
+  and put `OPENAI_API_KEY` in `.shipyard/.env`. For non-interactive init, pass
+  `--codex-auth api-key`.
+- Claude Code subscription authentication: run `claude setup-token` on the
+  host and put the result in `CLAUDE_CODE_OAUTH_TOKEN` in `.shipyard/.env`.
+- Claude Code API authentication: uncomment `ANTHROPIC_API_KEY` in
+  `.shipyard/.env` and put your API key there.
+- GitHub Issues authentication: set `GH_TOKEN` and `GH_REPO` in `.shipyard/.env`.
 
 Run it:
 
@@ -53,44 +71,101 @@ image when its definition has not changed:
 npx shipyard run --skip-build
 ```
 
-Inspect the generated branch strategy and start from a clean working tree. A
-completion marker means the agent stopped; inspect its commits and run the
-repository's checks before keeping the result.
-
-## JavaScript API
+Shipyard supports Codex and Claude Code agents, with Docker, Vercel Sandbox,
+and no-sandbox providers. `shipyard init` scaffolds Docker; configure Vercel
+Sandbox or no-sandbox mode through the JavaScript interface.
 
-The generated `.shipyard/main.ts` or `.shipyard/main.mts` is ordinary
-TypeScript:
+## Repository runner for GitHub Issues
 
-```ts
-import { CODEX_MODELS, codex, run } from "@snappedly-tools/shipyard";
-import { docker } from "@snappedly-tools/shipyard/sandboxes/docker";
+Shipyard can keep one repository ready for labelled GitHub Issues on a
+user-managed Mac. This deployment currently supports GitHub.com repositories
+on Apple Silicon macOS only. It uses GitHub's official self-hosted Actions
+runner as a wake-up transport; the foreground Shipyard controller owns the
+actual work outside the Actions job.
 
-const result = await run({
-  agent: codex(CODEX_MODELS.routine),
-  sandbox: docker(),
-  promptFile: ".shipyard/prompt.md",
-});
+Prerequisites are an initialized repository, Docker Desktop, `gh` authenticated
+to GitHub.com with repository-administration access, and the credentials needed
+by the selected agent in `.shipyard/.env`. Install from the repository root:
 
-console.log(result.commits);
+```sh
+npx shipyard runner install
+git add .github/workflows/shipyard-wake.yml .shipyard/.gitignore
+git commit -m "Add Shipyard wake workflow"
+git push
+npx shipyard runner start
 ```
 
-Use a dedicated branch when the scaffold has already been committed:
+`--registration-token` can supply the one-time registration credential, but it
+does not replace administrative `gh` access: Shipyard still uses that access to
+verify that the repository has no conflicting `shipyard` runner.
+
+Interactive `shipyard init` also offers installation after it creates a valid
+scaffold, defaulting to Yes. Non-interactive init skips installation unless
+`--install-runner true` is passed. Installation creates the workflow locally;
+it never commits or pushes it. In a terminal, installation shows a progress
+bar for validation, download, registration, and workflow setup. `runner start`
+requires the exact generated workflow on the repository's default branch.
+
+The activation label is the exact, lowercase label `shipyard`. Init attempts to
+create it, and start creates it if it is missing. Adding that label or manually
+dispatching the **Shipyard wake-up** workflow wakes the controller. Labels with
+different casing do not match. Issue edits and comments do not wake it.
+
+The controller first checks the current backlog, so restarting it recovers work
+labelled while the Mac was off. It invokes exactly `npx shipyard run`, then
+compares the eligible issue-number set. An empty set returns it to idle; a
+changed nonempty set starts another finite invocation; an unchanged set records
+no progress and returns it to idle instead of looping. A later label event,
+manual dispatch, or restart retries that backlog. Wake-ups delivered while
+Shipyard is busy are coalesced.
+
+The Actions job only reports whether its wake-up reached the controller. It
+does not report the later agent outcome and does not own the agent's runtime.
+The controller stays available only while `runner start` remains open in its
+foreground terminal. Ctrl-C, closing that terminal, or `runner stop` stops it
+and cancels active work; it does not start at login. A nonzero Shipyard exit or
+infrastructure failure records the error and takes the controller offline.
+
+Use these commands from the same repository root:
 
-```ts
-const result = await run({
-  agent: codex(CODEX_MODELS.routine),
-  sandbox: docker(),
-  promptFile: ".shipyard/prompt.md",
-  branchStrategy: { type: "branch", branch: "agent/my-task" },
-  maxIterations: 1,
-  logging: { type: "stdout" },
-});
+```sh
+npx shipyard runner status
+npx shipyard runner stop
+npx shipyard runner remove
 ```
 
-Shipyard supports Codex and Claude Code agents, with Docker, Vercel Sandbox,
-and no-sandbox providers. `shipyard init` scaffolds Docker; configure Vercel
-Sandbox or no-sandbox mode through the JavaScript interface.
