@deftai/directive-content 0.55.2 → 0.56.1

package/scripts/doctor.py

@@ -0,0 +1,2257 @@
+#!/usr/bin/env python3
+"""scripts/doctor.py -- canonical doctor implementation (Epic-1 #1335).
+
+This module now owns the core doctor logic previously in run::cmd_doctor
+and its helpers (parse flags, throttle via _doctor_state, install-integrity
+folding, AGENTS.md freshness, Taskfile include diagnostics, structure checks,
+--fix repair, --json / --session / --quiet / --full / --project-root modes).
+
+Thin shims remain in:
+  * run::cmd_doctor  (delegates here after sys.path insert)
+  * Taskfile.yml "doctor:" target (already a shim to `run doctor`)
+
+All new/moved code follows project testing guidelines; tests updated
+in tests/cli/test_cmd_doctor.py and siblings.
+
+See also: scripts/_doctor_state.py (throttle). Install-integrity logic
+previously in framework_doctor.py (retired #1336) now lives here.
+
+Story: #1335 / #1336 (paired in agent1 worktree).
+"""
+
+from __future__ import annotations
+
+import argparse
+import json
+import re
+import shutil
+import subprocess
+import sys
+from dataclasses import dataclass, field
+from datetime import UTC, datetime
+from pathlib import Path
+
+# --- Duplicated minimal CLI / path helpers (avoid importing heavy run) ---
+# These are small, stable, and let doctor.py stay self-contained.
+# Rich is optional; fall back to plain prints. Mirrors run's top-level setup.
+
+HAS_RICH = False
+
+console = None
+Panel = None
+Markdown = None
+try:
+    from rich.console import Console
+    from rich.markdown import Markdown as _Markdown
+    from rich.panel import Panel as _Panel
+    console = Console()
+    Panel = _Panel
+    Markdown = _Markdown
+    HAS_RICH = True
+except Exception:  # noqa: BLE001 -- rich optional
+    HAS_RICH = False
+
+def print_header(text: str):
+    if HAS_RICH and console and Panel:
+        console.print(Panel(f"[bold cyan]{text}[/bold cyan]", border_style="cyan"))
+    else:
+        print(f"\n{'=' * 60}")
+        print(f"  {text}")
+        print('=' * 60)
+
+def print_section(text: str):
+    if HAS_RICH and console and Markdown:
+        console.print(Markdown(f"## {text}"))
+    else:
+        print(f"\n{'-' * 60}")
+        print(f"  {text}")
+        print('-' * 60)
+
+def print_info(msg: str):
+    if HAS_RICH and console:
+        console.print(f"[blue]ℹ[/blue] {msg}")
+    else:
+        print(f"ℹ {msg}")
+
+def print_success(msg: str):
+    if HAS_RICH and console:
+        console.print(f"[green]✓[/green] {msg}")
+    else:
+        print(f"✓ {msg}")
+
+def print_warn(msg: str):
+    if HAS_RICH and console:
+        console.print(f"[yellow]⚠[/yellow] {msg}")
+    else:
+        print(f"⚠ {msg}")
+
+def print_error(msg: str):
+    if HAS_RICH and console:
+        console.print(f"[red]✗[/red] {msg}")
+    else:
+        print(f"✗ {msg}")
+
+# Legacy aliases for the extracted code that calls info/success etc.
+info = print_info
+success = print_success
+warn = print_warn
+error = print_error
+
+def get_script_dir() -> Path:
+    """Get the directory where this script is located (works for import and direct)."""
+    return Path(__file__).parent.absolute()
+
+def resolve_path(path_str: str) -> Path:
+    """Resolve a user-supplied path string to an absolute Path.
+    Expands ~ and resolves relative paths against cwd.
+    """
+    if not path_str:
+        return Path.cwd()
+    p = Path(path_str).expanduser()
+    if not p.is_absolute():
+        p = (Path.cwd() / p).resolve()
+    return p
+
+def _resolve_version() -> str:
+    """Best-effort version (duplicated for doctor self-containment)."""
+    try:
+        for cand in [
+            Path(__file__).parent.parent / 'VERSION',
+            Path(__file__).parent / 'VERSION',
+            Path.cwd() / '.deft-version',
+        ]:
+            if cand.exists():
+                return cand.read_text(encoding='utf-8').strip()
+    except Exception:
+        pass
+    return 'dev'
+
+VERSION = _resolve_version()
+
+# UV url constant (the _check_uv_available helper remains in run for other callers)
+UV_INSTALL_URL = "https://docs.astral.sh/uv/"
+
+# --- Install-integrity checks (ported from retired framework_doctor.py #1336) ---
+# Symbols (EXIT_*, run_checks, main, CheckResult, DoctorResult + 4 checks + impl)
+# are inserted below in small batches. Once complete, _run_install_integrity_checks
+# will delegate locally (no more self-import hack or double-scripts path).
+# This satisfies the Greptile P0 (missing symbols for tests + runtime NameError/AttributeError).
+# --- END PORTED CHECKS HEADER ---
+
+# --- Ported from framework_doctor.py: constants, regexes, dataclasses, low-level helpers ---
+EXIT_CLEAN = 0
+EXIT_DRIFT = 1
+EXIT_CONFIG_ERROR = 2
+
+
+# Marker contract -- mirrors run::_AGENTS_MANAGED_OPEN_RE. Kept inline so
+# this script stays pure-stdlib + cross-platform without importing run
+# (which has heavy import-time side effects).
+_AGENTS_MANAGED_OPEN_RE = re.compile(r"<!--\s*deft:managed-section\s+v(2|3)(?:\s+([^>]*?))?\s*-->")
+_AGENTS_MANAGED_CLOSE = "<!-- /deft:managed-section -->"
+
+# The canonical install-root declaration AGENTS.md carries one of:
+#   "Deft is installed in <root>/."
+#   "Full guidelines: <root>/main.md"
+# We parse both. The first match wins.
+_INSTALLED_IN_RE = re.compile(r"Deft is installed in\s+(\S+?)/?\.")
+_FULL_GUIDELINES_RE = re.compile(r"Full guidelines:\s+(\S+)/main\.md")
+
+# Pattern for referenced skill paths. Matches both ``deft/skills/<name>/SKILL.md``
+# (legacy) and ``.deft/core/skills/<name>/SKILL.md`` (canonical).
+_SKILL_PATH_RE = re.compile(r"(?P<root>[\w./-]+?)/skills/(?P<name>[a-z][\w-]*)/SKILL\.md")
+
+# Deprecation-redirect sentinels embedded in stub SKILL.md files (#411).
+# A skill path that resolves but is a redirect stub is treated as still
+# a fail -- the operator needs to act, not be told everything is fine.
+#
+# Important: current real skills legitimately mention the markdown
+# ``deft:deprecated-redirect`` sentinel when describing migrated
+# SPECIFICATION.md / PROJECT.md state. Redirect detection therefore keys on
+# the stub header shape, not substring presence anywhere in a skill body.
+_DEPRECATED_REDIRECT_SENTINEL = "<!-- deft:deprecated-redirect -->"
+_DEPRECATED_SKILL_REDIRECT_SENTINEL = "<!-- deft:deprecated-skill-redirect -->"
+_REDIRECT_STUB_HEADER_LINES = 8
+
+
+@dataclass
+class CheckResult:
+    """Outcome of a single doctor check.
+
+    ``status`` is one of:
+      * ``"pass"`` -- check succeeded; no action required.
+      * ``"fail"`` -- check failed; drift detected and operator action
+        is required.
+      * ``"skip"`` -- check was skipped because its precondition was
+        not met (e.g. manifest-agreement skips when neither file exists).
+      * ``"error"`` -- check could not run because of a config-level
+        problem (e.g. project root does not exist). Propagates to
+        exit code 2.
+    """
+
+    name: str
+    status: str
+    detail: str
+    data: dict = field(default_factory=dict)
+
+
+@dataclass
+class DoctorResult:
+    """Aggregated doctor outcome consumed by the CLI + gate hook."""
+
+    project_root: str
+    install_root: str | None
+    exit_code: int
+    checks: list[CheckResult]
+    errors: list[str] = field(default_factory=list)
+
+    def to_dict(self) -> dict:
+        return {
+            "project_root": self.project_root,
+            "install_root": self.install_root,
+            "exit_code": self.exit_code,
+            "checks": [
+                {
+                    "name": c.name,
+                    "status": c.status,
+                    "detail": c.detail,
+                    "data": c.data,
+                }
+                for c in self.checks
+            ],
+            "errors": list(self.errors),
+        }
+
+
+# ---------------------------------------------------------------------------
+# Helpers (ported)
+# ---------------------------------------------------------------------------
+
+
+def _read_text_safe(path: Path) -> str | None:
+    """Best-effort UTF-8 read; returns None on OSError."""
+    if not path.is_file():
+        return None
+    try:
+        return path.read_text(encoding="utf-8", errors="replace")
+    except OSError:
+        return None
+
+
+def _parse_install_root_from_agents_md(text: str) -> str | None:
+    """Return the install root AGENTS.md claims (e.g. ``.deft/core``).
+
+    Tries the ``Deft is installed in <root>/.`` form first, then falls back
+    to ``Full guidelines: <root>/main.md``. Returns None when neither matches.
+    Pure -- no I/O.
+    """
+    match = _INSTALLED_IN_RE.search(text)
+    if match:
+        return match.group(1).strip()
+    match = _FULL_GUIDELINES_RE.search(text)
+    if match:
+        return match.group(1).strip()
+    return None
+
+
+def _extract_managed_section(text: str) -> str | None:
+    """Return the bracketed managed-section block, or None when markers are absent."""
+    normalised = text.replace("\r\n", "\n")
+    open_match = _AGENTS_MANAGED_OPEN_RE.search(normalised)
+    if open_match is None:
+        return None
+    open_idx = open_match.start()
+    close_idx = normalised.find(_AGENTS_MANAGED_CLOSE, open_match.end())
+    if close_idx < 0:
+        return None
+    end = close_idx + len(_AGENTS_MANAGED_CLOSE)
+    return normalised[open_idx:end]
+
+
+_MANIFEST_LINE_RE = re.compile(r"^\s*(?P<key>[A-Za-z_][A-Za-z0-9_]*)\s*:\s*(?P<value>.*?)\s*$")
+
+
+def _parse_manifest(text: str) -> dict:
+    """Minimal YAML-ish ``key: value`` parser (#1046 PR-B AC-4).
+
+    Mirrors ``run::_parse_install_manifest``. Pure -- no I/O.
+    """
+    parsed: dict = {}
+    for line in text.splitlines():
+        stripped = line.strip()
+        if not stripped or stripped.startswith("#"):
+            continue
+        match = _MANIFEST_LINE_RE.match(stripped)
+        if match is None:
+            continue
+        key = match.group("key").strip().lower()
+        value = match.group("value").strip().strip("'\"")
+        if key:
+            parsed[key] = value
+    return parsed
+
+
+def _manifest_tag_to_version(manifest: dict) -> str | None:
+    """Derive the bare ``.deft-version`` value from a manifest dict."""
+    for key in ("tag", "ref"):
+        raw = manifest.get(key)
+        if not isinstance(raw, str):
+            continue
+        candidate = raw.strip().lstrip("v")
+        if candidate:
+            return candidate
+    return None
+
+
+def _manifest_candidate_paths(
+    project_root: Path, install_root: str | None
+) -> list[Path]:
+    """Return the canonical-first VERSION-manifest probe order (#1427).
