agent-bios 0.18.0 → 0.19.0

package/compose/corpus_setup.py

@@ -0,0 +1,674 @@
+"""Shared setup controller, read-only dependency inventory, and numbered client."""
+from __future__ import annotations
+
+import hashlib
+import json
+import os
+from pathlib import Path
+import platform
+import re
+import shlex
+import shutil
+import subprocess
+import sys
+from typing import Any, Callable, TextIO
+
+try:
+    from corpus_setup_i18n import choice_label, dependency_display, translate
+except ImportError:
+    from .corpus_setup_i18n import choice_label, dependency_display, translate
+
+
+class SetupError(RuntimeError):
+    pass
+
+
+class _Back(Exception):
+    pass
+
+
+class _Cancel(Exception):
+    pass
+
+
+def _display(value: str) -> str:
+    return re.sub(r"[\x00-\x1f\x7f-\x9f]", " ", value)[:240].strip()
+
+
+def dependency_inventory(repo: Path, environ: dict[str, str] | None = None, *,
+                         runner: Callable = subprocess.run,
+                         which: Callable = shutil.which,
+                         system: str | None = None) -> list[dict[str, Any]]:
+    """Probe local commands without installing, authenticating, or fetching data."""
+    env = dict(os.environ if environ is None else environ)
+    env["PYTHONDONTWRITEBYTECODE"] = "1"
+    home = Path(env.get("HOME", str(Path.home())))
+    system = system or platform.system()
+    supported = system in {"Darwin", "Linux"}
+    paths = {name: which(name, path=env.get("PATH", os.defpath))
+             for name in ("bash", "python3", "node", "npm", "brew", "git", "zsh", "claude", "codex", "cp", "mktemp")}
+
+    def probe(argv: list[str]) -> tuple[bool, str]:
+        try:
+            result = runner(argv, shell=False, stdin=subprocess.DEVNULL, capture_output=True,
+                            text=True, timeout=5, env=env)
+            text = (result.stdout or result.stderr or "").splitlines()
+            return result.returncode == 0, _display(text[0] if text else "")
+        except (OSError, subprocess.SubprocessError) as exc:
+            return False, _display(str(exc))
+
+    rows: list[dict[str, Any]] = []
+
+    def add(identifier: str, title: str, role: str, purpose: str, *,
+            path: str | None = None, argv: list[str] | None = None,
+            action: list[str] | None = None, reason: str = "", scope: str = "",
+            present: bool | None = None, version: str = "") -> dict[str, Any]:
+        okay, detail = probe(argv) if argv else (bool(path) if present is None else present, version)
+        row = {"id": identifier, "title": title, "role": role, "purpose": purpose,
+               "status": "available" if okay else "missing", "path": path, "version": detail,
+               "install_argv": action if not okay and supported else None,
+               "install_scope": scope, "manual_reason": reason if not okay else ""}
+        if not supported:
+            row["manual_reason"] = "This installer supports macOS and Linux."
+        rows.append(row)
+        return row
+
+    brew_row = add("homebrew", "Homebrew", "optional package manager", "Offers local package installation recipes when available.",
+        path=paths["brew"], argv=[paths["brew"], "--version"] if paths["brew"] else None,
+        reason="Optional: use an existing operating-system package manager or the official host installer.")
+    brew = paths["brew"] if brew_row["status"] == "available" else None
+
+    def formula(name: str) -> list[str] | None:
+        return [brew, "install", name] if brew else None
+
+    add("bash", "Bash", "runtime", "Runs the package entry point and bundled shell tools.",
+        path=paths["bash"], argv=[paths["bash"], "--version"] if paths["bash"] else None,
+        action=formula("bash"), scope="Homebrew prefix", reason="Install Bash using your operating system package manager.")
+    py = paths["python3"]
+    add("python3", "Python 3.11+", "runtime", "Runs installation, corpus storage, and terminal interfaces.", path=py,
+        argv=[py, "-c", "import sys; print(sys.version.split()[0]); raise SystemExit(sys.version_info < (3,11))"] if py else None,
+        action=formula("python"), scope="Homebrew prefix", reason="Install Python 3.11+ and ensure python3 resolves to it.")
+    node = paths["node"]
+    node_row = add("node", "Node.js 22+", "delivery / optional host install", "Supports npm host installation and optional slide rendering.", path=node,
+        argv=[node, "--version"] if node else None, action=formula("node"), scope="Homebrew prefix",
+        reason="Install a current Node.js distribution with npm; the corpus runtime itself does not need Node.")
+    node_major = re.match(r"v?(\d+)", node_row["version"])
+    major = int(node_major[1]) if node_major and node_row["status"] == "available" else 0
+    if node_row["status"] == "available" and major < 22:
+        node_row["status"] = "missing"
+        if supported:
+            node_row.update(install_argv=formula("node"), manual_reason="Node.js 22+ is required by the Claude npm installer.")