+Status reports local process state, GitHub connectivity, repository identity,
+and the last outcome without showing credentials. Runner binaries, credentials,
+state, and diagnostics are protected and ignored under `.shipyard/runner/`;
+normal removal unregisters the runner and deletes those files while preserving
+the Shipyard config, workflow, issues, logs, and worktrees. If GitHub
+unregistration is unavailable, retry after restoring access. As a last resort,
+`runner remove --force` deletes local files and prints the GitHub registration
+that must be removed manually.
+
+There is no Mac sleep/wake detector. GitHub can discard a queued self-hosted job
+after 24 hours, so after a long sleep use manual workflow dispatch or restart
+the controller. GitHub removes self-hosted runner registrations after 14 days
+offline; the next start automatically re-registers with the current
+administrative `gh` login. A Mac rename does not rename an existing
+registration. Remove and reinstall it explicitly.
+
+GitHub does not charge Actions minutes for the self-hosted wake job. The brief
+exact-case gate runs on `ubuntu-latest` and may consume hosted Actions minutes
+for private repositories. Model costs apply only when a preflight finds eligible
+issues and starts Shipyard; the host owner still pays for hardware, electricity,
+network, Docker, and model usage. GitHub warns that self-hosted runners on public repositories can be
+exposed to untrusted repository activity. Use this deployment only where label
+authority, workflows, collaborators, and agent credentials have an acceptable
+trust boundary. See GitHub's
+[self-hosted runner security guidance](https://docs.github.com/en/actions/reference/security/secure-use#hardening-for-self-hosted-runners).
+
+For setup failures, run `runner status`, inspect the foreground terminal and
+`.shipyard/runner/.shipyard-last-failure.json`, then verify Docker, GitHub
+authentication with `gh auth status --hostname github.com`, `.shipyard/.env`,
+the lowercase label, and the published workflow. The
+[Apple Silicon validation runbook](docs/runbooks/repository-runner-macos-validation.md)
+covers the complete lifecycle.
 
 To run directly on the host without isolation:
 
@@ -108,39 +183,6 @@ const result = await run({
 No-sandbox mode grants the agent the permissions of the Shipyard process. Use
 it only with trusted repositories and prompts.
 
-## Branch behavior
-
-Docker keeps the repository and Git metadata inside the sandbox. It starts
-from committed history and syncs changes back. The generated blank
-template omits `branchStrategy`, which defaults to `merge-to-head`: commits
-are transferred to a temporary host branch and merged into your current
-branch. Direct `head` mode is not supported by Docker or Vercel Sandbox.
-
-The explicit `branch` strategy keeps commits on the named branch for review.
-Commit input files before either strategy, or use `copyToWorktree` for specific
-untracked or ignored files.
-
-## Authentication
-
-`shipyard init` generates the environment variables and mounts required by
-the chosen agent. Keep `.shipyard/.env`, agent login files, logs, and recovery
-patches private.
-
-Use a subscription first when the selected agent supports it. If subscription
-authentication does not work in your environment, use the API-key fallback:
-
-- Codex subscription authentication: choose **Sign in with ChatGPT** during
-  interactive init and complete the browser login. The generated configuration
-  mounts `~/.codex/auth.json` read-only. For non-interactive init, run
-  `codex login` on the host, then pass `--codex-auth chatgpt`.
-- Codex API authentication: choose **OpenAI API key** during interactive init
-  and put `OPENAI_API_KEY` in `.shipyard/.env`. For non-interactive init, pass
-  `--codex-auth api-key`.
-- Claude Code subscription authentication: run `claude setup-token` on the
-  host and put the result in `CLAUDE_CODE_OAUTH_TOKEN` in `.shipyard/.env`.
-- Claude Code API authentication: uncomment `ANTHROPIC_API_KEY` in
-  `.shipyard/.env` and put your API key there.