+
+    The install provenance manifest is written to divergent paths by two
+    install rails: the Go installer writes the documented canonical
+    ``<install_root>/VERSION`` (``.deft/core/VERSION`` per #1062), while the
+    webinstaller writes ``.deft/VERSION`` (a 5-field manifest that omits the
+    #1062 ``install_root`` field). The ordering below is **canonical-first**
+    so an existing ``.deft/core/VERSION`` always wins over a stale
+    ``.deft/VERSION``:
+
+      1. ``<install_root>/VERSION`` -- the AGENTS.md / manifest-declared
+         install root, when known (skipped when ``install_root`` is None).
+      2. ``.deft/core/VERSION``    -- the v0.27+ canonical install (#1062).
+      3. ``.deft/VERSION``         -- the webinstaller-vendored location
+         (#1427); restores detection for that population.
+      4. ``deft/VERSION``          -- the pre-v0.27 legacy install.
+
+    Duplicates are removed while preserving order so an ``install_root`` of
+    ``.deft/core`` does not probe the same path twice. Pure -- builds paths
+    only; no filesystem access.
+    """
+    raw: list[Path] = []
+    if install_root:
+        raw.append(project_root / install_root / "VERSION")
+    raw.append(project_root / ".deft" / "core" / "VERSION")
+    raw.append(project_root / ".deft" / "VERSION")
+    raw.append(project_root / "deft" / "VERSION")
+    seen: set[str] = set()
+    ordered: list[Path] = []
+    for candidate in raw:
+        key = str(candidate)
+        if key not in seen:
+            seen.add(key)
+            ordered.append(candidate)
+    return ordered
+
+
+def _locate_manifest(project_root: Path, install_root: str | None) -> Path | None:
+    """Return the first existing VERSION manifest, canonical-first (#1427).
+
+    Walks :func:`_manifest_candidate_paths` in canonical-first order and
+    returns the first candidate that exists on disk, or ``None`` when no
+    manifest is present. Centralises the manifest-location contract so
+    ``_check_manifest_agreement``, ``_check_install_path_consistency``, and
+    the #1339 payload-staleness read path all agree on where a manifest may
+    live -- including the webinstaller's ``.deft/VERSION`` location.
+    """
+    for candidate in _manifest_candidate_paths(project_root, install_root):
+        if candidate.is_file():
+            return candidate
+    return None
+
+
+def _is_deprecation_redirect_stub(text: str) -> bool:
+    """Return True when a resolved skill file is an actual redirect stub."""
+    lines = text.replace("\r\n", "\n").lstrip().splitlines()
+    sentinels = {
+        _DEPRECATED_REDIRECT_SENTINEL,
+        _DEPRECATED_SKILL_REDIRECT_SENTINEL,
+    }
+    return any(line.strip() in sentinels for line in lines[:_REDIRECT_STUB_HEADER_LINES])
+
+
+# ---------------------------------------------------------------------------
+# Checks (ported from framework_doctor.py)
+# ---------------------------------------------------------------------------
+
+
+def _check_quick_start_resolves(project_root: Path, install_root: str | None) -> CheckResult:
+    """Check #1: QUICK-START.md resolves from the install root AGENTS.md claims."""
+    if install_root is None:
+        return CheckResult(
+            name="quick-start-resolves",
+            status="skip",
+            detail=(
+                "AGENTS.md does not declare an install root; cannot check "
+                "QUICK-START.md resolution."
+            ),
+        )
+    qs_path = project_root / install_root / "QUICK-START.md"
+    if qs_path.is_file():
+        return CheckResult(
+            name="quick-start-resolves",
+            status="pass",
+            detail=f"Found QUICK-START.md at {qs_path}.",
+            data={"path": str(qs_path), "install_root": install_root},
+        )
+    return CheckResult(
+        name="quick-start-resolves",
+        status="fail",
+        detail=(
+            f"QUICK-START.md not found at {qs_path}. AGENTS.md claims the "
+            f"install root is {install_root!r} but the file is missing. "
+            "Run `.deft/core/run agents:refresh` (Unix) / "
+            "`.deft\\core\\run agents:refresh` (Windows) to align AGENTS.md "
+            "with the on-disk install root, OR run `task upgrade` to "
+            "re-pull the framework if the on-disk install is missing. "
+            "See UPGRADING.md for the canonical drift-repair walkthrough."
+        ),
+        data={
+            "path": str(qs_path),
+            "install_root": install_root,
+            # Dual repair-path contract: ``suggested_fix`` is the AGENTS.md
+            # realignment (preferred when the on-disk framework is correct);
+            # ``suggested_fix_alt`` re-pulls the framework when the on-disk
+            # install is missing entirely. Mirrors the prose's two-option
+            # phrasing so programmatic consumers (sync skill / CI) see the
+            # same dual surface as humans (SLizard P1 on PR #1067).
+            "suggested_fix": ".deft/core/run agents:refresh",
+            "suggested_fix_alt": "task upgrade",
+        },
+    )
+
+
+def _check_skill_paths_resolve(project_root: Path, agents_md_text: str) -> CheckResult:
+    """Check #2: every <install>/skills/<name>/SKILL.md AGENTS.md references resolves."""
+    referenced = sorted({m.group(0) for m in _SKILL_PATH_RE.finditer(agents_md_text)})
+    if not referenced:
+        return CheckResult(
+            name="skill-paths-resolve",
+            status="skip",
+            detail="AGENTS.md references no skill paths to verify.",
+            data={"referenced": []},
+        )
+    missing: list[str] = []
+    redirect_stubs: list[str] = []
+    for rel in referenced:
+        candidate = project_root / rel
+        if not candidate.is_file():
+            missing.append(rel)
+            continue
+        text = _read_text_safe(candidate)
+        if text is not None and _is_deprecation_redirect_stub(text):
+            redirect_stubs.append(rel)
+    if not missing and not redirect_stubs:
+        return CheckResult(
+            name="skill-paths-resolve",
+            status="pass",
+            detail=f"All {len(referenced)} skill path(s) resolve.",
+            data={"referenced": referenced},
+        )
+    parts: list[str] = []
+    if missing:
+        parts.append(f"missing: {missing}")
+    if redirect_stubs:
+        parts.append(f"deprecation-redirect stubs: {redirect_stubs}")
+    return CheckResult(
+        name="skill-paths-resolve",
+        status="fail",
+        detail=(
+            f"{len(missing)} skill path(s) do not resolve; "
+            f"{len(redirect_stubs)} stub redirect(s). " + "; ".join(parts)
+            + ". Run `.deft/core/run agents:refresh` (Unix) / "
+            "`.deft\\core\\run agents:refresh` (Windows) to rewrite the "
+            "managed AGENTS.md block so skill paths match the on-disk "
+            "framework, OR run `task upgrade` if the on-disk skills are "
+            "missing entirely. See UPGRADING.md for the drift-repair walkthrough."
+        ),
+        data={
+            "referenced": referenced,
+            "missing": missing,
+            "redirect_stubs": redirect_stubs,
+            # Dual repair-path contract -- see ``_check_quick_start_resolves``
+            # for the rationale (SLizard P1 on PR #1067).
+            "suggested_fix": ".deft/core/run agents:refresh",
+            "suggested_fix_alt": "task upgrade",
+        },
+    )
+
+
+def _check_manifest_agreement(project_root: Path, install_root: str | None) -> CheckResult:
+    """Check #3: <install>/VERSION YAML manifest agrees with <root>/.deft-version.
+
+    The manifest is located via :func:`_locate_manifest` (#1427) so a
+    webinstaller-vendored install whose manifest is at ``.deft/VERSION`` is
+    found, canonical-first. ``install_root`` may be None (the webinstaller
+    population whose manifest omits the #1062 ``install_root`` field and
+    whose AGENTS.md therefore yields no install-root claim) -- the helper
+    still probes the canonical/legacy locations, so detection no longer
+    depends on the AGENTS.md install-root parse.
+
+    #1325: before the canonical-vs-bare reconciliation, detect when BOTH the
+    canonical ``.deft/core/VERSION`` and the legacy parent-level
+    ``.deft/VERSION`` exist AND disagree. Two install manifests that name
+    different versions is a stale source-of-truth hazard -- ``task upgrade``
+    migrates the legacy file (backing it up as ``.deft/VERSION.premigrate``).
+    """
+    core_manifest = project_root / ".deft" / "core" / "VERSION"
+    legacy_manifest = project_root / ".deft" / "VERSION"
+    core_dual_text = _read_text_safe(core_manifest)
+    legacy_dual_text = _read_text_safe(legacy_manifest)
+    if core_dual_text is not None and legacy_dual_text is not None:
+        core_ver = _manifest_tag_to_version(_parse_manifest(core_dual_text))
+        legacy_ver = _manifest_tag_to_version(_parse_manifest(legacy_dual_text))
+        if core_ver != legacy_ver:
+            return CheckResult(
+                name="manifest-agreement",
+                status="fail",
+                detail=(
+                    f"Two install manifests disagree: .deft/core/VERSION "
+                    f"(tag={core_ver!r}) vs legacy .deft/VERSION "
+                    f"(tag={legacy_ver!r}). The canonical manifest is "
+                    ".deft/core/VERSION -- run `task upgrade` to migrate the "
+                    "stale .deft/VERSION (backed up as .deft/VERSION.premigrate). "
+                    "See UPGRADING.md for the canonical drift-repair walkthrough."
+                ),
+                data={
+                    "dual_manifest_drift": True,
+                    "core_manifest_path": str(core_manifest),
+                    "legacy_manifest_path": str(legacy_manifest),
+                    "core_version": core_ver,
+                    "legacy_version": legacy_ver,
+                    "authoritative": "manifest",
+                    "suggested_fix": "task upgrade",
+                },
+            )
+    manifest_path = _locate_manifest(project_root, install_root)
+    # Canonical-first expected location for diagnostics when no manifest is
+    # found on disk (``_manifest_candidate_paths`` always returns >= 1 entry).
+    expected_manifest_path = (
+        manifest_path
+        if manifest_path is not None
+        else _manifest_candidate_paths(project_root, install_root)[0]
+    )
+    bare_candidates = [
+        project_root / "vbrief" / ".deft-version",
+        project_root / ".deft-version",
+    ]
+    bare_path: Path | None = next((p for p in bare_candidates if p.is_file()), None)
+    manifest_text = _read_text_safe(manifest_path) if manifest_path else None
+    bare_text = _read_text_safe(bare_path) if bare_path else None
+    if manifest_text is None and bare_text is None:
+        return CheckResult(
+            name="manifest-agreement",
+            status="skip",
+            detail=(
+                "Neither YAML manifest nor bare .deft-version exists; "
+                "nothing to reconcile (greenfield install)."
+            ),
+            data={
+                "manifest_path": str(manifest_path) if manifest_path else None,
+                "bare_path": str(bare_path) if bare_path else None,
+            },
+        )
+    if manifest_text is None:
+        return CheckResult(
+            name="manifest-agreement",
+            status="fail",
+            detail=(
+                f"Bare .deft-version exists at {bare_path} but YAML manifest "
+                f"is missing at {expected_manifest_path}. Run `task upgrade` to write "
+                "the canonical manifest (#1046 PR-B AC-4). See UPGRADING.md "
+                "for the v0.27.x -> v0.28 transition walkthrough."
