peaks-loop 4.0.0-beta.2 → 4.0.0-beta.21

package/dist/src/services/doctor/doctor-service.js

@@ -1,929 +0,0 @@
-import { join } from 'node:path';
-import { homedir } from 'node:os';
-import { existsSync, lstatSync, readFileSync, readdirSync } from 'node:fs';
-import { createRequire } from 'node:module';
-import { dirname, resolve as resolvePath } from 'node:path';
-import { readText } from '../../shared/fs.js';
-import { requiredSchemaFiles, requiredSkillNames, schemasDir } from '../../shared/paths.js';
-import { getErrorMessage } from '../../shared/result.js';
-import { loadSkillRegistry } from '../skills/skill-registry.js';
-import { getSkillPresence } from '../skills/skill-presence-service.js';
-import { planStatusLineInstall } from '../skills/statusline-settings-service.js';
-import { findProjectRoot } from '../config/config-safety.js';
-import { isValidSessionId } from '../workspace/sid-naming-guard.js';
-import { CLI_VERSION } from '../../shared/version.js';
-const CODEGRAPH_EXPECTED_VERSION = '0.7.10';
-const SKILL_PRESENCE_FRESHNESS_THRESHOLD_MS = 24 * 60 * 60 * 1000;
-function defaultCodegraphProbe() {
-    const require = createRequire(import.meta.url);
-    const packagePath = require.resolve('@colbymchenry/codegraph/package.json');
-    const pkg = require(packagePath);
-    const binaryPath = resolvePath(dirname(packagePath), 'dist', 'bin', 'codegraph.js');
-    return {
-        packagePath,
-        version: pkg.version ?? 'unknown',
-        binaryPath,
-        binaryExists: existsSync(binaryPath)
-    };
-}
-function defaultStatusLineInstalledProbe() {
-    const projectRoot = findProjectRoot(process.cwd());
-    // Check both scopes: a user may have installed the statusLine globally, which
-    // the project-only check would miss and falsely report as "not installed".
-    try {
-        if (projectRoot !== null && planStatusLineInstall('project', projectRoot).alreadyInstalled) {
-            return true;
-        }
-    }
-    catch { // TODO(g2): legacy silent catch — grace: 1 minor release (v2.14.0)
-        /* fall through to global */
-    }
-    try {
-        return planStatusLineInstall('global').alreadyInstalled;
-    }
-    catch {
-        return false;
-    }
-}
-function defaultWorkspaceInitializedProbe() {
-    const projectRoot = findProjectRoot(process.cwd());
-    if (projectRoot === null)
-        return false;
-    // Workspace is "initialized" when EITHER the canonical runtime-layer session
-    // binding (`.peaks/_runtime/session.json`, the home since slice
-    // 2026-06-05-peaks-runtime-layer) OR the legacy top-level binding
-    // (`.peaks/.session.json`, kept as read-only back-compat for one minor
-    // release) is present. The legacy check is what catches projects that ran
-    // `peaks workspace init` before the runtime-layer migration and have not yet
-    // been reconciled; both paths must continue to satisfy the doctor until the
-    // legacy location is removed.
-    return isWorkspaceInitializedAt(projectRoot);
-}
-/**
- * Pure helper extracted from `defaultWorkspaceInitializedProbe` so tests can
- * drive the filesystem check without monkey-patching `process.cwd()` or
- * `findProjectRoot`. Returns `true` when EITHER the canonical
- * `.peaks/_runtime/session.json` OR the legacy `.peaks/.session.json` exists.
- */
-export function isWorkspaceInitializedAt(projectRoot) {
-    return (existsSync(join(projectRoot, '.peaks', '_runtime', 'session.json')) ||
-        existsSync(join(projectRoot, '.peaks', '.session.json')));
-}
-/**
- * Pure helper that compares the published dist `CLI_VERSION` against the
- * source-of-truth `package.json#version`. Default readers fail-soft to `null`
- * on missing/unreadable/malformed input. Exported so tests can drive the
- * filesystem reads without monkey-patching `process.cwd()`.
- */
-export function compareDistVersion(opts) {
-    const distReader = opts.distVersionReader ?? defaultDistVersionReader;
-    const sourceReader = opts.sourceVersionReader ?? defaultSourceVersionReader;
-    const dist = safeRead(() => distReader(opts.projectRoot));
-    const source = safeRead(() => sourceReader(opts.projectRoot)) ?? 'unknown';
-    const distReadable = dist !== null;
-    return {
-        dist,
-        source,
-        match: distReadable && dist === source,
-        distReadable
-    };
-}
-function safeRead(reader) {
-    try {
-        return reader();
-    }
-    catch { // TODO(g2): legacy silent catch — grace: 1 minor release (v2.14.0)
-        return null;
-    }
-}
-function defaultDistVersionReader(projectRoot) {
-    // Synchronous read is fine: the dist version.js is small and on the
-    // local build pipeline's hot path. readFileSync + regex is cheaper
-    // than pulling in fs/promises for a single short file.