-
 ## Generated files
 
 | Path                              | Purpose                                                      |
@@ -152,6 +194,7 @@ authentication does not work in your environment, use the API-key fallback:
 | `.shipyard/logs/`                 | Run logs                                                     |
 | `.shipyard/worktrees/`            | Worktrees for separate-branch runs                           |
 | `.shipyard/patches/`              | Recovery artifacts preserved after some failures             |
+| `.shipyard/runner/`               | Protected self-hosted runner files and diagnostics           |
 
 ## Workflow templates
 

package/dist/{chunk-VDHZO5PP.js → chunk-EGYPJMLV.js}

@@ -1,5 +1,7 @@
-import { Display } from './chunk-2GT3OPO5.js';
+import { CONFIG_DIR, ConfigDirError, assertNoSymlinkComponents, Display } from './chunk-FDYOTN55.js';
 import { Effect } from 'effect';
+import { FileSystem } from '@effect/platform';
+import { join } from 'path';
 
 var formatErrorMessage = (error) => {
   switch (error._tag) {
@@ -107,7 +109,63 @@ var CODEX_MODELS = {
     effort: readEffort("strong")
   }
 };
+var parseEnvFile = (filePath) => Effect.gen(function* () {
+  const fs = yield* FileSystem.FileSystem;
+  const symlink = yield* fs.readLink(filePath).pipe(
+    Effect.map(() => true),
+    Effect.catchAll(() => Effect.succeed(false))
+  );
+  if (symlink) return {};
+  const content = yield* fs.readFileString(filePath).pipe(Effect.catchAll(() => Effect.succeed(null)));
+  if (content === null) return {};
+  const vars = {};
+  for (const line of content.split("\n")) {
+    const trimmed = line.trim();
+    if (!trimmed || trimmed.startsWith("#")) continue;
+    const eqIndex = trimmed.indexOf("=");
+    if (eqIndex === -1) continue;
+    const key = trimmed.slice(0, eqIndex).trim();
+    let value = trimmed.slice(eqIndex + 1).trim();
+    const isDoubleQuoted = value.length >= 2 && value[0] === '"' && value[value.length - 1] === '"';
+    const isSingleQuoted = value.length >= 2 && value[0] === "'" && value[value.length - 1] === "'";
+    if (isDoubleQuoted || isSingleQuoted) {
+      value = value.slice(1, -1);
+    }
+    if (isDoubleQuoted) {
+      value = value.replace(/\\([nrt\\])/g, (_, ch) => {
+        const escapes = {
+          n: "\n",
+          r: "\r",
+          t: "	",
+          "\\": "\\"
+        };
+        return escapes[ch] ?? ch;
+      });
+    }
+    vars[key] = value;
+  }
+  return vars;
+});
+var resolveEnv = (repoDir) => Effect.gen(function* () {
+  const configDir = join(repoDir, CONFIG_DIR);
+  const envPath = join(configDir, ".env");
+  yield* Effect.tryPromise({
+    try: () => assertNoSymlinkComponents(repoDir, envPath, "environment file"),
+    catch: (e) => new ConfigDirError({
+      message: `Refusing symlinked environment path: ${e instanceof Error ? e.message : String(e)}`
+    })
+  });
+  const shipyardEnv = yield* parseEnvFile(envPath);
+  const result = {};
+  for (const key of Object.keys(shipyardEnv)) {
+    const value = shipyardEnv[key] || process.env[key];
+    if (value) {
+      result[key] = value;
+    }
+  }
+  return result;
+});
 
-export { CODEX_MODELS, CODEX_REASONING_EFFORTS, formatErrorMessage, withFriendlyErrors };
-//# sourceMappingURL=chunk-VDHZO5PP.js.map
-//# sourceMappingURL=chunk-VDHZO5PP.js.map
+export { CODEX_MODELS, CODEX_REASONING_EFFORTS, formatErrorMessage, resolveEnv, withFriendlyErrors };
+//# sourceMappingURL=chunk-EGYPJMLV.js.map
+//# sourceMappingURL=chunk-EGYPJMLV.js.map

package/dist/chunk-EGYPJMLV.js.map

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{ Effect } from \"effect\";\nimport { Display } from \"./Display.js\";\nimport type { SandboxError } from \"./errors.js\";\n\n/**\n * Formats a tagged SandboxError into a user-friendly message with\n * context-specific hints about what went wrong and how to recover.\n */\nexport const formatErrorMessage = (error: SandboxError): string => {\n  switch (error._tag) {\n    case \"ExecError\":\n      return `Command failed in sandbox (${error.command}): ${error.message}`;\n    case \"ExecHostError\":\n      return `Command failed on host (${error.command}): ${error.message}`;\n    case \"CopyError\":\n      return `File copy failed: ${error.message}`;\n    case \"DockerError\":\n      return `Docker operation failed: ${error.message}. Is Docker running?