+    npm = paths["npm"]
+    npm_row = add("npm", "npm", "delivery / optional host install", "Installs the package and selected host CLIs.", path=npm,
+        argv=[npm, "--version"] if npm else None,
+        reason="npm comes with Node.js; install Node.js first and rerun setup.")
+    npm = npm if npm_row["status"] == "available" else None
+    for identifier, title, package, minimum in (("codex", "Codex CLI", "@openai/codex", 18),
+                                                  ("claude", "Claude Code", "@anthropic-ai/claude-code", 22)):
+        action = [brew, "install", "--cask", "codex" if identifier == "codex" else "claude-code"] if brew else (
+            [npm, "install", "-g", package] if npm and major >= minimum else None)
+        path = paths[identifier]
+        add(identifier, title, "selected host", "Required to launch this host; sign-in is a separate step.", path=path,
+            argv=[path, "--version"] if path else None, action=action,
+            scope="Homebrew prefix and required dependencies" if brew else "npm global prefix",
+            reason=f"Use the official installer, or install npm with Node.js {minimum}+ and rerun setup.")
+    for identifier, title, role, purpose in (
+        ("git", "Git", "workflow", "Clone updates, worktrees, and version-control workflows."),
+        ("zsh", "zsh", "optional shell connection", "Optional interception of bare host commands."),
+    ):
+        path = paths[identifier]
+        add(identifier, title, role, purpose, path=path, argv=[path, "--version"] if path else None,
+            action=formula(identifier), scope="Homebrew prefix", reason="Install with your operating system package manager.")
+    for identifier in ("cp", "mktemp"):
+        add(identifier, identifier, "shell adapters", "Required by optional shell worker adapters.", path=paths[identifier],
+            reason="Install the standard BSD or GNU command-line utilities for your system.")
+    venv = Path(env.get("AGENT_LAUNCH_VENV") or str(home / ".local/share/agent-launch/venv"))
+    vpy = venv / "bin/python"
+    configured_python = env.get("AGENT_LAUNCH_PYTHON")
+    bootstrap_python = which(configured_python, path=env.get("PATH", os.defpath)) if configured_python else py
+    provisioner = Path(repo) / "launch/provision-venv.sh"
+    pins = {}
+    if provisioner.is_file():
+        pins = dict(re.findall(r'\b(?:TEXTUAL|JSONSCHEMA)_PIN="([a-z]+)==([0-9][a-zA-Z0-9_.-]*)"', provisioner.read_text(encoding="utf-8")))
+        if set(pins) != {"textual", "jsonschema"}:
+            raise SetupError("Bundled managed dependency pins are incomplete; verify or reinstall the agent-bios package.")
+
+    def module_probe(interpreter: str, name: str, *, managed: bool = False) -> list[str]:
+        code = f"import {name}; import importlib.metadata; actual = importlib.metadata.version({name!r}); print(actual)"
+        if name == "jsonschema":
+            code += "; from jsonschema import Draft202012Validator"
+        if managed and name in pins:
+            code += f"; import sys; raise SystemExit(sys.version_info < (3, 11) or actual != {pins[name]!r})"
+        return [interpreter, "-c", code]
+
+    bootstrap = add("python-venv", "Python venv / pip bootstrap", "managed dependency prerequisite", "Creates the managed environment using AGENT_LAUNCH_PYTHON when set, otherwise python3.", path=bootstrap_python,
+        argv=[bootstrap_python, "-c", "import sys, venv, ensurepip; print('venv; bundled pip ' + ensurepip.version()); raise SystemExit(sys.version_info < (3, 11))"] if bootstrap_python else None,
+        reason="Install venv/ensurepip for Python 3.11+; check AGENT_LAUNCH_PYTHON if configured. An existing managed environment does not need this bootstrap.")