-    const distPath = join(projectRoot, 'dist', 'src', 'shared', 'version.js');
-    if (!existsSync(distPath)) {
-        return null;
-    }
-    const body = readFileSync(distPath, 'utf8');
-    const match = /export\s+const\s+CLI_VERSION\s*=\s*["']([^"']+)["']/.exec(body);
-    return match?.[1] ?? null;
-}
-function defaultSourceVersionReader(projectRoot) {
-    const pkgPath = join(projectRoot, 'package.json');
-    if (!existsSync(pkgPath)) {
-        return null;
-    }
-    const body = readFileSync(pkgPath, 'utf8');
-    const parsed = JSON.parse(body);
-    return typeof parsed.version === 'string' ? parsed.version : null;
-}
-function defaultDistVersionProbe() {
-    const projectRoot = findProjectRoot(process.cwd());
-    if (projectRoot === null) {
-        return { dist: null, source: 'unknown', match: false, distReadable: false };
-    }
-    return compareDistVersion({ projectRoot });
-}
-/**
- * Pure helper that inspects the on-disk workspace layout for
- * post-F3-canonical violations. The post-F3 canonical layout puts
- * session dirs under `.peaks/_runtime/<sid>/` and the runtime
- * binding at `.peaks/_runtime/session.json`; the legacy paths
- * (top-level `<YYYY-MM-DD-session-<hex>>/` dirs and the legacy
- * top-level `.peaks/.session.json` / `.peaks/.active-skill.json`
- * dotfiles) must be absent. This helper is exported so tests can
- * drive the filesystem walk without monkey-patching `process.cwd()`
- * or `findProjectRoot`.
- *
- * Both scanners fail-soft (return `[]` on read errors) so a flaky
- * filesystem read on a non-fatal probe path never escalates into a
- * doctor failure.
- */
-export function inspectWorkspaceLayout(opts) {
-    const topLevel = opts.topLevelScanner ?? defaultTopLevelSessionDirScanner;
-    const dotfiles = opts.dotfileScanner ?? defaultLegacyDotfileScanner;
-    const perChangeId = opts.perChangeIdScanner ?? defaultPerChangeIdDirScanner;
-    return {
-        topLevelSessionDirs: safeList(() => topLevel(opts.projectRoot)),
-        legacyDotfiles: safeList(() => dotfiles(opts.projectRoot)),
-        perChangeIdDirs: safeList(() => perChangeId(opts.projectRoot))
-    };
-}
-function safeList(reader) {
-    try {
-        const out = reader();
-        return Array.isArray(out) ? out : [];
-    }
-    catch {
-        return [];
-    }
-}
-const SESSION_DIR_PATTERN = /^\d{4}-\d{2}-\d{2}-session-[a-f0-9]+$/;
-function defaultTopLevelSessionDirScanner(projectRoot) {
-    const peaksRoot = join(projectRoot, '.peaks');
-    if (!existsSync(peaksRoot))
-        return [];
-    let names;
-    try {
-        names = readdirSync(peaksRoot);
-    }
-    catch {
-        return [];
-    }
-    const offenders = [];
-    for (const name of names) {
-        if (!SESSION_DIR_PATTERN.test(name))
-            continue;
-        const full = join(peaksRoot, name);
-        try {
-            const stat = existsSync(full) ? lstatSync(full) : null;
-            if (stat === null)
-                continue;
-            // Directories only — the regex should never match a dotfile or
-            // regular file, but be defensive against weird filesystem state
-            // (e.g. someone manually created a file whose name happens to
-            // match the session-id pattern).
-            if (stat.isDirectory()) {
-                offenders.push(join('.peaks', name) + '/');
-            }
-        }
-        catch {
-            continue;
-        }
-    }
-    return offenders;
-}
-const LEGACY_DOTFILES = ['.session.json', '.active-skill.json'];
-function defaultLegacyDotfileScanner(projectRoot) {
-    const peaksRoot = join(projectRoot, '.peaks');
-    if (!existsSync(peaksRoot))
-        return [];
-    const offenders = [];
-    for (const name of LEGACY_DOTFILES) {
-        if (existsSync(join(peaksRoot, name))) {
-            offenders.push(join('.peaks', name));
-        }
-    }
-    return offenders;
-}
-function defaultWorkspaceLayoutProbe() {
-    const projectRoot = findProjectRoot(process.cwd());
-    if (projectRoot === null) {
-        return { topLevelSessionDirs: [], legacyDotfiles: [], perChangeIdDirs: [] };
-    }
-    return inspectWorkspaceLayout({ projectRoot });
-}
-// Slice 007 — per-change-id top-level dir pattern. Matches the
-// F3-canonical (pre-canonicalization) layout the 5 already-shipped
-// slices left behind, e.g. `.peaks/001-2026-06-06-doctor-dist-version-check/`.
-// The pattern is intentionally narrow so it does NOT match the
-// post-F3 system dirs (`_runtime/`, `_dogfood/`, `retrospective/`,
-// `memory/`, `perf-baseline/`, `project-scan/`, `sops/`,
-// `0NN-session-...`, `YYYY-MM-DD-session-...`).