`;\n    case \"SyncError\":\n      return `Git sync failed: ${error.message}`;\n    case \"WorktreeError\":\n      return `Git worktree operation failed: ${error.message}`;\n    case \"PromptError\":\n      return `Failed to resolve prompt: ${error.message}`;\n    case \"AgentError\":\n      return `Agent invocation failed: ${error.message}`;\n    case \"ConfigDirError\":\n      return `${error.message}`;\n    case \"InitError\":\n      return `${error.message}`;\n    case \"AgentIdleTimeoutError\":\n    case \"WorktreeTimeoutError\":\n    case \"ContainerStartTimeoutError\":\n    case \"CopyToWorktreeTimeoutError\":\n    case \"CopyToWorktreeError\":\n    case \"SyncInTimeoutError\":\n    case \"HookTimeoutError\":\n    case \"GitSetupTimeoutError\":\n    case \"PromptExpansionTimeoutError\":\n    case \"CommitCollectionTimeoutError\":\n    case \"MergeToHostTimeoutError\":\n    case \"SessionCaptureError\":\n    case \"CwdError\":\n      return error.message;\n  }\n};\n\nconst showErrorAndExit = (error: SandboxError) =>\n  Effect.gen(function* () {\n    const d = yield* Display;\n    yield* d.status(formatErrorMessage(error), \"error\");\n    return yield* Effect.sync(() => process.exit(1) as never);\n  });\n\n/**\n * Wraps an effect so that any SandboxError is caught, displayed via the\n * Display service as an error-severity status message, then exits the process\n * with code 1. Non-SandboxError errors pass through unchanged.\n */\nexport const withFriendlyErrors = <A, E, R>(\n  effect: Effect.Effect<A, E, R>,\n): Effect.Effect<A, Exclude<E, SandboxError>, R | Display> =>\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  Effect.catchTags(effect as Effect.Effect<A, SandboxError, R>, {\n    ExecError: showErrorAndExit,\n    ExecHostError: showErrorAndExit,\n    CopyError: showErrorAndExit,\n    DockerError: showErrorAndExit,\n    SyncError: showErrorAndExit,\n    WorktreeError: showErrorAndExit,\n    PromptError: showErrorAndExit,\n    AgentError: showErrorAndExit,\n    ConfigDirError: showErrorAndExit,\n    InitError: showErrorAndExit,\n    AgentIdleTimeoutError: showErrorAndExit,\n    WorktreeTimeoutError: showErrorAndExit,\n    ContainerStartTimeoutError: showErrorAndExit,\n    CopyToWorktreeTimeoutError: showErrorAndExit,\n    CopyToWorktreeError: showErrorAndExit,\n    SyncInTimeoutError: showErrorAndExit,\n    HookTimeoutError: showErrorAndExit,\n    GitSetupTimeoutError: showErrorAndExit,\n    PromptExpansionTimeoutError: showErrorAndExit,\n    CommitCollectionTimeoutError: showErrorAndExit,\n    MergeToHostTimeoutError: showErrorAndExit,\n    SessionCaptureError: showErrorAndExit,\n    CwdError: showErrorAndExit,\n  }) as Effect.Effect<A, Exclude<E, SandboxError>, R | Display>;\n","/** Reasoning efforts accepted by the Codex CLI. */\nexport const CODEX_REASONING_EFFORTS = [\n  \"low\",\n  \"medium\",\n  \"high\",\n  \"xhigh\",\n  \"max\",\n] as const;\n\nexport type CodexReasoningEffort = (typeof CODEX_REASONING_EFFORTS)[number];\n\n/** A model identifier plus the reasoning policy used for that model role. */\nexport interface CodexModelConfig {\n  readonly model: string;\n  readonly effort: CodexReasoningEffort;\n}\n\n/**\n * Default values for Shipyard's built-in Codex roles.\n *\n * Runtime environment variables override these defaults:\n *   SHIPYARD_CODEX_ROUTINE_MODEL\n *   SHIPYARD_CODEX_ROUTINE_REASONING_EFFORT\n *   SHIPYARD_CODEX_STRONG_MODEL\n *   SHIPYARD_CODEX_STRONG_REASONING_EFFORT\n *\n * Keep the defaults here so runtime providers, generated templates, and the\n * repository workflows all use the same role definitions.\n */\nconst DEFAULT_CODEX_MODELS = {\n  routine: { model: \"gpt-5.6-luna\", effort: \"max\" },\n  strong: { model: \"gpt-5.6-sol\", effort: \"max\" },\n} as const satisfies Record<string, CodexModelConfig>;\n\nconst readModel = (role: keyof typeof DEFAULT_CODEX_MODELS): string =>\n  process.env[`SHIPYARD_CODEX_${role.toUpperCase()}_MODEL`]?.trim() ||\n  DEFAULT_CODEX_MODELS[role].model;\n\nconst readEffort = (\n  role: keyof typeof DEFAULT_CODEX_MODELS,\n): CodexReasoningEffort => {\n  const envName = `SHIPYARD_CODEX_${role.toUpperCase()}_REASONING_EFFORT`;\n  const value = process.env[envName]?.trim();\n  if (!value) return DEFAULT_CODEX_MODELS[role].effort;\n  if ((CODEX_REASONING_EFFORTS as readonly string[]).includes(value)) {\n    return value as CodexReasoningEffort;\n  }\n  throw new Error(\n    `${envName} must be one of ${CODEX_REASONING_EFFORTS.join(\", \")}; received \"${value}\"`,\n  );\n};\n\nexport const CODEX_MODELS = {\n  routine: {\n    model: readModel(\"routine\"),\n    effort: readEffort(\"routine\"),\n  },\n  strong: {\n    model: readModel(\"strong\"),\n    effort: readEffort(\"strong\"),\n  },\n} as const satisfies Record<string, CodexModelConfig>;\n","import { FileSystem } from \"@effect/platform\";\nimport { Effect } from \"effect\";\nimport { join } from \"node:path\";\n\nimport { ConfigDirError } from \"./errors.js\";\nimport { assertNoSymlinkComponents } from \"./pathSecurity.js\";\nimport { CONFIG_DIR } from \"./runtimeNames.js\";\n\nconst parseEnvFile = (\n  filePath: string,\n): Effect.Effect<Record<string, string>, never, FileSystem.FileSystem> =>\n  Effect.gen(function* () {\n    const fs = yield* FileSystem.FileSystem;\n    const symlink = yield* fs.readLink(filePath).pipe(\n      Effect.map(() => true),\n      Effect.catchAll(() => Effect.succeed(false)),\n    );\n    // A repository-controlled symlink could redirect this read to a host\n    // secret and then expose matching keys to the agent.\n    if (symlink) return {};\n    const content = yield* fs\n      .readFileString(filePath)\n      .pipe(Effect.catchAll(() => Effect.succeed(null)));\n    if (content === null) return {};\n    const vars: Record<string, string> = {};\n    for (const line of content.split(\"\\n\")) {\n      const trimmed = line.trim();\n      if (!trimmed || trimmed.startsWith(\"#\")) continue;\n      const eqIndex = trimmed.indexOf(\"=\");\n      if (eqIndex === -1) continue;\n      const key = trimmed.slice(0, eqIndex).trim();\n      let value = trimmed.slice(eqIndex + 1).trim();\n      const isDoubleQuoted =\n        value.length >= 2 &&\n        value[0] === '\"' &&\n        value[value.length - 1] === '\"';\n      const isSingleQuoted =\n        value.length >= 2 &&\n        value[0] === \"'\" &&\n        value[value.length - 1] === \"'\";\n      if (isDoubleQuoted || isSingleQuoted) {\n        value = value.slice(1, -1);\n      }\n      if (isDoubleQuoted) {\n        value = value.replace(/\\\\([nrt\\\\])/g, (_, ch: string) => {\n          const escapes: Record<string, string> = {\n            n: \"\\n\",\n            r: \"\\r\",\n            t: \"\\t\",\n            \"\\\\\": \"\\\\\",\n          };\n          return escapes[ch] ?? ch;\n        });\n      }\n      vars[key] = value;\n    }\n    return vars;\n  });\n\n/**\n * Resolve all env vars from .env files with process.env fallback.\n *\n * Precedence: .shipyard/.env > process.env\n * Only keys declared in .shipyard/.env are resolved from process.env.\n * Repo root .env is not part of the resolution chain.\n */\nexport const resolveEnv = (\n  repoDir: string,\n): Effect.Effect<\n  Record<string, string>,\n  ConfigDirError,\n  FileSystem.FileSystem\n> =>\n  Effect.gen(function* () {\n    const configDir = join(repoDir, CONFIG_DIR);\n    const envPath = join(configDir, \".env\");\n    yield* Effect.tryPromise({\n      try: () =>\n        assertNoSymlinkComponents(repoDir, envPath, \"environment file\"),\n      catch: (e) =>\n        new ConfigDirError({\n          message: `Refusing symlinked environment path: ${e instanceof Error ? e.message : String(e)}`,\n        }),\n    });\n    const shipyardEnv = yield* parseEnvFile(envPath);\n\n    const result: Record<string, string> = {};\n    for (const key of Object.keys(shipyardEnv)) {\n      // A blank placeholder falls back to process.env, so callers can source\n      // credentials from a host login for one invocation, e.g.\n      // `GH_TOKEN=\"$(gh auth token)\" npx shipyard run`. Only keys declared in\n      // .shipyard/.env are eligible for this fallback.\n      const value = shipyardEnv[key] || process.env[key];\n      if (value) {\n        result[key] = value;\n      }\n    }\n\n    return result;\n  });\n"]}

package/dist/{chunk-2GT3OPO5.js → chunk-FDYOTN55.js}

@@ -1,5 +1,5 @@
 import { toSessionTransferHandle, shellQuote } from './chunk-KMGNFXKN.js';
-import { existsSync, constants, statSync } from 'fs';
+import { existsSync, constants, lstatSync, realpathSync, statSync } from 'fs';
 import { mkdtemp, writeFile, chmod, mkdir, stat, copyFile, rm, readdir, lstat, readFile, open } from 'fs/promises';
 import * as clack from '@clack/prompts';
 import { FileSystem } from '@effect/platform';
@@ -29,6 +29,15 @@ var SilentDisplay = {
       ]),
       () => effect
     ),
+    progress: (title, effect) => Effect.gen(function* () {
+      const updates = [];
+      const result = yield* effect((update) => updates.push(update));
+      yield* Ref.update(ref, (entries) => [
+        ...entries,
+        { _tag: "progress", title, updates: [...updates] }
+      ]);
+      return result;
+    }),
     summary: (title, rows) => Ref.update(ref, (entries) => [
       ...entries,
       { _tag: "summary", title, rows }
@@ -127,6 +136,20 @@ var FileDisplay = {
           yield* appendToLog(`${message} done (${elapsed}s)`);
           return result;