+    can_provision = bool(paths["bash"] and provisioner.is_file() and (vpy.is_file() or bootstrap["status"] == "available"))
+    try:
+        from .corpus_ui_runtime import runtime_inventory
+    except ImportError:
+        from corpus_ui_runtime import runtime_inventory
+    ui = runtime_inventory(Path(repo))
+    bundle = str(Path(repo) / "compose/ui_runtime")
+    textual_version = next((row["version"] for row in ui.get("packages", []) if row["name"] == "textual"), "")
+    add("textual", "Textual (included)", "bundled UI runtime", "The terminal UI uses verified bundled packages without a system or managed Textual installation.",
+        path=bundle, present=ui["status"] == "available", version=textual_version,
+        scope="process-owned temporary directory",
+        reason="The shipped UI bundle is unavailable; verify or reinstall this agent-bios package. " + "; ".join(ui.get("issues", [])))
+    for package in ui.get("packages", []):
+        if package["name"] == "textual":
+            continue
+        add("ui-" + package["name"], package["name"] + " (included)", "bundled UI dependency",
+            "Included in the Textual runtime; no separate installation is needed.",
+            path=bundle, present=True, version=package["version"], scope="process-owned temporary directory")
+    learning_ready, learning_version = probe(module_probe(py, "jsonschema")) if py else (False, "")
+    learning_python = py
+    if not learning_ready and vpy.is_file():
+        learning_ready, learning_version = probe(module_probe(str(vpy), "jsonschema", managed=True))
+        learning_python = str(vpy)
+    add("jsonschema", "jsonschema", "learning capture", "Validates end-user learn submissions against JSON Schema Draft 2020-12, and also serves the author gate.",
+        path=learning_python, present=learning_ready, version=learning_version,
+        action=[paths["bash"], str(provisioner), "--learning-only"] if can_provision else None,
+        scope=str(venv), reason="Select the managed learning validator installation; learn uses it when system Python lacks jsonschema.")
+    for identifier, title, purpose in (
+        ("slide-playwright", "Playwright module", "Static slide jobs bind an explicit Playwright module file."),
+        ("slide-pdf-lib", "pdf-lib", "Static slide jobs resolve pdf-lib beside the selected Playwright module."),
+        ("slide-browser", "Chromium-family browser", "Static slide jobs bind an explicit browser executable."),
+        ("spreadsheet-processing", "Spreadsheet-processing skill", "Selected spreadsheet guidance can use this optional personal skill."),
+        ("mcp-servers", "User-specific MCP servers", "Only user-selected workflows require their configured external services."),
+    ):
+        row = add(identifier, title, "optional job / personal integration", purpose, present=False,
+                  reason="Configure this only for a workflow that requires it; setup cannot choose your job environment or account.")
+        row["status"] = "not assessed"
+    return rows
+
+
+def catalog_choices(installer: Any) -> list[dict[str, str]]:
+    if hasattr(installer, "setup_catalog"):
+        catalog = installer.setup_catalog()
+    else:
+        try:
+            from corpus_catalog import load_catalog
+        except ImportError:
+            from .corpus_catalog import load_catalog
+        catalog = load_catalog(installer.repo)
+    choices: list[dict[str, str]] = []
+    for package in catalog["packages"]:
+        package_id = package["package_id"]
+        choices.append({"target": package_id, "label": "All content in " + package_id})
+        for name, description in sorted(package.get("domains", {}).items()):
+            choices.append({"target": package_id + "/" + name, "label": f"{description} ({package_id}/{name})"})
+    if not choices:
+        raise SetupError("No corpus packages are available for selection.")
+    return choices
+
+
+def _indexes(value: str, count: int) -> list[int]:
+    if value.lower() in {"", "none"}:
+        return []
+    try:
+        indexes = sorted({int(part.strip()) - 1 for part in value.split(",")})
+    except ValueError as exc:
+        raise SetupError("Enter comma-separated numbers, or none.") from exc
+    if any(index < 0 or index >= count for index in indexes):
+        raise SetupError("A selected number is outside the displayed list.")
+    return indexes
+
+
+def format_setup_result(result: dict[str, Any], language: str = "en", *, interface: str = "terminal") -> str:
+    """Summarize completion without exposing the runtime file inventory."""
+    if interface not in {"terminal", "conversation"}:
+        raise ValueError("unknown setup presentation")
+    def t(message: str, **values: Any) -> str:
+        return translate(language, message, **values)
+
+    def recovery_hint() -> str:
+        return t("Use the returned review_id with agent-bios setup status or agent-bios setup resume before continuing.")
+
+    if result.get("cancelled"):
+        if result.get("cancelled_after_start"):
+            lines = [t("Setup stopped after the current operation finished.")]
+            completed = [row["id"] for row in result.get("dependency_results", []) if row.get("returncode") == 0]
+            if completed:
+                lines.append(t("Dependencies retained: {dependencies}.", dependencies=", ".join(completed)))
+            if result.get("installation_applied"):
+                lines.append(t("The private runtime installation is retained; remaining setup was not applied."))
+            else:
+                lines.append(t("The private runtime installation was not applied."))
+            if interface == "conversation":
+                lines.append(recovery_hint())
+            return "\n".join(lines)
+        return t("Setup cancelled. No installation changes were applied.")
+    if result.get("dry_run"):
+        return t("Setup preview complete. No installation changes were applied.")