-const PER_CHANGE_ID_PATTERN = /^\d{3}-\d{4}-\d{2}-\d{2}-[a-z][a-z0-9-]*[a-z0-9]$/;
-function defaultPerChangeIdDirScanner(projectRoot) {
-    const peaksRoot = join(projectRoot, '.peaks');
-    if (!existsSync(peaksRoot))
-        return [];
-    let names;
-    try {
-        names = readdirSync(peaksRoot);
-    }
-    catch {
-        return [];
-    }
-    const offenders = [];
-    for (const name of names) {
-        if (!PER_CHANGE_ID_PATTERN.test(name))
-            continue;
-        const full = join(peaksRoot, name);
-        try {
-            const stat = existsSync(full) ? lstatSync(full) : null;
-            if (stat === null)
-                continue;
-            // Directories only — the regex should never match a dotfile
-            // or regular file, but be defensive against weird filesystem
-            // state (e.g. someone manually created a file whose name
-            // happens to match the per-change-id pattern).
-            if (stat.isDirectory()) {
-                offenders.push(join('.peaks', name) + '/');
-            }
-        }
-        catch {
-            continue;
-        }
-    }
-    return offenders;
-}
-const DESTRUCTIVE_APPLY_PATTERNS = [
-    /peaks\s+memory\s+sync[^\n]*--apply/,
-    /peaks\s+memory\s+extract[^\n]*--apply/,
-    /peaks\s+artifacts\s+sync[^\n]*--apply/,
-    /peaks\s+openspec\s+archive[^\n]*--apply/,
-    /peaks\s+standards\s+(?:init|update)[^\n]*--apply/
-];
-const AUTHORIZATION_KEYWORDS_PATTERN = /authoriz|explicit|--dry-run|approv|only after|only when/i;
-function extractRunbookSection(body) {
-    const match = /## Default runbook\n+([\s\S]*?)(?=\n## |$)/.exec(body);
-    return match === null ? null : (match[1] ?? null);
-}
-function findDestructiveApplyLines(section) {
-    const lines = section.split(/\r?\n/);
-    return lines.filter((line) => DESTRUCTIVE_APPLY_PATTERNS.some((pattern) => pattern.test(line)));
-}
-// ---------------------------------------------------------------------------
-// 2026-06-10 — gateguard-fact-force integration check (NOT a peaks-loop hook).
-//
-// The `gateguard-fact-force` hook is a third-party PreToolUse hook that
-// fires on Edit / Write / MultiEdit and demands a 4-fact questionnaire
-// before allowing the edit. It is unrelated to peaks-loop, but when the
-// LLM is in a peaks-qa flow and edits `.peaks/_runtime/<sid>/qa/requests/
-// *.md`, the questionnaire demands facts that do not apply (no
-// importers, no public API, no data files, user instruction already
-// in the conversation context). The check below detects the hook in
-// `~/.claude/settings.json` and the project `.claude/settings.json`,
-// and warns when no `.peaks/**` skip is configured.
-//
-// Probing is split out of the check so the check itself stays a pure
-// mapping over `GateguardProbeResult`. Tests inject the probe to keep
-// `~/.claude/settings.json` from leaking into test fixtures.
-// ---------------------------------------------------------------------------
-/** Hook command fragments that identify the gateguard-fact-force hook. */
-const GATEGUARD_HOOK_NEEDLES = ['gateguard', 'fact-force', 'fact_force'];
-/** Token the gateguard hook exposes for "skip these paths" — the check
- *  treats any match against `.peaks` (path or globs) as a routed
- *  configuration. We accept a few common spellings because the third-
- *  party hook's CLI surface is not part of peaks-loop's contract. */
-const GATEGUARD_PEAKS_SKIP_NEEDLES = [
-    '.peaks',
-    'peaks-skip',
-    'skip-glob',
-    '--skip',
-    'skip_paths'
-];
-function commandMentionsGateguard(command) {
-    if (typeof command !== 'string' || command.length === 0)
-        return false;
-    const lower = command.toLowerCase();
-    return GATEGUARD_HOOK_NEEDLES.some((needle) => lower.includes(needle));
-}
-function entrySkipsPeaks(entry) {
-    const matcher = typeof entry.matcher === 'string' ? entry.matcher : '';
-    const matcherMentionsPeaks = matcher.toLowerCase().includes('.peaks');
-    if (matcherMentionsPeaks)
-        return true;
-    for (const hook of entry.hooks) {
-        const command = typeof hook.command === 'string' ? hook.command : '';
-        const lower = command.toLowerCase();
-        if (GATEGUARD_PEAKS_SKIP_NEEDLES.some((needle) => lower.includes(needle))) {
-            return true;
-        }
-    }
-    return false;
-}
-function extractGateguardEntries(source, sourcePath, settings) {
-    if (settings === null || typeof settings !== 'object')
-        return [];
-    const hooks = settings.hooks;
-    if (hooks === null || typeof hooks !== 'object')
-        return [];
-    const preToolUse = hooks.PreToolUse;
-    if (!Array.isArray(preToolUse))
-        return [];
-    const out = [];
-    for (const rawEntry of preToolUse) {
-        if (rawEntry === null || typeof rawEntry !== 'object')
-            continue;
-        const entry = rawEntry;
-        if (!Array.isArray(entry.hooks))
-            continue;
-        const hooks = [];
-        for (const rawHook of entry.hooks) {
-            if (rawHook === null || typeof rawHook !== 'object')
-                continue;
-            const h = rawHook;
-            const hookEntry = {};
-            if (typeof h.type === 'string')
-                hookEntry.type = h.type;
-            if (typeof h.command === 'string')
-                hookEntry.command = h.command;
-            hooks.push(hookEntry);
-        }