         }),
+        progress: (title, effect) => Effect.gen(function* () {
+          yield* appendToLog(`${title}...`);
+          const start = Date.now();
+          const updates = [];
+          const result = yield* effect((update) => updates.push(update));
+          for (const update of updates) {
+            yield* appendToLog(
+              `  ${update.message} (${update.current}/${update.total})`
+            );
+          }
+          const elapsed = ((Date.now() - start) / 1e3).toFixed(1);
+          yield* appendToLog(`${title} done (${elapsed}s)`);
+          return result;
+        }),
         summary: (title, rows) => {
           const lines = Object.entries(rows).map(([key, value]) => `  ${key}: ${value}`).join("\n");
           return appendToLog(`${title}
@@ -186,6 +209,34 @@ var ClackDisplay = {
         }
       })
     ),
+    progress: (title, effect) => Effect.acquireUseRelease(
+      Effect.sync(() => {
+        const progress2 = clack.progress({ max: 100 });
+        let percent = 0;
+        progress2.start(title);
+        const report = (update) => {
+          const total = Math.max(1, update.total);
+          const current = Math.min(total, Math.max(0, update.current));
+          const nextPercent = Math.round(current / total * 100);
+          const message = `${update.message} (${current}/${total})`;
+          if (nextPercent > percent) {
+            progress2.advance(nextPercent - percent, message);
+          } else {
+            progress2.message(message);
+          }
+          percent = nextPercent;
+        };
+        return { progress: progress2, report };
+      }),
+      ({ report }) => effect(report),
+      ({ progress: progress2 }, exit) => Effect.sync(() => {
+        if (exit._tag === "Success") {
+          progress2.stop(`${title} complete`);
+        } else {
+          progress2.error(`${title} failed`);
+        }
+      })
+    ),
     summary: (title, rows) => Effect.sync(() => {
       const lines = Object.entries(rows).map(([key, value]) => terminalStyle.summaryRow(key, value)).join("\n");
       clack.note(lines, terminalStyle.summaryTitle(title));
@@ -306,11 +357,14 @@ var SessionCaptureError = class extends Data.TaggedError(
 var PRODUCT_NAME = "Shipyard";
 var CLI_NAME = "shipyard";
 var RUNTIME_NAMESPACE = "shipyard";
+var ACTIVATION_LABEL = "shipyard";
 var CONFIG_DIR = ".shipyard";
 var LOGS_DIR = "logs";
 var WORKTREES_DIR = "worktrees";
 var PATCHES_DIR = "patches";
 var LOCKS_DIR = "locks";
+var RUNNER_DIR = "runner";
+var RUNNER_SANDBOX_MASK_DIR = "runner-sandbox-mask";
 var PARENT_GIT_SANDBOX_DIR = "/.shipyard-parent-git";
 var SYNC_BASE_REF = "refs/shipyard/sync-base";
 var CONTAINER_NAME_PREFIX = "shipyard-";
@@ -815,6 +869,79 @@ var pruneStale = (repoDir) => Effect.gen(function* () {
     })
   )
 );
+var PROTECTED_RUNNER_PATH = `${CONFIG_DIR}/${RUNNER_DIR}`;
+var pathKey = (value) => value.normalize("NFC").toLocaleLowerCase("en-US");
+var SAFE_RUNNER_ENV_KEYS = /* @__PURE__ */ new Set([
+  "HOME",
+  "LANG",
+  "LC_ALL",
+  "LOGNAME",
+  "PATH",
+  "SHELL",
+  "TEMP",
+  "TERM",
+  "TMP",
+  "TMPDIR",
+  "USER"
+]);
+var repositoryRunnerEnvironment = (source) => Object.fromEntries(
+  Object.entries(source).filter(
+    ([key, value]) => SAFE_RUNNER_ENV_KEYS.has(key) && value !== void 0
+  )
+);
+var assertExcludesRepositoryRunner = (relativePath) => {
+  const normalized = pathKey(
+    posix.normalize(relativePath.replace(/\\/g, "/")).replace(/^\.\//, "").replace(/\/$/, "")
+  );
+  const protectedPath = pathKey(PROTECTED_RUNNER_PATH);
+  if (normalized === "." || normalized === protectedPath || normalized.startsWith(`${protectedPath}/`) || protectedPath.startsWith(`${normalized}/`)) {
+    throw new Error(
+      `Copy path ${relativePath} would expose the protected repository runner to an agent sandbox.`
+    );
+  }
+};
+var assertSafeRepositoryRunnerDirectories = (repoDir) => {
+  const runnerDir = join(repoDir, CONFIG_DIR, RUNNER_DIR);
+  const maskDir = join(repoDir, CONFIG_DIR, RUNNER_SANDBOX_MASK_DIR);
+  for (const [name, path] of [
+    ["repository runner", runnerDir],
+    ["repository runner sandbox mask", maskDir]
+  ]) {
+    const stat2 = lstatSync(path);
+    if (stat2.isSymbolicLink() || !stat2.isDirectory()) {
+      throw new Error(
+        `The protected ${name} path must be a real directory: ${path}`
+      );
+    }
+  }
+  if (pathKey(realpathSync(runnerDir)) === pathKey(realpathSync(maskDir))) {
+    throw new Error(
+      "The protected repository runner and sandbox mask paths must be distinct directories."