+            ),
+            data={
+                "manifest_path": str(manifest_path) if manifest_path else None,
+                "expected_manifest_path": str(expected_manifest_path),
+                "bare_path": str(bare_path) if bare_path else None,
+                "bare_value": (bare_text or "").strip() if bare_text else None,
+                "suggested_fix": "task upgrade",
+            },
+        )
+    if bare_text is None:
+        # YAML present, bare missing -- not a drift in itself; cmd_upgrade
+        # will derive the bare file on next run. Report as pass with a note.
+        manifest = _parse_manifest(manifest_text)
+        derived = _manifest_tag_to_version(manifest)
+        return CheckResult(
+            name="manifest-agreement",
+            status="pass",
+            detail=(
+                f"YAML manifest at {manifest_path} present; bare .deft-version "
+                f"absent (derived value: {derived!r} from manifest tag). "
+                "Run `task upgrade` to regenerate the derivative."
+            ),
+            data={
+                "manifest_path": str(manifest_path),
+                "manifest": manifest,
+                "derived_version": derived,
+            },
+        )
+    manifest = _parse_manifest(manifest_text)
+    derived = _manifest_tag_to_version(manifest)
+    bare_value = bare_text.strip()
+    if derived is None:
+        return CheckResult(
+            name="manifest-agreement",
+            status="fail",
+            detail=(
+                f"YAML manifest at {manifest_path} has no parseable tag/ref "
+                "field; cannot reconcile with bare .deft-version."
+            ),
+            data={
+                "manifest_path": str(manifest_path),
+                "bare_path": str(bare_path),
+                "manifest": manifest,
+                "bare_value": bare_value,
+            },
+        )
+    if derived == bare_value:
+        return CheckResult(
+            name="manifest-agreement",
+            status="pass",
+            detail=(
+                f"YAML manifest (tag={derived!r}) agrees with bare .deft-version ({bare_value!r})."
+            ),
+            data={
+                "manifest_path": str(manifest_path),
+                "bare_path": str(bare_path),
+                "derived_version": derived,
+                "bare_value": bare_value,
+            },
+        )
+    return CheckResult(
+        name="manifest-agreement",
+        status="fail",
+        detail=(
+            f"Drift detected: YAML manifest tag={derived!r} does NOT agree "
+            f"with bare .deft-version={bare_value!r}. Per #1046 PR-B AC-4 "
+            "the YAML manifest is the canonical source -- run `task upgrade` "
+            "to regenerate the bare derivative from the manifest, OR "
+            f"manually update {manifest_path} if the bare value is correct. "
+            "See UPGRADING.md for the canonical drift-repair walkthrough."
+        ),
+        data={
+            "manifest_path": str(manifest_path),
+            "bare_path": str(bare_path),
+            "derived_version": derived,
+            "bare_value": bare_value,
+            "authoritative": "manifest",
+            "suggested_fix": "task upgrade",
+        },
+    )
+
+
+def _check_install_path_consistency(project_root: Path, install_root: str | None) -> CheckResult:
+    """Check #4: AGENTS.md install-root claim resolves to an on-disk directory.
+
+    Narrow scope by design (#1046 PR-B Greptile review #1057): this check
+    only verifies that the install root AGENTS.md declares is a real
+    directory on disk. The cross-check that the YAML manifest is
+    **co-located** at that root is the responsibility of check #3
+    (``manifest-agreement``) -- when the manifest lives at a different
+    install root (e.g. legacy ``deft/VERSION`` while AGENTS.md claims
+    ``.deft/core``), check #3 reports the drift with the manifest as the
+    authoritative source. Splitting the responsibility keeps each check
+    independently actionable: this one says "reinstall or fix AGENTS.md",
+    check #3 says "reconcile the manifest with the bare derivative".
+    """
+    effective_install_root = install_root
+    fallback_info_note = ""
+    source = "AGENTS.md"
+    # #1062: prefer the manifest-side ``install_root`` field when present --
+    # it is the single source of truth for the install-layout contract.
+    # Fall back to the legacy AGENTS.md parse only when the manifest exists
+    # but predates the field (legacy v0.28 shape) or no manifest exists.
+    # The ``source`` flag stays sticky across the manifest-found-but-empty
+    # path so the diagnostic prose later accurately names where the
+    # effective install root came from (Greptile P1 on PR #1063 -- prior
+    # heuristic compared values, which mislabelled when manifest and
+    # AGENTS.md happened to agree).
+    # #1427: probe the manifest canonical-first via the shared candidate
+    # list so a webinstaller-vendored ``.deft/VERSION`` is considered too
+    # (the prior shape probed only ``.deft/core/VERSION`` and legacy
+    # ``deft/VERSION``). Iterate the candidate list rather than call
+    # ``_locate_manifest`` so an existing-but-unreadable manifest (OSError /
+    # permission denial -> ``_read_text_safe`` returns None) falls through
+    # to the next candidate, preserving the ``continue``-on-unreadable
+    # resilience of the original two-path loop (Greptile P2 on PR #1431).
+    # The first READABLE manifest wins, matching the prior
+    # break-on-first-found semantics.
+    for manifest_path in _manifest_candidate_paths(project_root, install_root):
+        manifest_text = _read_text_safe(manifest_path)
+        if manifest_text is None:
+            continue
+        manifest = _parse_manifest(manifest_text)
+        manifest_install_root = manifest.get("install_root")
+        if isinstance(manifest_install_root, str) and manifest_install_root.strip():
+            effective_install_root = manifest_install_root.strip()
+            fallback_info_note = ""
+            source = "manifest"
+            break
+        # Manifest found but missing the #1062 ``install_root`` field
+        # (legacy v0.28 shape, or a webinstaller ``.deft/VERSION`` that
+        # omits it). Fall back to the AGENTS.md parse and note it.
+        # ``source`` stays "AGENTS.md" -- the manifest was found but did not
+        # carry the install_root field, so the effective value still came
+        # from the AGENTS.md parse.
+        fallback_info_note = (
+            f" INFO: manifest at {manifest_path} is missing install_root; "
+            "fell back to the legacy AGENTS.md install-root parse."
+        )
+        break
+    if effective_install_root is None:
+        return CheckResult(
+            name="install-path-consistency",
+            status="skip",
+            detail=(
+                "AGENTS.md does not declare an install root."
+                + fallback_info_note
+            ),
+            data={
+                "claimed_install_root": install_root,
+                "effective_install_root": effective_install_root,
+                "fallback_info_note": fallback_info_note or None,
+            },
+        )
+    claimed_dir = project_root / effective_install_root
+    if not claimed_dir.is_dir():
+        return CheckResult(
+            name="install-path-consistency",
+            status="fail",
+            detail=(
+                f"Install root is recorded as {effective_install_root!r} "
+                f"(source: {source}) but {claimed_dir} is not a directory. "
+                "Pick one of two repair paths: "
+                "(a) run `.deft/core/run agents:refresh` (Unix) / "
+                "`.deft\\core\\run agents:refresh` (Windows) to rewrite "
+                "AGENTS.md to match the on-disk framework -- pick this if "
+                "the framework on disk is correct; OR "
+                "(b) run `task relocate:relocate -- --confirm` to move the "
+                "framework to the path AGENTS.md / the manifest claims -- "
+                "pick this if AGENTS.md is correct. The YAML manifest (if "
+                "present) is authoritative for the install-layout contract. "
+                "See UPGRADING.md for the canonical drift-repair walkthrough."
+            ),
+            data={
+                "claimed_install_root": install_root,
+                "effective_install_root": effective_install_root,
+                "effective_install_root_source": source,
+                "claimed_dir": str(claimed_dir),
+                "claimed_dir_exists": False,
+                "fallback_info_note": fallback_info_note or None,
+                "suggested_fix": ".deft/core/run agents:refresh",
+                "suggested_fix_alt": "task relocate:relocate -- --confirm",
+            },
+        )
+    # Note: this check intentionally does NOT verify the YAML manifest
+    # is co-located at ``<claimed_dir>/VERSION`` -- that cross-check is
+    # owned by check #3 (``manifest-agreement``). See docstring for the
+    # rationale and the per-check responsibility split.
+    return CheckResult(
+        name="install-path-consistency",
+        status="pass",
+        detail=(
+            f"Install root ({effective_install_root!r}, source: {source}) "
+            f"matches an existing directory at {claimed_dir}."
+            + fallback_info_note
+        ),
+        data={
+            "claimed_install_root": install_root,
+            "effective_install_root": effective_install_root,
+            "effective_install_root_source": source,
+            "claimed_dir": str(claimed_dir),
+            "fallback_info_note": fallback_info_note or None,
+        },
+    )
+
+
+# ---------------------------------------------------------------------------
+# Top-level driver (ported) -- provides run_checks for tests + internal use
+# ---------------------------------------------------------------------------
+
+
+def run_checks(project_root: Path) -> dict:
+    """Run all four checks and return a structured payload.
+
+    Public API consumed by ``run::_maybe_run_framework_doctor`` (and tests).
+    Returns the DoctorResult dict shape directly. Best-effort -- any
+    individual check that fails to run converts to an ``error`` status and
+    propagates to exit code 2.
+    """
+    return _run_checks_impl(project_root).to_dict()
+
+
+def _run_checks_impl(project_root: Path) -> DoctorResult:
+    """Internal driver -- returns the dataclass form for richer testing."""
+    errors: list[str] = []
+    if not project_root.is_dir():
+        return DoctorResult(
+            project_root=str(project_root),
+            install_root=None,
+            exit_code=EXIT_CONFIG_ERROR,
+            checks=[],
+            errors=[f"project root does not exist: {project_root}"],
+        )
+
+    agents_md_path = project_root / "AGENTS.md"
+    agents_md_text = _read_text_safe(agents_md_path)
+    install_root: str | None = None
+    if agents_md_text is not None:
+        install_root = _parse_install_root_from_agents_md(agents_md_text)
+
+    checks: list[CheckResult] = []
+
+    # If AGENTS.md is missing entirely, the install-root-dependent checks
+    # all skip; surface this fact in a synthetic check so operators see
+    # the cause.
+    if agents_md_text is None:
+        checks.append(
+            CheckResult(
+                name="agents-md-present",
+                status="fail",
+                detail=(
+                    "AGENTS.md not found at project root -- run "
+                    "`.deft/core/run agents:refresh` to generate it from "
+                    "the canonical template."
+                ),
+                data={"agents_md_path": str(agents_md_path)},
+            )
+        )
+        # Still attempt the manifest agreement check (it can run without
+        # AGENTS.md for the greenfield case).
+        checks.append(_check_manifest_agreement(project_root, None))
+        return DoctorResult(
+            project_root=str(project_root),
+            install_root=None,
+            exit_code=_derive_exit_code(checks, errors),
+            checks=checks,
+            errors=errors,
+        )
+
+    checks.append(_check_quick_start_resolves(project_root, install_root))
+    checks.append(_check_skill_paths_resolve(project_root, agents_md_text))
+    checks.append(_check_manifest_agreement(project_root, install_root))
+    checks.append(_check_install_path_consistency(project_root, install_root))
+
+    return DoctorResult(
+        project_root=str(project_root),
+        install_root=install_root,
+        exit_code=_derive_exit_code(checks, errors),
+        checks=checks,
+        errors=errors,
+    )
+
+
+def _derive_exit_code(checks: list[CheckResult], errors: list[str]) -> int:
+    """Three-state exit code from check results + errors."""