-        if (!hooks.some((h) => commandMentionsGateguard(h.command)))
-            continue;
-        const outEntry = { hooks };
-        if (typeof entry.matcher === 'string')
-            outEntry.matcher = entry.matcher;
-        out.push({ source, sourcePath, entry: outEntry });
-    }
-    return out;
-}
-function readSettingsJson(path) {
-    if (!existsSync(path))
-        return null;
-    try {
-        return JSON.parse(readFileSync(path, 'utf8'));
-    }
-    catch { // TODO(g2): legacy silent catch — grace: 1 minor release (v2.14.0)
-        return null;
-    }
-}
-function defaultGateguardProbe() {
-    const projectRoot = findProjectRoot(process.cwd());
-    const globalPath = join(homedir(), '.claude', 'settings.json');
-    const projectPath = projectRoot === null ? null : join(projectRoot, '.claude', 'settings.json');
-    return {
-        globalSettingsPath: globalPath,
-        globalSettings: readSettingsJson(globalPath),
-        projectSettingsPath: projectPath,
-        projectSettings: projectPath === null ? null : readSettingsJson(projectPath)
-    };
-}
-export function collectGateguardEntries(probe) {
-    const fromGlobal = extractGateguardEntries('global', probe.globalSettingsPath ?? '~/.claude/settings.json', probe.globalSettings);
-    const fromProject = probe.projectSettingsPath === null
-        ? []
-        : extractGateguardEntries('project', probe.projectSettingsPath, probe.projectSettings);
-    return [...fromGlobal, ...fromProject];
-}
-export async function runDoctor(options = {}) {
-    const checks = [];
-    const registry = await loadSkillRegistry(options.skillsBaseDir);
-    const skills = registry.skills;
-    const skillNames = new Set(skills.map((skill) => skill.name));
-    for (const requiredSkill of requiredSkillNames) {
-        checks.push({
-            id: `skill:${requiredSkill}`,
-            ok: skillNames.has(requiredSkill),
-            message: skillNames.has(requiredSkill)
-                ? `Required skill ${requiredSkill} exists`
-                : `Missing required skill ${requiredSkill}`
-        });
-    }
-    for (const skill of skills) {
-        checks.push({
-            id: `skill-name:${skill.directory}`,
-            ok: skill.name === skill.directory,
-            message: skill.name === skill.directory
-                ? `Skill ${skill.name} matches its directory`
-                : `Skill ${skill.directory} declares mismatched name ${skill.name}`
-        });
-    }
-    for (const failure of registry.failures) {
-        checks.push({
-            id: `skill-parse:${failure.directory}`,
-            ok: false,
-            message: `Skill ${failure.directory} has invalid metadata: ${failure.message}`
-        });
-    }
-    const requiredSkillNameSet = new Set(requiredSkillNames);
-    for (const skill of skills) {
-        if (!requiredSkillNameSet.has(skill.name)) {
-            continue;
-        }
-        try {
-            const body = await readText(skill.skillPath);
-            const hasRunbook = /## Default runbook\s/.test(body);
-            checks.push({
-                id: `skill-runbook:${skill.name}`,
-                ok: hasRunbook,
-                message: hasRunbook
-                    ? `Skill ${skill.name} declares a Default runbook`
-                    : `Skill ${skill.name} is missing a ## Default runbook section`
-            });
-            const runbookSection = extractRunbookSection(body);
-            if (runbookSection !== null) {
-                const destructiveLines = findDestructiveApplyLines(runbookSection);
-                if (destructiveLines.length === 0) {
-                    checks.push({
-                        id: `skill-apply-note:${skill.name}`,
-                        ok: true,
-                        message: `Skill ${skill.name} runbook has no destructive --apply commands to gate`
-                    });
-                }
-                else {
-                    const hasAuthorizationNote = AUTHORIZATION_KEYWORDS_PATTERN.test(runbookSection);
-                    checks.push({
-                        id: `skill-apply-note:${skill.name}`,
-                        ok: hasAuthorizationNote,
-                        message: hasAuthorizationNote
-                            ? `Skill ${skill.name} gates ${destructiveLines.length} destructive --apply command(s) with an authorization note`
-                            : `Skill ${skill.name} has ${destructiveLines.length} destructive --apply command(s) without an authorization/dry-run note in the runbook section`
-                    });
-                }
-            }
-        }
-        catch (error) {
-            checks.push({
-                id: `skill-runbook:${skill.name}`,
-                ok: false,
-                message: `Skill ${skill.name} runbook check failed: ${getErrorMessage(error)}`
-            });
-        }
-    }
-    const schemaRoot = options.schemasBaseDir ?? schemasDir;
-    for (const schemaFile of requiredSchemaFiles) {
-        try {
-            JSON.parse(await readText(join(schemaRoot, schemaFile)));
-            checks.push({ id: `schema:${schemaFile}`, ok: true, message: `Schema ${schemaFile} is valid JSON` });
-        }
-        catch (error) {
-            checks.push({
-                id: `schema:${schemaFile}`,
-                ok: false,
-                message: `Schema ${schemaFile} is missing or invalid: ${getErrorMessage(error)}`
-            });
-        }