+    );
+  }
+};
+var assertProtectedDirectoryIdentities = async (runnerDir, maskDir, inspect) => {
+  if (!inspect) return;
+  const runner = await inspect(runnerDir);
+  const mask = await inspect(maskDir);
+  if (!runner.directory || runner.symbolicLink) {
+    throw new Error(
+      `The protected repository runner path must be a real directory: ${runnerDir}`
+    );
+  }
+  if (!mask.directory || mask.symbolicLink) {
+    throw new Error(
+      `The protected repository runner sandbox mask path must be a real directory: ${maskDir}`
+    );
+  }
+  if (pathKey(runner.realPath) === pathKey(mask.realPath)) {
+    throw new Error(
+      "The protected repository runner and sandbox mask paths must be distinct directories."
+    );
+  }
+};
+
+// src/CopyToWorktree.ts
 var COPY_TO_WORKTREE_TIMEOUT_MS = 6e4;
 var getCopyOnWriteFlags = (platform) => platform === "darwin" ? ["-cR"] : ["-R", "--reflink=auto"];
 var copyToWorktree = (paths, hostRepoDir, worktreePath, timeoutMs) => {
@@ -825,6 +952,7 @@ var copyToWorktree = (paths, hostRepoDir, worktreePath, timeoutMs) => {
       let src;
       let dest;
       try {
+        assertExcludesRepositoryRunner(relativePath);
         src = resolveSafeRelativePath(hostRepoDir, relativePath, "copy path");
         dest = resolveSafeRelativePath(worktreePath, relativePath, "copy path");
       } catch (error) {
@@ -1109,7 +1237,35 @@ var syncOut = (hostRepoDir, handle) => Effect.gen(function* () {
   const hasUntracked = lsFilesResult.stdout.length > 0;
   const untrackedFiles = hasUntracked ? lsFilesResult.stdout.split("\0").filter((f) => f.length > 0) : [];
   yield* Effect.try({
-    try: () => untrackedFiles.forEach(assertSafeGitWorktreePath),
+    try: () => untrackedFiles.forEach((path) => {
+      assertSafeGitWorktreePath(path);
+      assertExcludesRepositoryRunner(path);
+    }),
+    catch: (error) => new SyncError({ message: String(error) })
+  });
+  const changedPaths = [];
+  if (hasCommits) {
+    const committedNames = yield* execOk(
+      handle,
+      `git diff --name-only -z ${shellQuote(`${base}..HEAD`)}`,
+      { cwd: worktreePath }
+    );
+    changedPaths.push(
+      ...committedNames.stdout.split("\0").filter((path) => path.length > 0)
+    );
+  }
+  if (hasDiff) {
+    const uncommittedNames = yield* execOk(
+      handle,
+      "git diff --name-only -z HEAD",
+      { cwd: worktreePath }
+    );
+    changedPaths.push(
+      ...uncommittedNames.stdout.split("\0").filter((path) => path.length > 0)
+    );
+  }
+  yield* Effect.try({
+    try: () => changedPaths.forEach(assertExcludesRepositoryRunner),
     catch: (error) => new SyncError({ message: String(error) })
   });
   if (!hasCommits && !hasDiff && !hasUntracked) {
@@ -1727,6 +1883,18 @@ ${result.stderr}`
   )
 );
 var syncIn = (hostRepoDir, handle) => Effect.gen(function* () {
+  const protectedRunnerPath = `${CONFIG_DIR}/${RUNNER_DIR}`;
+  const runnerObjects = yield* execHostGit3(
+    ["rev-list", "--objects", "--all", "--", protectedRunnerPath],
+    hostRepoDir
+  );
+  if (runnerObjects.trim().length > 0) {
+    return yield* Effect.fail(
+      new SyncError({
+        message: `Refusing to copy repository history into the sandbox because it contains protected repository runner files under ${protectedRunnerPath}. Remove those files from all refs before retrying.`
+      })
+    );
+  }
   const branch = (yield* execHostGit3(