+    if errors or any(c.status == "error" for c in checks):
+        return EXIT_CONFIG_ERROR
+    if any(c.status == "fail" for c in checks):
+        return EXIT_DRIFT
+    return EXIT_CLEAN
+
+
+# --- Extracted doctor logic (from run, markers removed, now owned here) ---
+# (start of logic extracted from monolithic run per #1335)
+# The block from this marker through DOCTOR-EXTRACTION-END (the end of
+# cmd_doctor, just before def cmd_update) is extracted verbatim into
+# scripts/doctor.py . After extraction, this region is replaced by a
+# thin shim that does the path-insert + import + delegation.
+# The scripts/doctor.py now owns the core doctor logic.
+# ===
+
+# ── #1272 root Taskfile.yml include diagnostics ──────────────────────────
+#
+# A freshly installed directive project does not have a working `task X`
+# surface from the project root until the consumer wires their
+# root-level Taskfile.yml to include `.deft/core/Taskfile.yml`. The
+# install policy in `main.md` correctly prohibits silent mutation of
+# the consumer's existing Taskfile.yml, but the framework should still
+# *diagnose* the missing-include / missing-file shapes the moment the
+# operator runs doctor. Interactive `run doctor --fix` may offer to
+# create a Taskfile.yml when one is absent (explicit consent required);
+# the default and `--session` paths NEVER mutate filesystem state.
+#
+# The canonical snippet is mirrored verbatim from `.deft/core/main.md`
+# ("Publishing deft tasks in your project root") so doctor's output and
+# the prose documentation never drift.
+
+# Canonical YAML snippet emitted by doctor's diagnostic output and
+# written verbatim when the operator opts in to interactive repair.
+# Kept as a module-level constant so tests can compare against the
+# exact bytes a write would produce.
+_TASKFILE_INCLUDE_SNIPPET = (
+    "version: '3'\n"
+    "\n"
+    "includes:\n"
+    "  deft:\n"
+    "    taskfile: ./.deft/core/Taskfile.yml\n"
+    "    optional: true\n"
+)
+
+# Matches a top-level YAML ``includes:`` declaration. Used by the
+# indentation-aware state machine in :func:`_includes_block_has_deft_taskfile`
+# to anchor the scan: a ``taskfile:`` line that lives inside any other
+# block (e.g. ``vars:``, ``tasks:`` cmds, a YAML comment, a long string
+# scalar) MUST NOT count as a valid deft framework include, otherwise
+# the diagnostic mis-reports ``ok`` on a Taskfile that mentions the
+# string ``taskfile: ./.deft/core/Taskfile.yml`` in unrelated context
+# (a comment, an example block, an echo cmd). See #1303 review.
+_TASKFILE_INCLUDES_KEY_RE = re.compile(
+    r"^(?P<indent>[\t ]*)includes\s*:\s*(?:#.*)?$",
+    re.IGNORECASE,
+)
+
+# Matches ``taskfile: <path-to-deft-framework-Taskfile>`` value lines that
+# appear under the ``includes:`` mapping. Tolerates leading ``./``,
+# surrounding whitespace, optional single/double quotes around the value,
+# and an inline ``# ...`` comment trailing the value. Case-insensitive so
+# both ``Taskfile.yml`` and ``taskfile.yml`` match. Indent MUST be > 0
+# under a top-level ``includes:`` block.
+_TASKFILE_INCLUDE_VALUE_RE = re.compile(
+    r"^[\t ]+taskfile\s*:\s*[\"']?\.?/?(?:\.deft/core|deft)/Taskfile\.ya?ml[\"']?"
+    r"\s*(?:#.*)?$",
+    re.IGNORECASE,
+)
+
+
+def _includes_block_has_deft_taskfile(text: str) -> bool:
+    """Return True iff a top-level ``includes:`` mapping points at deft.
+
+    Walks ``text`` line-by-line with a small indentation-aware state
+    machine: anchors on a top-level (indent 0) ``includes:`` key, then
+    scans the strictly-greater-indent body for a ``taskfile:`` property
+    whose value resolves to either the canonical ``./.deft/core/Taskfile.yml``
+    or the pre-v0.27 legacy ``./deft/Taskfile.yml``. Lines whose indent
+    is less-than-or-equal-to the ``includes:`` indent end the block.
+
+    Stdlib-only: ``run`` is the bootstrap entry point and cannot assume
+    PyYAML is installed. A full YAML walk would be more robust but adds
+    a runtime dependency we deliberately avoid here.
+    """
+    includes_indent: int | None = None
+    in_includes = False
+    for raw_line in text.splitlines():
+        stripped = raw_line.strip()
+        if not stripped or stripped.startswith("#"):
+            continue
+        indent = len(raw_line) - len(raw_line.lstrip(" \t"))
+        if not in_includes:
+            match = _TASKFILE_INCLUDES_KEY_RE.match(raw_line)
+            if match is not None and indent == 0:
+                includes_indent = indent
+                in_includes = True
+            continue
+        if indent <= (includes_indent or 0):
+            in_includes = False
+            match = _TASKFILE_INCLUDES_KEY_RE.match(raw_line)
+            if match is not None and indent == 0:
+                includes_indent = indent
+                in_includes = True
+            continue
+        if _TASKFILE_INCLUDE_VALUE_RE.match(raw_line):
+            return True
+    return False
+
+
+def _resolve_consumer_taskfile(
+    project_root: Path | None = None,
+) -> Path | None:
+    """Return the consumer project's root Taskfile path, or None if absent.
+
+    Recognises both ``Taskfile.yml`` and ``Taskfile.yaml`` so the
+    diagnostic accepts whichever spelling the consumer chose. Returns
+    the first candidate that exists on disk; returns ``None`` when
+    neither file is present so callers can distinguish the
+    missing-file case from the missing-include case.
+
+    ``project_root`` defaults to ``Path.cwd()`` when omitted so existing
+    callers stay backward-compatible; the explicit-argument shape is the
+    canonical form so :func:`cmd_doctor` can honour a user-supplied
+    ``--project-root <path>`` (#1303 review).
+    """
+    if project_root is None:
+        project_root = Path.cwd()
+    for name in ("Taskfile.yml", "Taskfile.yaml"):
+        candidate = project_root / name
+        if candidate.is_file():
+            return candidate
+    return None
+
+
+def _classify_taskfile_include(project_root: Path) -> str:
+    """Classify the consumer's root Taskfile include health (#1272).
+
+    Returns one of:
+        ``ok``              -- root Taskfile.yml present and includes the
+                               deft framework Taskfile (``./.deft/core/Taskfile.yml``
+                               or the legacy ``./deft/Taskfile.yml``).
+        ``missing-file``    -- neither ``Taskfile.yml`` nor ``Taskfile.yaml``
+                               exists at the project root. Interactive
+                               ``run doctor --fix`` may create one with
+                               explicit consent.
+        ``missing-include`` -- a root Taskfile exists but contains no
+                               include pointing at the deft framework
+                               Taskfile. Doctor NEVER mutates an
+                               existing user-owned Taskfile -- diagnose
+                               only; the operator pastes the snippet.
+        ``unreadable``      -- a root Taskfile exists but could not be
+                               read (permission error, etc.). Diagnose;
+                               do not repair.
+
+    Pure -- read-only filesystem probe + indentation-aware string walk.
+    Never mutates state.
+    """
+    taskfile = _resolve_consumer_taskfile(project_root)
+    if taskfile is None:
+        return "missing-file"
+    try:
+        # ``utf-8-sig`` transparently strips a leading UTF-8 BOM if present.
+        # Windows editors (Notepad, some VS Code configurations) persist YAML
+        # with a BOM byte at the head; ``utf-8`` would keep the ``\ufeff``
+        # prefix in ``text`` and defeat the ``^[\t ]*includes`` anchor in
+        # :func:`_includes_block_has_deft_taskfile`, producing a spurious
+        # ``missing-include`` diagnostic on a legitimately wired Taskfile.
+        # See #1303 pass-2 review.
+        text = taskfile.read_text(encoding="utf-8-sig", errors="replace")
+    except OSError:
+        return "unreadable"
+    if _includes_block_has_deft_taskfile(text):
+        return "ok"
+    return "missing-include"
+
+
+def _format_missing_include_snippet() -> str:
+    """Return the paste-ready `includes:` fragment for an existing Taskfile.
+
+    Used by doctor's ``missing-include`` diagnostic so the operator
+    sees the exact YAML they need to paste under their existing
+    ``includes:`` block, without the ``version: '3'`` header (which
+    their existing file already supplies).
+    """
+    return (
+        "  deft:\n"
+        "    taskfile: ./.deft/core/Taskfile.yml\n"
+        "    optional: true\n"
+    )
+
+
+def _parse_doctor_flags(args: list[str]) -> dict:
+    """Parse the doctor-specific CLI flags (#1272, #1303 review).
+
+    Recognises (whitelist; unknown tokens surface as ``unknown``):
+        ``--session``                -- diagnose-only, session-safe mode.
+                                        NEVER prompts, NEVER mutates
+                                        filesystem state. Suitable for
+                                        invocation from session-start
+                                        rituals.
+        ``--fix`` / ``--repair`` /   -- offer interactive repair when
+        ``--repair-taskfile``           actionable (currently: create
+                                        missing root Taskfile.yml with
+                                        the canonical include). Requires
+                                        an interactive TTY AND explicit
+                                        operator approval at the prompt;
+                                        ignored when ``--session`` is
+                                        also passed.
+        ``--json``                   -- emit a single JSON object on
+                                        stdout describing the findings;
+                                        suppresses the human-readable
+                                        prose surface. Exit code is
+                                        still 0 (clean) / 1 (errors).
+        ``--quiet``                  -- suppress the per-check success
+                                        lines; errors and warnings still
+                                        surface.
+        ``--project-root <path>`` /  -- override the project root used
+        ``--project-root=<path>``       for the Taskfile diagnostic.
+                                        Defaults to :func:`Path.cwd`.
+        ``-h`` / ``--help``          -- accepted (caller decides how to
+                                        render help text); does not run
+                                        the diagnostics.
+
+    Unknown tokens are collected into ``flags["unknown"]`` so the caller
+    can exit non-zero with a useful error message rather than silently
+    swallowing a typo (e.g. ``--repare`` instead of ``--repair`` -- the
+    pre-review behaviour shipped diagnostics that ignored the typo,
+    masking the fact that the user never opted into repair).
+    """
+    flags = {
+        "session": False,
+        "fix": False,
+        "json": False,
+        "quiet": False,
+        "full": False,
+        "help": False,
+        "project_root": None,
+        "unknown": [],
+    }
+    i = 0
+    while i < len(args):
+        token = args[i]
+        if token == "--session":
+            flags["session"] = True
+        elif token in ("--fix", "--repair", "--repair-taskfile"):
+            flags["fix"] = True
+        elif token == "--json":
+            flags["json"] = True
+        elif token == "--quiet":
+            flags["quiet"] = True
+        elif token == "--full":
+            # #1308: bypass the 24h/4h throttle and always run the full
+            # check. Operators reach for this when the prior run was
+            # dirty (errors) and they want to re-probe after fixing,
+            # OR when they want to re-confirm a clean run before
+            # publishing a swarm.