+    completed = [row["id"] for row in result.get("dependency_results", []) if row.get("returncode") == 0]
+    if result.get("installation_error"):
+        lines = [t("Private runtime installation needs attention: {error}", error=str(result["installation_error"]))]
+        if completed:
+            lines.append(t("Dependencies retained: {dependencies}.", dependencies=", ".join(completed)))
+        lines.append(recovery_hint() if interface == "conversation" else t("Inspect the reported state and rerun agent-bios install."))
+        return "\n".join(lines)
+    if result.get("dependency_failed"):
+        lines = [t("Dependency installation failed: {dependency}. The private runtime was not installed by this setup.", dependency=result["dependency_failed"])]
+        if completed:
+            lines.append(t("Dependencies already installed: {dependencies}.", dependencies=", ".join(completed)))
+        lines.append(recovery_hint() if interface == "conversation" else t("Resolve the dependency error and run agent-bios install --interactive again."))
+        return "\n".join(lines)
+    if result.get("extras_error"):
+        lines = [t("Private runtime installed; app registration or instruction capture needs attention."),
+                 str(result["extras_error"])]
+        if (result.get("extras") or {}).get("app_bridge", {}).get("registered"):
+            lines.append(t("The app command registration is retained; instruction capture did not complete."))
+        if completed:
+            lines.append(t("Dependencies installed: {dependencies}.", dependencies=", ".join(completed)))
+        lines.append(recovery_hint() if interface == "conversation" else t("Open Corpus Studio: agent-bios corpus (terminal or Codex app terminal panel)."))
+        return "\n".join(lines)
+    if not result.get("applied"):
+        return t("Setup did not complete.")
+    plan = result.get("plan", {})
+    lines = [t("Setup complete. Private runtime installed.")]
+    if completed:
+        lines.append(t("Dependencies installed: {dependencies}.", dependencies=", ".join(completed)))
+    mode, targets = plan.get("selection_mode"), plan.get("targets") or []
+    if mode == "none":
+        lines.append(t("Corpus for future activated sessions: none."))
+    elif mode == "selected":
+        corpus = t("all available corpus") if targets == ["all"] else ", ".join(targets)
+        lines.append(t("Corpus for future activated sessions: {corpus}.", corpus=corpus))
+    elif mode == "default":
+        lines.append(t("Corpus policy: core, infrastructure and personal corpus; selected domains: {domains}.", domains=", ".join(targets))
+                     if targets else t("Corpus policy: core, infrastructure and personal corpus."))
+    else:
+        lines.append(t("Saved corpus policy and item choices preserved."))
+    extras = result.get("extras") or {}
+    bridge = extras.get("app_bridge") or (result.get("installation") or {}).get("app_bridge") or {}
+    if bridge.get("needs_action"):
+        lines.append(t("Codex app bridge needs attention; existing files were preserved:"))
+        lines.extend("- " + str(message) for message in bridge["needs_action"])
+    if bridge.get("registered"):
+        lines.append(t("Codex app bridge registered: use $agent-bios for per-task preview/use/off and corpus management."))
+    captured = extras.get("import") or {}
+    if captured.get("capture_id"):
+        count = captured.get("source_count")
+        lines.append(t("Instruction capture: {capture_id} ({count} source files). Model review is required before activation.",
+                       capture_id=captured["capture_id"], count=count) if count is not None else
+                     t("Instruction capture: {capture_id}. Model review is required before activation.", capture_id=captured["capture_id"]))
+        if captured.get("next_command"):
+            lines.append(t("Next: {command}", command=str(captured["next_command"])))
+        if bridge.get("registered") and captured.get("app_request"):
+            request = str(captured["app_request"])
+            if request == f"Use $agent-bios to import capture {captured['capture_id']}":
+                request = t("Use $agent-bios to import capture {capture_id}", capture_id=captured["capture_id"])
+            lines.append(t("In Codex: {request}", request=request))
+    lines.append(t("Continue in the conversation using the returned verified entrypoint.") if interface == "conversation"
+                 else t("Open Corpus Studio: agent-bios corpus (terminal or Codex app terminal panel)."))
+    return "\n".join(lines)
+
+
+def review_summary(plan: dict[str, Any], dependencies: list[dict[str, Any]],
+                   choices: list[dict[str, Any]], language: str = "en") -> str:
+    """Render the shared human review without importing a UI framework."""