-    }
-    const userConfigPath = join(homedir(), '.peaks', 'config.json');
-    const hasUserConfig = existsSync(userConfigPath);
-    checks.push({
-        id: 'config:user',
-        ok: true,
-        message: hasUserConfig ? 'User config exists at ~/.peaks/config.json' : 'Optional user config not found at ~/.peaks/config.json'
-    });
-    const presenceProbe = options.skillPresenceProbe ?? getSkillPresence;
-    const freshnessThresholdMs = options.skillPresenceFreshnessThresholdMs ?? SKILL_PRESENCE_FRESHNESS_THRESHOLD_MS;
-    let presence = null;
-    try {
-        presence = presenceProbe();
-    }
-    catch {
-        presence = null;
-    }
-    if (presence === null) {
-        checks.push({
-            id: 'skill-presence:current',
-            ok: true,
-            message: 'No active Peaks skill presence (.peaks/.active-skill.json absent or invalid)'
-        });
-        checks.push({
-            id: 'skill-presence:freshness',
-            ok: true,
-            message: 'No active Peaks skill presence to age-check'
-        });
-    }
-    else {
-        const modePart = presence.mode !== undefined ? `, mode ${presence.mode}` : '';
-        const gatePart = presence.gate !== undefined ? `, gate ${presence.gate}` : '';
-        checks.push({
-            id: 'skill-presence:current',
-            ok: true,
-            message: `Active Peaks skill presence: ${presence.skill}${modePart}${gatePart} (set ${presence.setAt})`
-        });
-        const setAtMs = Date.parse(presence.setAt);
-        if (Number.isNaN(setAtMs)) {
-            checks.push({
-                id: 'skill-presence:freshness',
-                ok: false,
-                message: `Skill presence ${presence.skill} has invalid setAt: ${presence.setAt}`
-            });
-        }
-        else {
-            const ageMs = Date.now() - setAtMs;
-            if (ageMs > freshnessThresholdMs) {
-                const ageHours = Math.round(ageMs / (60 * 60 * 1000));
-                checks.push({
-                    id: 'skill-presence:freshness',
-                    ok: false,
-                    message: `Skill presence ${presence.skill} is stale (set ${presence.setAt}, ~${ageHours}h ago); run peaks skill presence:clear if the role has ended`
-                });
-            }
-            else {
-                checks.push({
-                    id: 'skill-presence:freshness',
-                    ok: true,
-                    message: `Skill presence ${presence.skill} is fresh (set ${presence.setAt})`
-                });
-            }
-        }
-    }
-    // Workspace guard: an active workflow presence (peaks-code) with no workspace
-    // session means the skill was anchored but `peaks workspace init` never ran —
-    // the #1 reported failure where .peaks/ artifacts are never created. This
-    // turns the SKILL.md "MUST create the workspace" prose into an executable check.
-    const workspaceProbe = options.workspaceInitializedProbe ?? defaultWorkspaceInitializedProbe;
-    let workspaceInitialized = false;
-    try {
-        workspaceInitialized = workspaceProbe();
-    }
-    catch {
-        workspaceInitialized = false;
-    }
-    if (presence !== null && !workspaceInitialized) {
-        checks.push({
-            id: 'skill-presence:workspace',
-            ok: false,
-            message: `Skill ${presence.skill} is active but no workspace session exists (.peaks/_runtime/session.json missing); run \`peaks workspace init --project <repo>\` — peaks-code Step 0 must anchor the workspace before any work`
-        });
-    }
-    else {
-        checks.push({
-            id: 'skill-presence:workspace',
-            ok: true,
-            message: presence === null
-                ? 'No active skill presence; workspace guard not applicable'
-                : `Workspace session present for active skill ${presence.skill}`
-        });
-    }
-    // Discoverability nudge: when a skill is actively orchestrating but the
-    // out-of-band statusLine isn't installed, the user has no terminal-level
-    // signal that Peaks is in control. Suggest installing it (non-failing).
-    const statusLineProbe = options.statusLineInstalledProbe ?? defaultStatusLineInstalledProbe;
-    let statusLineInstalled = false;
-    try {
-        statusLineInstalled = statusLineProbe();
-    }
-    catch {
-        statusLineInstalled = false;
-    }
-    if (presence !== null && !statusLineInstalled) {
-        checks.push({
-            id: 'statusline:install',
-            ok: true,
-            message: 'A Peaks skill is active but the statusLine is not installed; run `peaks statusline install` so the active skill shows in the terminal status bar'
-        });
-    }
-    else {
-        checks.push({
-            id: 'statusline:install',
-            ok: true,
-            message: statusLineInstalled
-                ? 'Peaks statusLine is installed'
-                : 'Peaks statusLine not installed (no active skill; install optional)'
-        });
-    }
-    // Runtime/platform diagnostic for the "statusLine shows nothing" reports.
-    // Surfaces (a) the running peaks version — a stale global install predating
-    // the statusLine feature is a common cause — and (b) on Windows, the fact that
-    // the bare `peaks statusline` command must resolve in the shell Claude Code
-    // spawns, which fails when the npm global bin dir is not on that shell's PATH.