+            flags["full"] = True
+        elif token in ("-h", "--help"):
+            flags["help"] = True
+        elif token == "--project-root":
+            if i + 1 >= len(args):
+                flags["unknown"].append("--project-root (missing value)")
+            else:
+                i += 1
+                flags["project_root"] = args[i]
+        elif token.startswith("--project-root="):
+            value = token.split("=", 1)[1]
+            if value:
+                flags["project_root"] = value
+            else:
+                flags["unknown"].append("--project-root= (empty value)")
+        else:
+            flags["unknown"].append(token)
+        i += 1
+    return flags
+
+
+# Allowed flag set for ``run doctor`` -- surfaced in the error message
+# emitted when ``_parse_doctor_flags`` collects an unknown token (#1303
+# review correctness #3). Keep in sync with the registered branches in
+# :func:`_parse_doctor_flags`.
+_DOCTOR_ALLOWED_FLAGS = (
+    "--session",
+    "--fix",
+    "--repair",
+    "--repair-taskfile",
+    "--json",
+    "--quiet",
+    "--full",
+    "--project-root",
+    "-h",
+    "--help",
+)
+
+
+def _load_doctor_state_module():
+    """Lazy-import ``scripts/_doctor_state`` (#1308)."""
+    try:
+        # Inside scripts/doctor.py, get_script_dir() already returns the
+        # scripts/ dir containing sibling _doctor_state.py. Do not append
+        # another "/scripts" (would resolve to scripts/scripts/ and break
+        # throttle state load when doctor.py is the entry point).
+        scripts_dir = get_script_dir()
+        if str(scripts_dir) not in sys.path:
+            sys.path.insert(0, str(scripts_dir))
+        import _doctor_state  # type: ignore[import-not-found]
+        return _doctor_state
+    except Exception:  # noqa: BLE001 -- state load MUST NOT break doctor
+        return None
+
+
+def _evaluate_doctor_throttle(project_root: Path):
+    """Read doctor state and compute the 24h/4h throttle decision (#1308)."""
+    mod = _load_doctor_state_module()
+    if mod is None:
+        return None
+    try:
+        state = mod.read_state(project_root)
+        return mod.decide_throttle(state)
+    except Exception:  # noqa: BLE001 -- state read MUST NOT break doctor
+        return None
+
+
+# --- Ported from run (required by cmd_doctor / freshness / throttle paths) ---
+# These were left behind during the initial extraction; without them every
+# `run doctor` (non-throttled path) hits NameError before any check runs.
+# Small batch ports; supporting constants/defs included where referenced.
+
+# Minimal local read_yn (used only in interactive --fix Taskfile repair path
+# under isatty + fix_mode). Closes the "undefined" gap Greptile summary
+# flagged on the post-7a0606c head. Full ask_confirm lives in run; this is
+# the smallest non-crashing implementation sufficient for doctor.
+def read_yn(prompt_text: str, default: bool = False) -> bool:
+    """Yes/No prompt (read_yn alias to run's ask_confirm)."""
+    try:
+        suffix = " (Y/n): " if default else " (y/N): "
+        resp = input(f"{prompt_text}{suffix}").strip().lower()
+        if not resp:
+            return default
+        return resp[0] in ("y", "yes")
+    except (EOFError, KeyboardInterrupt):
+        return default
+
+
+def _load_agents_md_module():
+    """Lazy-import the shared ``scripts/_agents_md`` helpers (#1389).
+
+    ``get_script_dir()`` already returns the ``scripts/`` directory holding
+    the sibling ``_agents_md.py``, so mirror ``_load_doctor_state_module``
+    and insert it on ``sys.path`` before importing. The freshness probe can
+    then share ``run``'s exact managed-section verdict logic instead of the
+    interim stub that always reported ``unreadable``.
+    """
+    scripts_dir = get_script_dir()
+    if str(scripts_dir) not in sys.path:
+        sys.path.insert(0, str(scripts_dir))
+    import _agents_md  # type: ignore[import-not-found]
+    return _agents_md
+
+
+def _agents_refresh_plan(project_root: Path) -> dict:
+    """Compute the real AGENTS.md managed-section freshness verdict (#1389).
+
+    Delegates to the shared, pure ``scripts/_agents_md._agents_refresh_plan``
+    -- the same implementation ``run`` uses -- so a consumer whose managed
+    section is present, readable and current reports ``state == "current"``
+    (no freshness warning) instead of the previous interim stub that
+    unconditionally returned ``{"state": "unreadable"}`` and produced a
+    spurious warning on every ``task doctor`` run. Genuinely stale sections
+    report ``stale`` (the freshness check then points the operator at
+    ``deft agents:refresh``); a genuinely unreadable / template-missing
+    state still surfaces a warning.
+    """
+    return _load_agents_md_module()._agents_refresh_plan(project_root)
+
+
+def _now_utc() -> datetime:
+    """Return UTC-aware ``datetime.now`` (split out for test monkeypatching)."""
+    return datetime.now(UTC)
+
+
+# Post-#1875 content/ move: these framework-internal markers now live under
+# content/ in the SOURCE repo. They identify a deft source checkout (a consumer
+# would never reproduce them); the C1 flatten means a consumer deposit has no
+# content/ dir, so the absence of content/ here is itself consistent with the
+# "not a source checkout" branch.
+_DEFT_REPO_POSITIVE_MARKERS = (
+    Path("content") / "templates" / "agents-entry.md",
+    Path("content") / "skills" / "deft-directive-build" / "SKILL.md",
+)
+
+
+def _running_inside_deft_repo(project_root: Path) -> bool:
+    """Heuristic: True when `run` is invoked from inside the deft repo itself.
+
+    Consumer projects embed deft as ``./deft/`` (legacy) or ``./.deft/core/``
+    (canonical) and consume the framework's published surface; the deft
+    source repo carries ``main.md`` at its root, has neither install
+    location materialised inside its own checkout, AND ships a set of
+    framework-internal artefacts (notably ``templates/agents-entry.md`` and
+    ``skills/deft-directive-build/SKILL.md``) a consumer would have no
+    reason to mirror.
+
+    The heuristic fires only when ALL of the following hold:
+      * ``main.md`` is present at ``project_root`` (the documented entry
+        point a consumer never reproduces verbatim).
+      * NEITHER ``./deft`` (legacy install) NOR ``./.deft/core`` (canonical
+        install) exists at the project root -- both indicate the deft
+        framework was installed INTO this directory rather than that this
+        directory IS the framework.
+      * ALL of the markers in ``_DEFT_REPO_POSITIVE_MARKERS`` resolve --
+        framework-internal paths a consumer would never reproduce.
+
+    The original heuristic (#1272 baseline) checked only ``main.md`` plus
+    the absence of ``./deft``; that mis-fired on a consumer who happened
+    to carry a root-level ``main.md`` for unrelated reasons OR who
+    installed canonically to ``./.deft/core`` and so genuinely had no
+    ``./deft`` subdirectory -- doctor would then silently skip the
+    Taskfile-include diagnostic in exactly the place it was meant to
+    surface (#1303 review SLizard P1, Greptile carryover).
+
+    Skipping the gate here avoids nagging deft maintainers on every
+    ``run`` invocation against the framework checkout itself.
+    """
+    if not (project_root / "main.md").is_file():
+        return False
+    if (project_root / "deft").is_dir():
+        return False
+    if (project_root / ".deft" / "core").is_dir():
+        return False
+    return all((project_root / marker).is_file() for marker in _DEFT_REPO_POSITIVE_MARKERS)
+
+
+# --- Extracted doctor logic (from run, markers removed, now owned here) ---
+
+def _format_iso_z(when) -> str:
+    """Render a UTC-aware datetime as YYYY-MM-DDTHH:MM:SSZ."""
+    if when is None:
+        return ""
+    if when.tzinfo is None:
+        when = when.replace(tzinfo=UTC)
+    return when.astimezone(UTC).strftime("%Y-%m-%dT%H:%M:%SZ")
+
+
+def _render_doctor_status_line(decision) -> str:
+    """Render the human-readable throttle-skip line (#1308)."""
+    age_h = max(int(decision.age_hours), 0)
+    if decision.dirty:
+        errs = decision.last_error_count
+        warns = max(decision.last_finding_count - decision.last_error_count, 0)
+        err_phrase = f"{errs} error{'s' if errs != 1 else ''}"
+        warn_phrase = f"{warns} warning{'s' if warns != 1 else ''}"
+        return (
+            f"[doctor] ran {age_h}h ago, {err_phrase} / {warn_phrase} "
+            "-- UNRESOLVED; run `deft doctor --full` to re-probe or "
+            "address findings."
+        )
+    remaining = decision.next_eligible_at - _now_utc()
+    remaining_h = max(int(remaining.total_seconds() // 3600), 0)
+    return (
+        f"[doctor] ran {age_h}h ago, clean; next eligible in "
+        f"{remaining_h}h; --full forces."
+    )
+
+
+def _emit_doctor_throttle_skip(decision, *, json_mode: bool) -> int:
+    """Print the throttle-skip surface and return the gated exit code (#1308)."""
+    hint = (
+        "run `deft doctor --full` to re-probe or address findings"
+        if decision.dirty
+        else "--full forces"
+    )
+    if json_mode:
+        payload = {
+            "status": "throttle-skipped",
+            "last_run_at": _format_iso_z(decision.last_run_at),
+            "last_exit_code": decision.last_exit_code,
+            "last_error_count": decision.last_error_count,
+            "last_finding_count": decision.last_finding_count,
+            "next_eligible_at": _format_iso_z(decision.next_eligible_at),
+            "hint": hint,
+        }
+        print(json.dumps(payload, sort_keys=True))
+    else:
+        print(_render_doctor_status_line(decision))
+    return 1 if decision.dirty else 0
+
+
+def _persist_doctor_state(
+    project_root: Path,
+    *,
+    exit_code: int,
+    findings: list[dict],
+) -> None:
+    """Best-effort write of doctor-state.json after a full check (#1308).
+
+    ``last_finding_count`` is persisted as the count of findings that
+    *mattered* -- ``severity == "skip"`` findings (e.g. the AGENTS.md
+    freshness check's "no managed-section markers (likely maintainer
+    repo)" skip) are EXCLUDED (#1316). Counting a skip would make
+    ``_render_doctor_status_line`` over-report warnings by one on a
+    dirty throttle-skip, because it derives the warning tally as
+    ``last_finding_count - last_error_count`` and a skip carries no
+    error/warning weight. See ``scripts/_doctor_state.py`` for the
+    persisted-schema contract.
+    """
+    mod = _load_doctor_state_module()
+    if mod is None:
+        return
+    try:
+        mod.write_state(
+            project_root,
+            exit_code=int(exit_code),
+            finding_count=sum(
+                1 for f in findings if f.get("severity") != "skip"
+            ),
+            error_count=sum(1 for f in findings if f.get("severity") == "error"),
+        )
+    except Exception:  # noqa: BLE001 -- state write MUST NOT break doctor
+        return
+
+
+def _run_install_integrity_checks(
+    project_root: Path,
+    *,
+    emit_success,
+    emit_warn,
+    emit_error,
+    emit_info,
+    add_finding,
+) -> None:
+    """Install-integrity checks (ex-framework_doctor.py) folded into
+    canonical doctor (#1308, #1336 retirement).
+    """
+    if _running_inside_deft_repo(project_root):
+        emit_info(
+            "Skipping install-integrity checks -- running inside the deft "
+            "framework repo (no install manifest in the source checkout)."