     ["rev-parse", "--abbrev-ref", "HEAD"],
     hostRepoDir
@@ -1823,12 +1991,33 @@ var startNoSandbox = (options) => Effect.tryPromise({
 );
 var startBindMountSandbox = (options) => Effect.tryPromise({
   try: () => {
+    const usesRunnerMask = options.worktreeOrRepoPath === options.hostRepoDir && existsSync(join(options.hostRepoDir, CONFIG_DIR, RUNNER_DIR)) && existsSync(
+      join(options.hostRepoDir, CONFIG_DIR, RUNNER_SANDBOX_MASK_DIR)
+    );
+    if (usesRunnerMask) {
+      assertSafeRepositoryRunnerDirectories(options.hostRepoDir);
+    }
     const rawMounts = [
       {
         hostPath: options.worktreeOrRepoPath,
         sandboxPath: options.repoDir
       },
-      ...options.gitMounts
+      ...options.gitMounts,
+      ...usesRunnerMask ? [
+        {
+          hostPath: join(
+            options.hostRepoDir,
+            CONFIG_DIR,
+            RUNNER_SANDBOX_MASK_DIR
+          ),
+          sandboxPath: posix.join(
+            options.repoDir,
+            CONFIG_DIR,
+            RUNNER_DIR
+          ),
+          readonly: true
+        }
+      ] : []
     ];
     const mounts = normalizeMounts(
       rawMounts,
@@ -1895,6 +2084,7 @@ var startIsolatedSandbox = (options) => Effect.gen(function* () {
           let hostPath;
           let sandboxPath;
           try {
+            assertExcludesRepositoryRunner(relativePath);
             hostPath = resolveSafeRelativePath(
               options.sourceRepoDir ?? options.hostRepoDir,
               relativePath,
@@ -2615,6 +2805,6 @@ var registerShutdown = (teardown) => {
   };
 };
 
-export { AgentError, AgentIdleTimeoutError, CLI_NAME, CONFIG_DIR, ClackDisplay, ConfigDirError, CwdError, Display, DockerError, ExecHostError, FileDisplay, InitError, LOCKS_DIR, LOGS_DIR, PRODUCT_NAME, PromptError, PromptExpansionTimeoutError, SANDBOX_REPO_DIR, SandboxConfig, SandboxFactory, SessionCaptureError, SilentDisplay, WorktreeDockerSandboxFactory, assertIsolatedWorkspaceMounts, assertNoSymlinkComponents, copyToWorktree, create, defaultImageName, formatVolumeMount, generateTempBranchName, getCurrentBranch, hasUncommittedChanges, makeSandboxFromHandle, patchGitMountsForWindows, processFileMountParents, pruneStale, registerShutdown, remove, resolveCwd, resolveGitMounts, resolveUserMounts, runHostHooks, startSandbox, syncOut, withSandboxLifecycle };
-//# sourceMappingURL=chunk-2GT3OPO5.js.map
-//# sourceMappingURL=chunk-2GT3OPO5.js.map
+export { ACTIVATION_LABEL, AgentError, AgentIdleTimeoutError, CLI_NAME, CONFIG_DIR, ClackDisplay, ConfigDirError, CwdError, Display, DockerError, ExecHostError, FileDisplay, InitError, LOCKS_DIR, LOGS_DIR, PRODUCT_NAME, PromptError, PromptExpansionTimeoutError, RUNNER_DIR, RUNNER_SANDBOX_MASK_DIR, SANDBOX_REPO_DIR, SandboxConfig, SandboxFactory, SessionCaptureError, SilentDisplay, WorktreeDockerSandboxFactory, assertIsolatedWorkspaceMounts, assertNoSymlinkComponents, assertProtectedDirectoryIdentities, copyToWorktree, create, defaultImageName, formatVolumeMount, generateTempBranchName, getCurrentBranch, hasUncommittedChanges, makeSandboxFromHandle, patchGitMountsForWindows, processFileMountParents, pruneStale, registerShutdown, remove, repositoryRunnerEnvironment, resolveCwd, resolveGitMounts, resolveUserMounts, runHostHooks, startSandbox, syncOut, withSandboxLifecycle };
+//# sourceMappingURL=chunk-FDYOTN55.js.map
+//# sourceMappingURL=chunk-FDYOTN55.js.map