-    const platform = options.platform ?? process.platform;
-    if (platform === 'win32') {
-        checks.push({
-            id: 'statusline:runtime',
-            ok: true,
-            message: `peaks ${CLI_VERSION} (win32): if the statusLine shows nothing in git bash, verify \`peaks\` resolves on PATH in the shell Claude Code uses (run \`peaks -v\` there), reinstall globally with \`npm i -g peaks-loop@latest\` if the version is older than ${CLI_VERSION}, then re-run \`peaks statusline install\` and reload Claude Code`
-        });
-    }
-    else {
-        checks.push({
-            id: 'statusline:runtime',
-            ok: true,
-            message: `peaks ${CLI_VERSION} (${platform}): statusLine command is \`peaks statusline\``
-        });
-    }
-    const probe = options.codegraphProbe ?? defaultCodegraphProbe;
-    try {
-        const result = probe();
-        const versionOk = result.version === CODEGRAPH_EXPECTED_VERSION;
-        if (!versionOk) {
-            checks.push({
-                id: 'capability:codegraph',
-                ok: false,
-                message: `@colbymchenry/codegraph version mismatch: expected ${CODEGRAPH_EXPECTED_VERSION}, resolved ${result.version} at ${result.packagePath}`
-            });
-        }
-        else if (!result.binaryExists) {
-            checks.push({
-                id: 'capability:codegraph',
-                ok: false,
-                message: `@colbymchenry/codegraph@${result.version} resolved at ${result.packagePath} but binary is missing at ${result.binaryPath}`
-            });
-        }
-        else {
-            checks.push({
-                id: 'capability:codegraph',
-                ok: true,
-                message: `@colbymchenry/codegraph@${result.version} resolves with binary at ${result.binaryPath}`
-            });
-        }
-    }
-    catch (error) {
-        checks.push({
-            id: 'capability:codegraph',
-            ok: false,
-            message: `@colbymchenry/codegraph not resolvable: ${getErrorMessage(error)}`
-        });
-    }
-    // Build-hygiene check: the published `dist/` ships a different CLI_VERSION
-    // than the source-of-truth `src/shared/version.ts` / `package.json#version`
-    // whenever the user runs `npx peaks` or `node bin/peaks.js` after `pnpm
-    // install` but before `pnpm build`. This is the silent-stale-CLI failure
-    // mode reported in `.peaks/2026-06-05-session-fecddb/txt/dogfood-2026-06-04-05.md`
-    // (F1). A missing dist/ is treated as informational (fresh clone, not broken)
-    // so the check does not flip the summary to red on a clean checkout.
-    const distProbe = options.distVersionProbe ?? defaultDistVersionProbe;
-    try {
-        const result = distProbe();
-        if (!result.distReadable) {
-            checks.push({
-                id: 'build:dist-version-matches-source',
-                ok: true,
-                message: `dist/ is not present; run \`pnpm build\` to populate dist/src/shared/version.js (source version ${result.source})`
-            });
-        }
-        else if (result.match) {
-            checks.push({
-                id: 'build:dist-version-matches-source',
-                ok: true,
-                message: `dist/src/shared/version.js ships CLI_VERSION ${result.dist} matching source ${result.source}`
-            });
-        }
-        else {
-            checks.push({
-                id: 'build:dist-version-matches-source',
-                ok: false,
-                message: `dist/src/shared/version.js ships CLI_VERSION ${result.dist} but source ${result.source} is in src/shared/version.ts; run \`pnpm build\` to refresh dist/`
-            });
-        }
-    }
-    catch (error) {
-        checks.push({
-            id: 'build:dist-version-matches-source',
-            ok: false,
-            message: `dist version check failed: ${getErrorMessage(error)}`
-        });
-    }
-    // Build-hygiene check: a non-canonical post-F3 workspace layout is
-    // the silent-regression failure mode that slice 003 explicitly chose
-    // to allow (the current session binding was kept at top-level as a
-    // safety measure). This check surfaces any leftover top-level
-    // session dirs, the legacy runtime dotfiles (`.peaks/.session.json`,
-    // `.peaks/.active-skill.json`), OR per-change-id top-level dirs
-    // (`.peaks/NNN-YYYY-MM-DD-<slug>/`) so a future contributor who
-    // manually recreates one of them is warned. The check is read-only;
-    // the fix path is `peaks workspace migrate --to-runtime --project
-    // <repo> --apply`.
-    //
-    // Slice 007 broadened this check to flag per-change-id top-level
-    // dirs (the 5 already-shipped slices left them behind). Until
-    // slice 008's migration consolidates them, the check reports
-    // `ok: false` for any repo that still has the legacy per-change-id
-    // layout.
-    const layoutProbe = options.workspaceLayoutProbe ?? defaultWorkspaceLayoutProbe;
-    try {
-        const layout = layoutProbe();
-        // Back-compat: probes injected by older tests (pre-slice-007)
-        // return a 2-field shape (no perChangeIdDirs). Treat missing
-        // field as empty.