+        )
+        return
+    try:
+        # Direct call to the local (ported) implementation -- no self-import
+        # hack, no path munging. The four checks now run for real.
+        result = run_checks(project_root)
+    except Exception as exc:  # noqa: BLE001 -- probe failure is a warning
+        message = f"Install-integrity probe unavailable: {type(exc).__name__}: {exc}"
+        emit_warn(message)
+        add_finding("warning", message, check="install-integrity")
+        return
+    for entry in result.get("checks", []) or []:
+        name = entry.get("name", "install-integrity")
+        status = entry.get("status", "")
+        detail = entry.get("detail", "")
+        if status == "pass":
+            emit_success(f"{name}: pass")
+            continue
+        if status == "skip":
+            emit_info(f"{name}: skip -- {detail}")
+            continue
+        if status == "error":
+            emit_error(f"{name}: error -- {detail}")
+        else:
+            emit_error(f"{name}: fail -- {detail}")
+        add_finding(
+            "error",
+            detail or f"{name} {status}",
+            check=f"install-integrity:{name}",
+            install_check=name,
+            status=status,
+            data=entry.get("data", {}),
+        )
+
+
+def _has_v3_managed_marker(project_root: Path) -> bool:
+    """True iff AGENTS.md carries a deft:managed-section v3 marker (#1308)."""
+    agents_md = project_root / "AGENTS.md"
+    if not agents_md.is_file():
+        return False
+    try:
+        text = agents_md.read_text(encoding="utf-8", errors="replace")
+    except OSError:
+        return False
+    return re.search(
+        r"<!--\s*deft:managed-section\s+v3(?:\s+[^>]*?)?\s*-->",
+        text,
+    ) is not None
+
+
+def _run_agents_md_freshness_check(
+    project_root: Path,
+    *,
+    emit_success,
+    emit_warn,
+    emit_info,
+    add_finding,
+) -> None:
+    """Probe AGENTS.md managed-section freshness via cmd_agents_refresh internals (#1308)."""
+    check_name = "agents-md-managed-section-fresh"
+    if _running_inside_deft_repo(project_root) or not _has_v3_managed_marker(
+        project_root
+    ):
+        skip_reason = "no managed-section markers (likely maintainer repo)"
+        emit_info(f"{check_name}: skip -- {skip_reason}")
+        add_finding(
+            "skip",
+            skip_reason,
+            check=check_name,
+            status="skip",
+        )
+        return
+    try:
+        plan = _agents_refresh_plan(project_root)
+    except Exception as exc:  # noqa: BLE001 -- never break doctor
+        message = f"{check_name}: probe failed -- {type(exc).__name__}: {exc}"
+        emit_warn(message)
+        add_finding("warning", message, check=check_name)
+        return
+    state = plan.get("state", "")
+    if state == "current":
+        emit_success(f"{check_name}: current")
+        return
+    if state in ("stale", "missing", "absent"):
+        message = (
+            f"AGENTS.md managed section is {state} -- "
+            "run `deft agents:refresh` to bring it to the current template."
+        )
+        emit_warn(message)
+        add_finding(
+            "warning",
+            message,
+            check=check_name,
+            status=state,
+            suggestion="deft agents:refresh",
+        )
+        return
+    message = (
+        f"AGENTS.md freshness check could not run (state={state!r}). "
+        "Inspect the framework template or AGENTS.md file permissions."
+    )
+    emit_warn(message)
+    add_finding("warning", message, check=check_name, status=state)
+
+
+def _run_payload_staleness_check(
+    project_root: Path,
+    *,
+    emit_warn,
+    emit_info,
+    add_finding,
+) -> None:
+    """#1339 (Epic-5): Detect when the installed framework payload is behind its
+    manifest-recorded ref/sha. Reads the canonical <deftDir>/VERSION manifest
+    (single source of truth per #1062), resolves the corresponding remote SHA
+    via git ls-remote, and surfaces the canonical headless upgrade command
+    `deft-install --yes --upgrade --repo-root . --json` (#1409) when the shas
+    diverge. Skips gracefully inside the deft repo or when git / network /
+    manifest unavailable (non-fatal, best-effort).
+    """
+    check_name = "payload-staleness"
+    # Self-contained "inside deft repo" probe (avoids dependency on private
+    # _running_inside_deft_repo helper that may be scoped inside cmd_doctor).
+    try:
+        agents = project_root / "AGENTS.md"
+        is_deft = agents.exists() and (
+            "Deft — Development Framework (deft repo)" in
+            agents.read_text(encoding="utf-8", errors="ignore")
+        )
+        if is_deft:
+            emit_info(f"{check_name}: skip -- running inside deft framework repo")
+            add_finding(
+                "skip", "inside framework repo (no install manifest)",
+                check=check_name, status="skip",
+            )
+            return
+    except Exception:
+        pass
+
+    # Locate a plausible manifest. Prefer the one next to the scripts/doctor.py
+    # we are running from (when invoked via the installed layout); fall back to
+    # common canonical/legacy locations under project_root.
+    manifest_path = None
+    try:
+        # When doctor.py lives at <deftDir>/scripts/doctor.py the manifest is at <deftDir>/VERSION
+        candidate = get_script_dir().parent / "VERSION"
+        if candidate.exists():
+            manifest_path = candidate
+    except Exception:
+        pass
+    if manifest_path is None:
+        # #1427: probe canonical-first via the shared helper so a
+        # webinstaller-vendored ``.deft/VERSION`` manifest is found too
+        # (the prior list probed only ``.deft/core/VERSION`` and legacy
+        # ``deft/VERSION``).
+        manifest_path = _locate_manifest(project_root, None)
+    if manifest_path is None:
+        # Legacy bare marker -- not a full manifest, but the last-resort
+        # provenance source for a pre-v0.28 install. Kept out of
+        # ``_locate_manifest`` because that helper returns VERSION-manifest
+        # paths only.
+        legacy_marker = project_root / ".deft-version"
+        if legacy_marker.exists():
+            manifest_path = legacy_marker
+    if manifest_path is None or not manifest_path.exists():
+        emit_info(f"{check_name}: skip -- no install manifest found (pre-v0.28 or legacy state)")
+        add_finding("skip", "no manifest", check=check_name, status="skip")
+        return
+
+    try:
+        text = manifest_path.read_text(encoding="utf-8", errors="replace")
+        manifest = _parse_install_manifest(text)
+    except Exception as exc:  # noqa: BLE001
+        emit_info(f"{check_name}: skip -- could not read manifest: {exc}")
+        add_finding("skip", f"manifest unreadable: {exc}", check=check_name, status="skip")
+        return
+
+    installed_sha = manifest.get("sha", "").strip()
+    # Greptile P1 on #1384: do NOT fall back to "HEAD" when ref/tag are
+    # absent. `git ls-remote origin HEAD` returns the current remote
+    # default-branch tip, which almost certainly differs from the locally
+    # installed sha for development builds without a ref/tag pinned, and
+    # the check would then emit a permanent false-stale warning. Skip
+    # cleanly when the manifest does not declare a ref/tag.
+    ref = (manifest.get("ref") or manifest.get("tag") or "").strip()
+    if not installed_sha:
+        emit_info(f"{check_name}: skip -- manifest has no sha (incomplete provenance)")
+        add_finding("skip", "no sha in manifest", check=check_name, status="skip")
+        return
+    if not ref:
+        emit_info(
+            f"{check_name}: skip -- manifest has no ref or tag (cannot resolve remote sha)"
+        )
+        add_finding("skip", "no ref/tag in manifest", check=check_name, status="skip")
+        return
+
+    # Resolve current remote SHA for the ref (best effort, may be tag or branch).
+    # Use ls-remote to avoid needing a local fetch or modifying state.
+    try:
+        # Determine the deft dir from manifest location (parent of VERSION)
+        deft_dir = manifest_path.parent
+        # ls-remote origin <ref> (works for branches and tags)
+        proc = subprocess.run(
+            ["git", "-C", str(deft_dir), "ls-remote", "origin", ref],
+            capture_output=True,
+            text=True,
+            timeout=15,
+        )
+        if proc.returncode != 0:
+            emit_info(f"{check_name}: skip -- git ls-remote failed (no network or no origin)")
+            add_finding("skip", "ls-remote unavailable", check=check_name, status="skip")
+            return
+        # Output is "<sha>\t<refname>"
+        # For annotated tags, ls-remote returns TWO lines:
+        #   <tag-object-sha>	refs/tags/<tag>
+        #   <commit-sha>	refs/tags/<tag>^{}
+        # Prefer the peeled ^{} commit SHA when present (the one that matches
+        # what the installer recorded in the manifest). Fall back to first line.
+        # See Greptile P1 on #1384 (annotated-tag false-positive staleness).
+        remote_sha = ""
+        peeled_sha = ""
+        for line in proc.stdout.splitlines():
+            parts = line.strip().split()
+            if len(parts) >= 2:
+                refname = parts[1]
+                if refname.endswith("^{}"):
+                    peeled_sha = parts[0]
+                elif not remote_sha:
+                    remote_sha = parts[0]
+        if peeled_sha:
+            remote_sha = peeled_sha
+        elif not remote_sha:
+            # last-resort: first token of first line
+            first_line = next((ln for ln in proc.stdout.splitlines() if ln.strip()), "")
+            parts = first_line.strip().split()
+            if parts:
+                remote_sha = parts[0]
+        if not remote_sha:
+            emit_info(f"{check_name}: skip -- ls-remote produced no sha")
+            add_finding("skip", "no remote sha", check=check_name, status="skip")
+            return
+    except Exception as exc:  # noqa: BLE001 -- network/git optional
+        emit_info(f"{check_name}: skip -- could not probe remote ({type(exc).__name__})")
+        add_finding("skip", f"remote probe failed: {exc}", check=check_name, status="skip")
+        return
+
+    if installed_sha == remote_sha:
+        # Current
+        emit_info(f"{check_name}: current (sha matches remote)")
+        return
+
+    # Stale! Emit the EXACT canonical headless upgrade command (#1409) so a
+    # normal consumer can copy-paste one line and end up with a fresh payload
+    # plus updated metadata -- not just the metadata-only `task upgrade` ack.
+    recommended_command = "deft-install --yes --upgrade --repo-root . --json"
+    msg = (
+        f"Framework payload is stale (installed sha {installed_sha[:8]}... "
+        f"behind remote {remote_sha[:8]}... for ref '{ref}'). "
+        f"Recommendation: run the canonical headless upgrader "
+        f"`{recommended_command}` from your project root to pull the latest "
+        f"payload (drop `--json` for human-readable output). On an installer "
+        f"binary predating the headless flags, download the latest deft-install "
+        f"from GitHub Releases first."
+    )
+    emit_warn(msg)
+    add_finding(
+        "warning",
+        msg,
+        check=check_name,
+        status="stale",
+        installed_sha=installed_sha,
+        remote_sha=remote_sha,
+        ref=ref,
+        suggestion=recommended_command,
+    )
+
+
+def _parse_install_manifest(text: str) -> dict:
+    """Tiny tolerant parser for the single-key: 'value' YAML shape used by the
+    install manifest (#1062). Mirrors the shape expected by run::_parse_install_manifest
+    but kept local here so scripts/doctor.py stays self-contained for the handoff.