+    def t(message: str, **values: Any) -> str:
+        return translate(language, message, **values)
+    labels = {row["target"]: choice_label(language, row) for row in choices}
+    labels["all"] = t("All available corpus")
+    mode, targets = plan.get("selection_mode"), plan.get("targets") or []
+    if mode is None:
+        corpus = t("Keep the saved corpus policy and item choices")
+    elif mode == "none":
+        corpus = t("No active corpus")
+    elif targets == ["all"]:
+        corpus = t("All available corpus")
+    else:
+        corpus = ", ".join(labels.get(value, value) for value in targets) or t("No selected items")
+    selected = set(plan.get("dependencies") or [])
+    installs = [dependency_display(language, row) for row in dependencies if row["id"] in selected]
+    lines = [t("Ready to apply"), "", t("Corpus: {selection}", selection=corpus),
+             t("App connection: {connection}", connection=t("Register $agent-bios for explicit task use") if plan.get("app_bridge") else t("No new app registration"))]
+    if installs:
+        lines.append(t("Install:"))
+        lines.extend("  " + row["title"] + (" — " + row["install_scope"] if row.get("install_scope") else "") for row in installs)
+    else:
+        lines.append(t("Install dependencies: none"))
+    sources = plan.get("import_paths") or []
+    lines.append(t("Prepare for model review: {count} instruction file(s)", count=len(sources)))
+    lines.extend("  " + path for path in sources)
+    lines.extend(["", t("Native global and project instruction files are preserved."),
+                  t("This setup does not add corpus to the current app task."),
+                  t("Library files remain stored privately when active corpus is off.")])
+    if sources:
+        lines.append(t("Captured instructions need a separate semantic review before import."))
+    return re.sub(r"[\x00-\x08\x0b-\x1f\x7f-\x9f]", " ", "\n".join(lines))
+
+
+class SetupController:
+    """One read-only plan and selected execution path for installation clients."""
+
+    FIELDS = {"selection_mode", "targets", "dependencies", "app_bridge", "import_paths", "project_roots"}
+
+    def __init__(self, installer: Any, *, runner: Callable = subprocess.run,
+                 inventory: list[dict[str, Any]] | None = None, extras_handler: Callable | None = None):
+        self.installer = installer
+        self.runner = runner
+        self.dependencies = inventory if inventory is not None else dependency_inventory(installer.repo, installer.env, runner=runner)
+        self.choices = catalog_choices(installer)
+        self.handler = extras_handler or getattr(installer, "setup_extras", None)
+        identifiers = [row["id"] for row in self.dependencies]
+        if len(identifiers) != len(set(identifiers)):
+            raise SetupError("Dependency inventory has duplicate identifiers.")
+
+    def default_plan(self, selection_mode: str | None = None, targets: list[str] | None = None) -> dict[str, Any]:
+        if selection_mode is None and targets is None:
+            status = getattr(self.installer, "status", None)
+            selection_mode = None if callable(status) and status().get("installed") else "none"
+        return {"selection_mode": selection_mode,
+                "targets": list(targets) if targets is not None else (None if selection_mode is None else []),
+                "dependencies": [], "app_bridge": False, "import_paths": [], "project_roots": []}
+
+    def discover(self, project_roots: list[str]) -> dict[str, Any]:
+        if not isinstance(project_roots, list) or not all(isinstance(value, str) and Path(value).is_absolute()
+                                                         and Path(value).is_dir() for value in project_roots):
+            raise SetupError("Project roots must be existing absolute directories.")
+        discovery = getattr(self.installer, "setup_discover", None)
+        if not callable(discovery):
+            raise SetupError("Instruction discovery is unavailable in this installer.")
+        found = discovery(project_roots)
+        return found if isinstance(found, dict) else {"sources": found, "omitted": []}
+
+    def _plan(self, value: dict[str, Any]) -> dict[str, Any]:
+        if not isinstance(value, dict) or set(value) - self.FIELDS - {"dependency_actions"}:
+            raise SetupError("Installation plan contains unsupported fields.")
+        if not self.FIELDS <= set(value):
+            raise SetupError("Installation plan is incomplete.")
+        plan = {key: value[key] for key in self.FIELDS}
+        mode, targets = plan["selection_mode"], plan["targets"]
+        if (mode is not None and not isinstance(mode, str)) or mode not in {None, "default", "selected", "none"}:
+            raise SetupError("Unsupported corpus selection mode.")
+        if targets is not None and (not isinstance(targets, list) or not all(isinstance(x, str) and x for x in targets)):
+            raise SetupError("Corpus targets must be a list of qualified names.")
+        if mode == "selected" and not targets:
+            raise SetupError("Select at least one corpus, or choose no active corpus.")
+        if mode == "none" and targets:
+            raise SetupError("No active corpus cannot include selected targets.")
+        if mode is None and targets:
+            raise SetupError("Keeping saved selection cannot specify new targets.")
+        if type(plan["app_bridge"]) is not bool:
+            raise SetupError("App registration must be an explicit boolean choice.")