-        const perChangeIdDirs = layout.perChangeIdDirs ?? [];
-        if (layout.topLevelSessionDirs.length === 0 && layout.legacyDotfiles.length === 0 && perChangeIdDirs.length === 0) {
-            checks.push({
-                id: 'build:workspace-layout-canonical',
-                ok: true,
-                message: 'Workspace layout is canonical: no top-level session dirs, no legacy runtime dotfiles, no per-change-id top-level dirs'
-            });
-        }
-        else {
-            const offenders = [
-                ...layout.topLevelSessionDirs.map((p) => `top-level session dir: ${p}`),
-                ...layout.legacyDotfiles.map((p) => `legacy dotfile: ${p}`),
-                ...perChangeIdDirs.map((p) => `per-change-id top-level dir: ${p}`)
-            ];
-            checks.push({
-                id: 'build:workspace-layout-canonical',
-                ok: false,
-                message: `Workspace layout is not canonical. Offenders: ${offenders.join('; ')}. Run \`peaks workspace migrate --to-runtime --project <repo> --apply\` to consolidate.`
-            });
-        }
-    }
-    catch (error) {
-        checks.push({
-            id: 'build:workspace-layout-canonical',
-            ok: false,
-            message: `Workspace layout check failed: ${getErrorMessage(error)}`
-        });
-    }
-    // 2026-06-10 — gateguard-fact-force integration check. The hook is a
-    // third-party PreToolUse that fires on Edit / Write and demands a
-    // 4-fact questionnaire; when the LLM is in a peaks-qa flow updating
-    // `.peaks/_runtime/<sid>/qa/requests/*.md` the facts do not apply.
-    // We warn when the hook is installed and no `.peaks/**` skip is
-    // configured. The check stays a pure mapping over the probe result
-    // so tests can drive it without touching the real `~/.claude/`.
-    const gateguardProbe = options.gateguardProbe ?? defaultGateguardProbe;
-    try {
-        const probe = gateguardProbe();
-        const offending = collectGateguardEntries(probe);
-        if (offending.length === 0) {
-            checks.push({
-                id: 'integration:gateguard-peaks-conflict',
-                ok: true,
-                message: 'No gateguard-fact-force PreToolUse hook detected in ~/.claude/settings.json or project .claude/settings.json; the Edit/Write fact-forcing flow will not interfere with peaks-qa .peaks/ artifact writes'
-            });
-        }
-        else {
-            const unrouted = offending.filter((location) => !entrySkipsPeaks(location.entry));
-            if (unrouted.length === 0) {
-                checks.push({
-                    id: 'integration:gateguard-peaks-conflict',
-                    ok: true,
-                    message: `gateguard-fact-force hook is installed in ${offending.map((l) => l.source).join(' + ')} but a .peaks/** skip pattern is configured; peaks-qa .peaks/ artifact writes are not blocked`
-                });
-            }
-            else {
-                const sources = Array.from(new Set(unrouted.map((u) => u.sourcePath))).join(' + ');
-                const matchers = unrouted.map((u) => u.entry.matcher ?? '*').join(', ');
-                checks.push({
-                    id: 'integration:gateguard-peaks-conflict',
-                    ok: false,
-                    message: `gateguard-fact-force PreToolUse hook is installed (${sources}, matcher: ${matchers}) with no .peaks/** skip pattern; every Edit/Write of a peaks-qa envelope (.peaks/_runtime/<sid>/qa/requests/*.md) will be intercepted and demand a 4-fact questionnaire that does not apply to QA templates. Workaround: set \`ECC_DISABLED_HOOKS=pre:edit-write:gateguard-fact-force\` for the session, OR add a paired PreToolUse entry whose matcher restricts the hook to non-.peaks paths. peaks-loop is NOT the source of this hook.`
-                });
-            }
-        }
-    }
-    catch (error) {
-        checks.push({
-            id: 'integration:gateguard-peaks-conflict',
-            ok: true,
-            message: `gateguard probe failed (${getErrorMessage(error)}); skipping check`
-        });
-    }
-    try {
-        const schemaText = await readText(join(schemaRoot, 'doctor-report.schema.json'));
-        const schema = JSON.parse(schemaText);
-        const patternSource = schema.properties?.checks?.items?.properties?.id?.pattern;
-        if (typeof patternSource === 'string') {
-            const pattern = new RegExp(patternSource);
-            const mismatches = checks.filter((check) => !pattern.test(check.id)).map((check) => check.id);
-            checks.push({
-                id: 'doctor-self:check-id-pattern',
-                ok: mismatches.length === 0,
-                message: mismatches.length === 0
-                    ? 'All doctor check IDs match the doctor-report schema pattern'
-                    : `Doctor check IDs missing from schema pattern: ${mismatches.join(', ')}`
-            });
-        }
-        else {
-            checks.push({
-                id: 'doctor-self:check-id-pattern',
-                ok: false,
-                message: 'doctor-report.schema.json does not declare a check.id pattern'
-            });
-        }
-    }
-    catch (error) {
-        checks.push({
-            id: 'doctor-self:check-id-pattern',
-            ok: false,
-            message: `Failed to load doctor-report.schema.json for self-validation: ${getErrorMessage(error)}`
-        });
-    }
-    // Slice L3.2: project doctor MVP — 2 new diagnostic checks.
-    //   1. L3:l3-orphan-sessions — flags bare sids in .peaks/_runtime/ that
-    //      fail isValidSessionId. Reuses the Slice 0.5 sid-naming-guard.
-    //   2. L3:l3-memory-health — verifies .peaks/memory/index.json is
-    //      well-formed JSON with the expected schema_version field and
-    //      references real files on disk.