+    """
+    data: dict[str, str] = {}
+    for line in text.splitlines():
+        line = line.strip()
+        if not line or ":" not in line:
+            continue
+        k, v = [x.strip() for x in line.split(":", 1)]
+        v = v.strip().strip("'\"")
+        data[k] = v
+    return data
+
+def cmd_doctor(args: list[str]):
+    """Thin shim (#1335) -- core doctor logic now owned by scripts/doctor.py.
+
+    This entry point (and therefore `task doctor`) is a thin delegation layer.
+    The implementation, modes (--session, reporting, --json, --fix, --quiet,
+    --full, --project-root), throttle, and checks live in scripts/doctor.py
+    (the single owner per Epic-1). During the carve transition the bodies
+    remain in this file for stability; scripts/doctor.py is the documented
+    import surface and will receive the logic in follow-on increments.
+
+    See scripts/doctor.py header + vbrief/active/*1335*.vbrief.json .
+    """
+
+    # Real implementation body follows (transition). After full extraction
+    # this will be a 4-line import + call to scripts.doctor.cmd_doctor.
+    # The body below is the current home (being migrated).
+    """Canonical doctor surface for task-surface health (#1272, #1303 review).
+
+    Diagnoses (and optionally repairs, with explicit consent):
+
+    1. Required tools on PATH (uv, git) and optional tools (task,
+       python3, go, node) -- the existing #792 dependency probe.
+    2. Expected framework directory layout (#792).
+    3. Consumer root Taskfile.yml include health (#1272). When run
+       inside a consumer project, doctor detects:
+         * missing root Taskfile.yml          -> diagnose + print snippet;
+                                                 interactive ``--fix``
+                                                 may CREATE the file after
+                                                 explicit operator consent.
+         * root Taskfile.yml exists, no       -> diagnose + print snippet;
+           deft include                          NEVER mutates the existing
+                                                 user-owned Taskfile.
+         * include present                    -> OK.
+
+    Flags (parsed via :func:`_parse_doctor_flags`):
+        ``--session``       diagnose-only, session-safe; no prompt, no
+                            mutation.
+        ``--fix``           interactive repair offered when actionable
+                            (Taskfile creation only); ignored under
+                            ``--session``.
+        ``--json``          emit a single JSON object on stdout and
+                            suppress the human-readable prose; exit
+                            code unchanged.
+        ``--quiet``         suppress per-check success lines; errors
+                            and warnings still surface.
+        ``--project-root``  override the project root used for the
+                            Taskfile diagnostic. Defaults to
+                            :func:`Path.cwd`.
+
+    Returns:
+        ``0`` on a clean check OR a warning-only check (warnings are
+        informational and never exit-failing).
+        ``1`` on a hard error (missing required tool OR Taskfile drift
+        detected).
+        ``2`` on argument-parse failure (an unknown flag was passed --
+        the doctor refuses to run the diagnostics so the typo cannot
+        masquerade as a clean check).
+
+    Non-zero return is informational -- doctor's role is to surface
+    the failure, not to block the upgrade gate.
+
+    Throttle-state count semantics (#1316): when a full run completes,
+    ``_persist_doctor_state`` writes ``last_finding_count`` as the count
+    of findings that *mattered* -- ``severity == "skip"`` findings are
+    EXCLUDED. A skip (e.g. the AGENTS.md freshness check reporting "no
+    managed-section markers (likely maintainer repo)") is neither an
+    error nor a warning, so counting it would make the next throttle-skip
+    status line over-report warnings by one (the line derives warnings as
+    ``last_finding_count - last_error_count``). The in-run ``--json``
+    ``summary`` block already counts only ``error`` / ``warning``
+    findings, so this keeps the persisted tally consistent with it.
+    """
+    flags = _parse_doctor_flags(args)
+
+    # Reject unknown flags loudly. The previous shape silently swallowed
+    # typos (`--repare` instead of `--repair`), so an operator who
+    # mistyped never realised they had not opted into repair -- the
+    # diagnostic still ran in default mode and the prose suggested the
+    # repair was offered. Surface the unknown tokens, list the allowed
+    # set, and exit 2 so CI wrappers can distinguish a malformed
+    # invocation from a real diagnostic failure (#1303 review #3).
+    if flags.get("unknown"):
+        error(
+            "Unknown flag(s): "
+            + ", ".join(flags["unknown"])
+        )
+        info(
+            "Allowed: " + ", ".join(_DOCTOR_ALLOWED_FLAGS)
+        )
+        return 2
+
+    session_mode = flags["session"]
+    fix_mode = flags["fix"] and not session_mode
+    json_mode = flags["json"]
+    quiet_mode = flags["quiet"]
+    full_mode = flags["full"]
+
+    # ``--project-root`` lets operators invoke doctor against an
+    # arbitrary directory rather than ``Path.cwd``. Defaults to the
+    # current working directory so existing callers (``task doctor``,
+    # the ``run doctor`` CLI without overrides) are unaffected. The
+    # path is normalised through :func:`resolve_path` so ``~`` and
+    # relative paths work (#1303 review #5).
+    project_root_arg = flags.get("project_root")
+    project_root = (
+        resolve_path(project_root_arg) if project_root_arg else Path.cwd()
+    )
+
+    # #1308: throttle gate. Default = full check, but a recent run
+    # within the 24h-clean / 4h-dirty window short-circuits to a
+    # one-line status surface. ``--full`` bypasses the throttle. The
+    # ritual halts on a dirty-within-window state (exit 1) so a
+    # persistent-dirty install is never silently ignored.
+    if not full_mode:
+        decision = _evaluate_doctor_throttle(project_root)
+        if decision is not None and decision.skip:
+            return _emit_doctor_throttle_skip(decision, json_mode=json_mode)
+
+    # Findings are the single source of truth for the summary, the
+    # JSON payload, and the exit code (#1303 review #1 / #4). Replaces
+    # the prior ``errors += 1`` / ``errors -= 1`` accounting pair that
+    # was brittle when the interactive ``--fix`` path repaired a
+    # missing-file finding -- the decrement coupled two unrelated
+    # branches and made the summary easy to mis-read.
+    findings: list[dict] = []
+
+    def _add_finding(severity: str, message: str, **extras: object) -> None:
+        entry: dict = {"severity": severity, "message": message}
+        entry.update(extras)
+        findings.append(entry)
+
+    def _emit_info(msg: str) -> None:
+        if not json_mode:
+            info(msg)
+
+    def _emit_success(msg: str) -> None:
+        if json_mode or quiet_mode:
+            return
+        success(msg)
+
+    def _emit_warn(msg: str) -> None:
+        if not json_mode:
+            warn(msg)
+
+    def _emit_error(msg: str) -> None:
+        if not json_mode:
+            error(msg)
+
+    if not json_mode:
+        print_header(f"Deft CLI v{VERSION} - Doctor")
+        print()
+    _emit_info("Checking system dependencies...")
+    if not json_mode:
+        print()
+
+    # Check for required tools.  Errors and warnings are tracked
+    # separately (#792) so a missing required tool surfaces above
+    # optional-tool warnings in the summary and forces a non-zero
+    # return code.
+    def check_command(cmd: str, name: str, required: bool = False,
+                       install_url: str = ""):
+        if shutil.which(cmd):
+            _emit_success(f"{name} is installed")
+            return
+        url_hint = f" - install: {install_url}" if install_url else ""
+        if required:
+            message = f"{name} not found - required{url_hint}"
+            _emit_error(message)
+            _add_finding(
+                "error",
+                message,
+                check="dependency",
+                tool=cmd,
+                suggestion=install_url or None,
+            )
+            return
+        if cmd == "task":
+            message = f"{name} not found - install from https://taskfile.dev"
+        else:
+            message = f"{name} not found{url_hint}"
+        _emit_warn(message)
+        _add_finding(
+            "warning",
+            message,
+            check="dependency",
+            tool=cmd,
+            suggestion=install_url or None,
+        )
+
+    # uv is required: every deft task script invokes `uv run python ...`,
+    # so a green doctor on a machine without uv would mask an adoption
+    # blocker (#792).  Surface it before optional tools so the error is
+    # the first thing a fresh-machine user sees.
+    check_command(
+        "uv",
+        "uv (Astral Python runner)",
+        required=True,
+        install_url=UV_INSTALL_URL,
+    )
+    check_command("git", "git", required=True)
+    check_command("python3", "python3")
+    check_command("go", "go")
+    check_command("node", "node")
+
+    # #1308 / #1336: install-integrity checks now owned by scripts/doctor.py
+    # (the four checks formerly in framework_doctor.py). cmd_doctor folds
+    # them under ``install-integrity:<name>`` keys. Skipped in the deft
+    # maintainer repo (no install manifest in the source checkout).
+    if not json_mode:
+        print()
+    _emit_info("Checking install integrity...")
+    _run_install_integrity_checks(
+        project_root,
+        emit_success=_emit_success,
+        emit_warn=_emit_warn,
+        emit_error=_emit_error,
+        emit_info=_emit_info,
+        add_finding=_add_finding,
+    )
+
+    # #1308: AGENTS.md managed-section freshness. Reuses the
+    # cmd_agents_refresh --check byte-compare via _agents_refresh_plan;
+    # emits a skip finding with reason "no managed-section markers
+    # (likely maintainer repo)" when AGENTS.md carries no v3 markers.
+    # Stale templates surface as a warning (zero exit) -- the operator
+    # runs `deft agents:refresh` to bring them current.
+    if not json_mode:
+        print()
+    _emit_info("Checking AGENTS.md managed-section freshness...")
+    _run_agents_md_freshness_check(
+        project_root,
+        emit_success=_emit_success,
+        emit_warn=_emit_warn,
+        emit_info=_emit_info,
+        add_finding=_add_finding,
+    )
+
+    # #1339 (Epic-5): payload staleness from the install manifest. Runs after
+    # AGENTS freshness so the handoff from installer always surfaces a clear
+    # "re-run the installer" recommendation when the cloned payload sha lags
+    # the remote (deterministic, works in --session --json mode for agents).
+    if not json_mode:
+        print()
+    _emit_info("Checking payload staleness from install manifest...")
+    _run_payload_staleness_check(
+        project_root,
+        emit_warn=_emit_warn,
+        emit_info=_emit_info,
+        add_finding=_add_finding,
+    )
+
+    # Check directory structure.  Updated to the v0.20+ canonical
+    # layout (#792); pre-v0.20 entries (core, interfaces, tools, swarm,
+    # meta) were dropped because they no longer reflect the framework's
+    # current top-level layout and produced spurious 'Missing directory'
+    # warnings on every clean checkout.  Cross-referenced with
+    # `skills/deft-directive-setup/SKILL.md` § Environment Preflight
+    # (vbrief lifecycle requirement) and the project tree on master.
+    if not json_mode:
+        print()
+    _emit_info("Checking Deft structure...")
+
+    # Use .parent so the check anchors at the framework root (the directory
+    # containing scripts/doctor.py), restoring the pre-extraction semantics
+    # from run.get_script_dir() (which returned repo root in source layout).
+    # This eliminates the false-positive "Missing directory" warnings for all
+    # seven canonical framework subdirectories on every `run doctor` / `task doctor`
+    # invocation (Greptile framework-layout issue on 7a0606c).
+    framework_root = get_script_dir().parent
+    # Post-#1875 content/ move: shippable content dirs live under content/ in
+    # the SOURCE repo and are flattened back to the framework root in a CONSUMER
+    # deposit (C1). ``content_root`` resolves both contexts; engine/lifecycle
+    # dirs (tasks/, scripts/, vbrief/) always stay at the framework root.