+        for key in ("dependencies", "import_paths", "project_roots"):
+            items = plan[key]
+            if not isinstance(items, list) or not all(isinstance(x, str) and x for x in items) or len(set(items)) != len(items):
+                raise SetupError(f"{key} must be a list of distinct values.")
+        available = {row["id"]: row for row in self.dependencies}
+        for name in plan["dependencies"]:
+            if name not in available or not available[name].get("install_argv"):
+                raise SetupError(f"Dependency has no reviewed installation recipe: {name}")
+        if (plan["app_bridge"] or plan["import_paths"]) and not callable(self.handler):
+            raise SetupError("The requested app/import integration is unavailable.")
+        return json.loads(json.dumps(plan))
+
+    def _sources(self, plan: dict[str, Any]) -> list[dict[str, str]]:
+        if not plan["import_paths"]:
+            return []
+        found = self.discover(plan["project_roots"])
+        allowed = {row["path"]: row for row in found["sources"]}
+        if not set(plan["import_paths"]) <= set(allowed):
+            raise SetupError("Instruction selection is outside the current discovery set.")
+        try:
+            from .corpus_import import _read_source
+        except ImportError:
+            from corpus_import import _read_source
+        return [{"path": path, "sha256": hashlib.sha256(_read_source(allowed[path])[0]).hexdigest()}
+                for path in plan["import_paths"]]
+
+    def _install(self, plan: dict[str, Any], dry_run: bool) -> dict[str, Any]:
+        if plan["selection_mode"] is None:
+            return self.installer.install(dry_run=dry_run)
+        return self.installer.install(dry_run=dry_run, selection_mode=plan["selection_mode"], targets=plan["targets"])
+
+    def preview(self, value: dict[str, Any]) -> dict[str, Any]:
+        plan = self._plan(value)
+        actions = [row for row in self.dependencies if row["id"] in plan["dependencies"]]
+        concrete = dict(plan, dependency_actions=[{"id": row["id"], "argv": list(row["install_argv"]),
+                                                  "scope": row["install_scope"]} for row in actions])
+        sources = self._sources(plan)
+        result = {"plan": concrete, "installation": self._install(plan, True),
+                  "extras": self.handler(plan, dry_run=True) if plan["app_bridge"] or plan["import_paths"] else None,
+                  "source_versions": sources}
+        revision = getattr(self.installer, "setup_revision", None)
+        if callable(revision):
+            result["state_revision"] = revision()
+        result["review_id"] = hashlib.sha256(json.dumps(result, sort_keys=True, ensure_ascii=False).encode()).hexdigest()
+        return result
+
+    def apply(self, value: dict[str, Any], preview: dict[str, Any] | None = None, *,
+              progress: Callable[[dict[str, Any]], None] | None = None,
+              should_cancel: Callable[[], bool] | None = None,
+              reuse_installation: bool = False) -> dict[str, Any]:
+        if type(reuse_installation) is not bool:
+            raise SetupError("reuse_installation must be boolean")
+        checked = self.preview(value)
+        if preview is not None and checked != preview:
+            raise SetupError("Installation inputs changed after review; inspect a fresh plan before Apply.")
+        plan = self._plan(checked["plan"])
+        result: dict[str, Any] = {"applied": False, "plan": checked["plan"], "dependency_results": []}
+
+        def emit(stage: str, message: str, **extra) -> None:
+            if progress:
+                progress({"stage": stage, "message": message, **extra})
+
+        def cancelled() -> bool:
+            if should_cancel and should_cancel():
+                result.update(cancelled=True, cancelled_after_start=bool(result["dependency_results"] or result.get("installation_applied")))
+                return True
+            return False
+
+        for action in checked["plan"]["dependency_actions"]:
+            if cancelled():
+                return result
+            emit("dependency", "Installing " + action["id"], dependency=action["id"], phase="started")
+            try:
+                process = self.runner(action["argv"], shell=False, stdin=subprocess.DEVNULL,
+                                      env=dict(self.installer.env), check=False, capture_output=True,
+                                      text=True, errors="replace")
+            except OSError as exc:
+                outcome = {"id": action["id"], "returncode": None, "stdout": "", "stderr": str(exc)}
+                result["dependency_results"].append(outcome)
+                result["dependency_failed"] = action["id"]
+                emit("dependency", "Could not start " + action["id"], phase="not_started", **outcome)
+                return result
+            outcome = {"id": action["id"], "returncode": process.returncode,
+                       "stdout": (getattr(process, "stdout", "") or "")[-16000:],
+                       "stderr": (getattr(process, "stderr", "") or "")[-16000:]}
+            result["dependency_results"].append(outcome)
+            emit("dependency", "Finished " + action["id"], phase="completed" if process.returncode == 0 else "failed", **outcome)
+            if process.returncode:
+                result["dependency_failed"] = action["id"]
+                return result
+        if cancelled():
+            return result
+        emit("install", "Installing the private runtime", phase="checking")
+        try:
+            revision = getattr(self.installer, "setup_revision", None)
+            if callable(revision) and revision() != checked.get("state_revision"):
+                raise SetupError("Private state changed after review; review the remaining installation again.")