-    // Slice L3.2: project doctor MVP — 2 new diagnostic checks.
-    //   1. L3:l3-orphan-sessions — flags bare sids in .peaks/_runtime/ that
-    //      fail isValidSessionId. Reuses the Slice 0.5 sid-naming-guard.
-    //   2. L3:l3-memory-health — verifies .peaks/memory/index.json is
-    //      well-formed JSON with the expected schema_version field and
-    //      references real files on disk.
-    //
-    // Round 2 (slice 2026-06-24-doctor-1xdetector-residual): the reducer
-    // must skip canonical system subdirs that intentionally live under
-    // `.peaks/_runtime/` — used by `request-artifact-service` /
-    // `workflow-autonomous-service` to route reviewable artifacts under
-    // session-axis dirs. Excluding these from the orphan scan is a
-    // reducer-level narrowing of which entries are subject to the check;
-    // it does NOT change the pass/fail rule for actual session ids.
-    const RUNTIME_SYSTEM_SUBDIRS = new Set(['change']);
-    const l3ProjectRoot = options.l3ProjectRoot ?? findProjectRoot(process.cwd()) ?? process.cwd();
-    try {
-        const runtimeDir = join(l3ProjectRoot, '.peaks/_runtime');
-        if (existsSync(runtimeDir)) {
-            const entries = readdirSync(runtimeDir, { withFileTypes: true })
-                .filter((e) => e.isDirectory())
-                .map((e) => e.name)
-                .filter((name) => !RUNTIME_SYSTEM_SUBDIRS.has(name));
-            const validSids = entries.filter((sid) => isValidSessionId(sid));
-            const invalidSids = entries.filter((sid) => !isValidSessionId(sid));
-            checks.push({
-                id: 'L3:l3-orphan-sessions',
-                ok: invalidSids.length === 0,
-                message: invalidSids.length === 0
-                    ? `All ${validSids.length} session(s) under .peaks/_runtime/ are valid (isValidSessionId)`
-                    : `${invalidSids.length} orphan session(s) under .peaks/_runtime/ fail isValidSessionId: ${invalidSids.slice(0, 5).join(', ')}${invalidSids.length > 5 ? '...' : ''}. Run \`peaks workspace clean --project <repo>\` to archive.`
-            });
-        }
-        else {
-            checks.push({
-                id: 'L3:l3-orphan-sessions',
-                ok: true,
-                message: 'No .peaks/_runtime/ directory; nothing to check.'
-            });
-        }
-    }
-    catch (error) {
-        checks.push({
-            id: 'L3:l3-orphan-sessions',
-            ok: true,
-            message: `L3:l3-orphan-sessions probe failed (${getErrorMessage(error)}); skipping check`
-        });
-    }
-    try {
-        const memoryIndexPath = join(l3ProjectRoot, '.peaks/memory/index.json');
-        if (existsSync(memoryIndexPath)) {
-            const raw = readFileSync(memoryIndexPath, 'utf8');
-            try {
-                // Slice 2026-06-13-repair-pre-existing-test-failures: the
-                // production MemoryIndex schema (see
-                // src/services/memory/project-memory-service.ts) uses
-                // `version: 1` as the schema marker, NOT `schema_version`.
-                // Accept BOTH names for back-compat with any external index
-                // writers (e.g. a future `schema_version: '2.0.0'` form).
-                const parsed = JSON.parse(raw);
-                const schemaMarker = parsed.schema_version ?? parsed.version;
-                if (schemaMarker === undefined) {
-                    checks.push({
-                        id: 'L3:l3-memory-health',
-                        ok: false,
-                        message: '.peaks/memory/index.json missing schema_version / version field'
-                    });
-                }
-                else {
-                    const hotCount = Object.values(parsed.hot ?? {}).reduce((sum, arr) => sum + (Array.isArray(arr) ? arr.length : 0), 0);
-                    const warmCount = Object.values(parsed.warm ?? {}).reduce((sum, arr) => sum + (Array.isArray(arr) ? arr.length : 0), 0);
-                    checks.push({
-                        id: 'L3:l3-memory-health',
-                        ok: true,
-                        message: `.peaks/memory/index.json is well-formed JSON; version=${schemaMarker}; ${hotCount} hot + ${warmCount} warm memory entries`
-                    });
-                }
-            }
-            catch (parseError) {
-                checks.push({
-                    id: 'L3:l3-memory-health',
-                    ok: false,
-                    message: `.peaks/memory/index.json is not valid JSON: ${getErrorMessage(parseError)}`
-                });
-            }
-        }
-        else {
-            checks.push({
-                id: 'L3:l3-memory-health',
-                ok: true,
-                message: 'No .peaks/memory/index.json yet (no memories extracted)'
-            });
-        }
-    }
-    catch (error) {
-        checks.push({
-            id: 'L3:l3-memory-health',
-            ok: true,
-            message: `L3:l3-memory-health probe failed (${getErrorMessage(error)}); skipping check`
-        });
-    }
-    const failed = checks.filter((check) => !check.ok).length;
-    return {
-        checks,
-        summary: {
-            ok: failed === 0,
-            passed: checks.length - failed,
-            failed
-        }
-    };
-}