+    scripts_dir = get_script_dir()
+    if str(scripts_dir) not in sys.path:
+        sys.path.insert(0, str(scripts_dir))
+    from _content_root import content_root  # noqa: PLC0415
+
+    content_base = content_root(framework_root)
+    expected_dirs = [
+        ("languages", content_base),
+        ("strategies", content_base),
+        ("skills", content_base),
+        ("templates", content_base),
+        ("tasks", framework_root),
+        ("scripts", framework_root),
+        ("vbrief", framework_root),
+    ]
+
+    for dir_name, base in expected_dirs:
+        dir_path = base / dir_name
+        if dir_path.is_dir():
+            _emit_success(f"Directory: {dir_name}/")
+        else:
+            message = f"Missing directory: {dir_name}/"
+            _emit_warn(message)
+            _add_finding(
+                "warning",
+                message,
+                check="framework-layout",
+                directory=dir_name,
+            )
+
+    # #1272 root Taskfile.yml include health. Skip when invoked from
+    # inside the deft framework repo itself -- the deft repo's own
+    # Taskfile.yml is the source of truth for its surface and does not
+    # need (and must not declare) a `deft:` include to itself.
+    if not json_mode:
+        print()
+    _emit_info("Checking optional root Taskfile.yml include...")
+    if _running_inside_deft_repo(project_root):
+        _emit_info(
+            "Skipping Taskfile include check -- running inside the deft "
+            "framework repo (the repo's own Taskfile.yml is the surface)."
+        )
+    else:
+        # ``include_missing`` is True until a successful interactive
+        # repair flips it off. Replaces the prior ``errors -= 1``
+        # gymnastic on the missing-file branch (#1303 review #1).
+        include_status = _classify_taskfile_include(project_root)
+        if include_status == "ok":
+            _emit_success("Root Taskfile.yml includes the deft framework")
+        elif include_status == "missing-file":
+            include_missing = True
+            target = project_root / "Taskfile.yml"
+            message = (
+                "Root Taskfile.yml missing. This is OK for package-manager "
+                "installs that use the `deft X` surface directly. To also "
+                f"enable the optional `task deft:X` surface, paste this into {target}:"
+            )
+            _emit_info(message)
+            if not json_mode:
+                print()
+                print(_TASKFILE_INCLUDE_SNIPPET)
+            # Interactive repair path. All gates MUST hold before any
+            # write: (1) --fix was requested AND we are not under
+            # --session (both folded into ``fix_mode`` -- see
+            # ``fix_mode = flags["fix"] and not session_mode`` above);
+            # (2) stdin is a TTY (so we can prompt); (3) we are not
+            # emitting JSON (JSON mode is diagnose-only). Even then,
+            # the operator must explicitly approve at the prompt.
+            # #1303 pass-3 review (Greptile run:4664-4669 -- redundant
+            # session_mode guard): the prior shape repeated
+            # ``and not session_mode`` here, but fix_mode already
+            # incorporates that condition; the duplicate gate could
+            # never change the outcome and invited confusion.
+            if (
+                fix_mode
+                and not json_mode
+                and sys.stdin.isatty()
+            ):
+                if read_yn(
+                    f"Create {target} with the canonical include now?",
+                    default=False,
+                ):
+                    try:
+                        # ``newline="\n"`` enforces LF line endings on
+                        # every host -- ``write_text`` otherwise honours
+                        # the platform default, which produces CRLF on
+                        # Windows and breaks the byte-equality contract
+                        # tests rely on (#1303 review #6).
+                        target.write_text(
+                            _TASKFILE_INCLUDE_SNIPPET,
+                            encoding="utf-8",
+                            newline="\n",
+                        )
+                        _emit_success(f"Wrote {target}")
+                        # The drift was just repaired -- flip the
+                        # boolean so the summary reflects the
+                        # post-repair state (replaces the prior
+                        # ``errors -= 1`` decrement pair).
+                        include_missing = False
+                    except OSError as exc:
+                        _emit_error(f"Failed to write {target}: {exc}")
+                else:
+                    _emit_info(
+                        "Skipped Taskfile.yml creation -- paste the "
+                        "snippet above when you are ready."
+                    )
+            if include_missing:
+                _add_finding(
+                    "warning",
+                    "Root Taskfile.yml missing; optional Taskfile include unavailable",
+                    check="taskfile-include",
+                    file=str(target),
+                    suggestion=_TASKFILE_INCLUDE_SNIPPET,
+                )
+        elif include_status == "missing-include":
+            message = (
+                "Root Taskfile.yml exists but does not include the deft "
+                "framework. The `deft X` surface still works; add this to "
+                "the Taskfile `includes:` block only if you want the optional "
+                "`task deft:X` surface (doctor NEVER mutates an existing "
+                "user-owned Taskfile):"
+            )
+            _emit_warn(message)
+            if not json_mode:
+                print()
+                print(_format_missing_include_snippet())
+            taskfile_path = _resolve_consumer_taskfile(project_root)
+            _add_finding(
+                "warning",
+                "Root Taskfile.yml does not include the deft framework",
+                check="taskfile-include",
+                file=str(taskfile_path) if taskfile_path else None,
+                suggestion=_format_missing_include_snippet(),
+            )
+        elif include_status == "unreadable":
+            # Resolve the actual Taskfile path so a consumer who chose the
+            # ``.yaml`` spelling sees the right file name in the error
+            # message and in the JSON `file` field (#1303 review,
+            # Greptile #2). Falls back to ``Taskfile.yml`` only if the
+            # resolver returns None -- which shouldn't happen here
+            # because the `unreadable` branch is only reached when a
+            # candidate file was found, but the fallback keeps the
+            # diagnostic informative under any future code drift.
+            taskfile_path = (
+                _resolve_consumer_taskfile(project_root)
+                or (project_root / "Taskfile.yml")
+            )
+            message = (
+                f"Root Taskfile.yml at {taskfile_path} "
+                "exists but could not be read -- check file permissions."
+            )
+            _emit_warn(message)
+            _add_finding(
+                "warning",
+                message,
+                check="taskfile-include",
+                file=str(taskfile_path),
+            )
+
+    error_count = sum(1 for f in findings if f["severity"] == "error")
+    warning_count = sum(1 for f in findings if f["severity"] == "warning")
+    exit_code = 1 if error_count else 0
+
+    # #1308: persist doctor-state.json so the next invocation can
+    # consult the throttle gate. Best-effort -- a write failure is
+    # silently swallowed by the state module so the doctor itself
+    # never breaks because of a state-file bug.
+    _persist_doctor_state(
+        project_root,
+        exit_code=exit_code,
+        findings=findings,
+    )
+
+    if json_mode:
+        payload = {
+            "status": "completed",
+            "ok": exit_code == 0,
+            "findings": findings,
+            "summary": {
+                "errors": error_count,
+                "warnings": warning_count,
+            },
+            "project_root": str(project_root),
+        }
+        print(json.dumps(payload, sort_keys=True))
+        return exit_code
+
+    print()
+    if error_count == 0 and warning_count == 0:
+        success("System check passed!")
+        return 0
+    if error_count:
+        # Errors first so missing-uv (or git) is not buried under
+        # optional-tool warnings.
+        error(
+            f"System check failed with {error_count} error(s)"
+            + (f" and {warning_count} warning(s)" if warning_count else "")
+            + "."
+        )
+        return 1
+    warn(f"System check completed with {warning_count} warning(s).")
+    return 0
+
+# (end of extracted region; now maintained in this file)
+# End of block extracted to scripts/doctor.py (see START marker above).
+# The thin shim below this point in the final state will replace the
+# extracted region.
+# ===
+# --- End of extracted doctor logic (Epic-1 #1335) ---
+
+# --- Ported CLI surface (main, _build_parser, _format_text_report) from
+# retired framework_doctor.py to satisfy test expectations for fd.main(),
+# UTF-8 reconfigure (#814), --json/--quiet/--project-root, and the 3-state
+# exit codes. The primary user surface remains cmd_doctor (new extraction).
+# ---
+
+
+def _build_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(
+        prog="framework_doctor.py",
+        description=(
+            "Local install-integrity probe (#1046 PR-B AC-3). Four checks: "
+            "QUICK-START resolves, skill paths resolve, manifest agreement, "
+            "install-path consistency. Three-state exit: 0 clean / 1 drift "
+            "detected / 2 config error."
+        ),
+    )
+    parser.add_argument(
+        "--project-root",
+        default=".",
+        help="Project root path (default: current working directory).",
+    )
+    parser.add_argument(
+        "--json",
+        action="store_true",
+        help="Emit a single JSON object on stdout instead of human-readable text.",
+    )
+    parser.add_argument(
+        "--quiet",
+        action="store_true",
+        help="Suppress the success summary; failure detail still prints.",
+    )
+    return parser
+
+
+def _format_text_report(result: DoctorResult) -> str:
+    """Render a human-readable summary of the doctor result."""
+    lines: list[str] = []
+    if result.exit_code == EXIT_CLEAN:
+        lines.append(
+            "\u2713 deft framework:doctor -- all checks pass "
+            f"(install_root={result.install_root!r})."
+        )
+    elif result.exit_code == EXIT_DRIFT:
+        lines.append(
+            "\u26a0 deft framework:doctor -- drift detected "
+            f"(install_root={result.install_root!r})."
+        )
+    else:
+        lines.append("\u2717 deft framework:doctor -- config error.")
+    for c in result.checks:
+        if c.status == "pass":
+            sym = "\u2713"
+        elif c.status == "skip":
+            sym = "\u2022"
+        elif c.status == "fail":
+            sym = "\u2717"
+        else:  # error
+            sym = "!"
+        lines.append(f"  {sym} {c.name}: {c.detail}")
+    for err in result.errors:
+        lines.append(f"  ! {err}")
+    return "\n".join(lines)
+
+
+def main(argv: list[str] | None = None) -> int:
+    # #814: Force UTF-8 stdout/stderr at script entry. Windows Python
+    # defaults stdout/stderr to cp1252 when invoked under git hooks,
+    # which has no glyph for the U+2713 success marker. Without this
+    # reconfigure the doctor crashes with UnicodeEncodeError on the
+    # success summary. Guarded by hasattr because reconfigure only
+    # exists on TextIOWrapper streams. errors='replace' is a
+    # belt-and-suspenders fallback for the rare environment that still
+    # cannot render UTF-8.
+    if hasattr(sys.stdout, "reconfigure"):
+        sys.stdout.reconfigure(encoding="utf-8", errors="replace")
+    if hasattr(sys.stderr, "reconfigure"):
+        sys.stderr.reconfigure(encoding="utf-8", errors="replace")
+
+    parser = _build_parser()
+    args = parser.parse_args(argv)
+    project_root = Path(args.project_root).resolve()
+    result = _run_checks_impl(project_root)
+    if args.json:
+        print(json.dumps(result.to_dict(), sort_keys=True))
+    else:
+        if not (args.quiet and result.exit_code == EXIT_CLEAN):
+            print(_format_text_report(result))
+    return result.exit_code
+
+
+if __name__ == "__main__":
+    # python -m scripts.doctor [args] or direct python scripts/doctor.py [args]
+    args = sys.argv[1:]
+    if args and args[0].lower() == 'doctor':
+        args = args[1:]
+    sys.exit(cmd_doctor(args))