+            if self._sources(plan) != checked["source_versions"]:
+                raise SetupError("Instruction sources changed after review; select and review them again.")
+            if self._install(plan, True) != checked["installation"]:
+                raise SetupError("Package or corpus selection changed after review; inspect a fresh plan.")
+            if reuse_installation:
+                verified = self.installer.verify()
+                status = self.installer.status()
+                installed_root = status.get("package_root")
+                digest = Path(installed_root).name if isinstance(installed_root, str) else None
+                if verified.get("stored") is not True or digest != checked["installation"].get("release_digest"):
+                    raise SetupError("the reviewed package does not match the retained installation")
+                result["installation"] = {**status, "verified": verified, "release_digest": digest}
+                result["installation_reused"] = True
+            else:
+                emit("install", "Installing the private runtime", phase="started")
+                result["installation"] = self._install(plan, False)
+                result["installation_applied"] = True
+            emit("install", "Installing the private runtime", phase="completed", installation=result["installation"],
+                 reused=reuse_installation)
+        except (OSError, RuntimeError, ValueError) as exc:
+            result["installation_error"] = str(exc)
+            return result
+        if cancelled():
+            return result
+        try:
+            if plan["app_bridge"] or plan["import_paths"]:
+                emit("extras", "Preparing app registration and selected instruction capture", phase="checking")
+                if self._sources(plan) != checked["source_versions"]:
+                    raise SetupError("Instruction sources changed after review; review a new capture before continuing.")
+                source_digests = {row["path"]: row["sha256"] for row in checked["source_versions"]}
+                emit("extras", "Preparing app registration and selected instruction capture", phase="started")
+                result["extras"] = self.handler(dict(plan, _expected_source_digests=source_digests), dry_run=False)
+                emit("extras", "Preparing app registration and selected instruction capture", phase="completed", extras=result["extras"])
+            else:
+                result["extras"] = None
+        except (OSError, RuntimeError, ValueError) as exc:
+            result["extras_error"] = str(exc)
+            if getattr(exc, "completed_extras", None):
+                result["extras"] = exc.completed_extras
+            return result
+        result["applied"] = True
+        emit("complete", "Setup complete")
+        return result
+
+
+def run_setup(installer: Any, *, input_fn: Callable[[str], str] | None = None,
+              input_stream: TextIO | None = None, output_stream: TextIO | None = None,
+              runner: Callable = subprocess.run, dry_run: bool = False,
+              inventory: list[dict[str, Any]] | None = None,
+              extras_handler: Callable | None = None) -> dict[str, Any]:
+    """Collect a complete plan, then apply only the user's explicit selection."""
+    out = output_stream or sys.stdout
+    source = input_stream or sys.stdin
+    controller = SetupController(installer, runner=runner, inventory=inventory, extras_handler=extras_handler)
+    dependencies = controller.dependencies
+    choices = controller.choices
+    plan: dict[str, Any] = {"selection_mode": "none", "targets": [], "dependencies": [],
+                            "app_bridge": False, "import_paths": [], "project_roots": []}
+
+    def write(text: str = "") -> None:
+        print(text, file=out, flush=True)
+
+    def ask(prompt: str) -> str:
+        try:
+            if input_fn is not None:
+                answer = input_fn(prompt)
+            else:
+                print(prompt, end="", file=out, flush=True)
+                answer = source.readline()
+                if not answer:
+                    raise _Cancel()
+            value = answer.strip()
+            if value.lower() in {"cancel", "q", "quit"}:
+                raise _Cancel()
+            if value.lower() in {"back", "b"}:
+                raise _Back()
+            return value
+        except (EOFError, KeyboardInterrupt, StopIteration):
+            raise _Cancel() from None
+
+    write("agent-bios setup — back returns to the previous step; cancel exits without applying.")
+    write("Native AGENTS.md and CLAUDE.md remain user-owned. Corpus choices govern future activated sessions.")
+    step = 0
+    applying = False
+    while True:
+        try:
+            if step == 0:
+                write("\nDependencies (probes do not install or sign in):")
+                available_actions = []
+                for row in dependencies:
+                    write(f"  {row['title']} — {row['status']} [{row['role']}] {row.get('version', '')}")
+                    write("    " + row["purpose"])
+                    if row.get("install_argv"):
+                        available_actions.append(row)
+                        write(f"    Install {len(available_actions)}: {shlex.join(row['install_argv'])} ({row['install_scope']})")
+                    elif row.get("manual_reason"):
+                        write("    " + row["manual_reason"])
+                selected = _indexes(ask("Install numbers, or none [none]: "), len(available_actions))
+                plan["dependencies"] = [available_actions[index]["id"] for index in selected]
+                step = 1
+            elif step == 1:
+                write("\nCorpus: 1 no active corpus; 2 all available corpus; 3 selected packages/domains; 4 keep saved/default selection")
+                value = ask("Corpus choice [1]: ") or "1"
+                if value not in {"1", "2", "3", "4"}:
+                    raise SetupError("Choose 1, 2, 3, or 4.")
+                plan["selection_mode"] = {"1": "none", "2": "selected", "3": "selected", "4": None}[value]
+                plan["targets"] = ["all"] if value == "2" else (None if value == "4" else [])
+                step = 2 if value == "3" else 3
+            elif step == 2:
+                for index, choice in enumerate(choices, 1):
+                    write(f"  {index}. {choice['label']}")
+                selected = _indexes(ask("Corpus numbers: "), len(choices))
+                if not selected:
+                    raise SetupError("Select at least one corpus, or go back to choose no active corpus.")
+                plan["targets"] = [choices[index]["target"] for index in selected]
+                step = 3
+            elif step == 3:
+                write("\nCodex app bridge supports per-task corpus preview/use/off and corpus management through $agent-bios.")
+                write("The TUI runs in a terminal or the Codex app terminal panel.")
+                value = ask("Register the Codex app bridge? [y/N]: ").lower()
+                if value not in {"", "n", "no", "y", "yes"}:
+                    raise SetupError("Enter yes or no.")
+                plan["app_bridge"] = value in {"y", "yes"}
+                step = 4
+            elif step == 4:
+                write("\nPrepare existing instructions for personal corpus review. Source files are preserved.")
+                write("Enter explicit project directories as JSON, for example [\"/path/to/project\"].")
+                raw = ask("Project directories [skip; globals = global sources only]: ")
+                if raw.lower() in {"", "skip", "none"}:
+                    plan["project_roots"], plan["import_paths"] = [], []
+                    step = 6
+                    continue
+                try:
+                    roots = [] if raw.lower() == "globals" else json.loads(raw)
+                except ValueError as exc:
+                    raise SetupError("Enter a JSON list of absolute project directories, globals, or skip.") from exc
+                if not isinstance(roots, list) or not all(isinstance(root, str) and Path(root).is_absolute() and Path(root).is_dir() for root in roots):
+                    raise SetupError("Project roots must be existing absolute directories.")
+                plan["project_roots"] = list(dict.fromkeys(roots))
+                discovery = getattr(installer, "setup_discover", None)
+                if not callable(discovery):
+                    raise SetupError("Instruction discovery is unavailable in this installer.")
+                found = discovery(plan["project_roots"])
+                candidates = found.get("sources", []) if isinstance(found, dict) else found
+                candidates = [dict(row) if isinstance(row, dict) else {"path": str(row)} for row in candidates]
+                if not candidates:
+                    write("No eligible instruction files were found in those locations.")
+                    plan["import_paths"] = []
+                    step = 6
+                    continue
+                step = 5
+            elif step == 5:
+                for index, row in enumerate(candidates, 1):
+                    write(f"  {index}. {row['path']}")
+                selected = _indexes(ask("Instruction file numbers to capture, or none [none]: "), len(candidates))
+                plan["import_paths"] = [str(candidates[index]["path"]) for index in selected]
+                step = 6
+            else:
+                preview = controller.preview(plan)
+                write("\nReview installation plan:")
+                write(json.dumps(preview, ensure_ascii=False, indent=2))
+                if plan["import_paths"]:
+                    write("Captured instructions require model review before choosing consumption surfaces. Capture alone does not activate them.")
+                if dry_run:
+                    return {"applied": False, "dry_run": True, **preview}
+                value = ask("Type apply to execute this plan, back to revise, or cancel: ").lower()
+                if value != "apply":
+                    raise SetupError("Nothing was applied. Type apply, back, or cancel.")
+                applying = True
+                return controller.apply(plan, preview=preview, progress=lambda event: write(event["message"]))
+        except _Back:
+            step = {0: 0, 1: 0, 2: 1, 3: 2 if plan["selection_mode"] == "selected" and plan["targets"] != ["all"] else 1,
+                    4: 3, 5: 4, 6: 4}.get(step, 4)
+        except _Cancel:
+            write("Setup cancelled; no installation plan was applied.")
+            return {"cancelled": True, "applied": False}
+        except SetupError as exc:
+            if applying:
+                raise
+            write(str(exc))