@warpgogol/forge 1.1.0 → 2.1.0

package/dist/src/onboarding/doctor.js

@@ -1,1108 +0,0 @@
-/*
-<MODULE_CONTRACT>
-<purpose>forge.doctor — diagnoses forge state in an existing project.
-Checks for forge.yaml, AGENTS.md, PREFERENCES.md, .agents/skills/, docs/rfcs/,
-@warpgogol/* import autonomy guard, and bindings contract (RFC-0393).</purpose>
-<non-goals>
-  <item>Do not modify files — doctor is read-only diagnostics.</item>
-</non-goals>
-</MODULE_CONTRACT>
-<CHANGE_SUMMARY>
-  <item>Initial forge.doctor handler for autonomy refactor.</item>
-  <item>RFC-0391: added @warpgogol/* forbidden-imports autonomy guard.</item>
-  <item>RFC-0393: added bindings validation — resolved/absent/invalid reporting.</item>
-  <item>RFC-0524: added stale knowledge file detection — compares source and .agents/ copies.</item>
-  <item>RFC-0539: extended knowledge file check to iterate pack skills via discoverPackSkills. Added pack-skills check for stale/missing copies and skillPacks config validation.</item>
-  <item>RFC-0540: added defaultable-binding-null notices for forge-CLI-backed bindings.</item>
-  <item>RFC-0611: added nested AGENTS.md checks — missing, stale (dryRun comparison), hand-written improvement.</item>
-  <item>RFC-0640: added domain reporting, invariant listing (reported-only), terminology resolution, --strict flag, and software-specific check skipping for non-software domains.</item>
-  <item>RFC-0675: upgraded domain-invariants check from advisory to enforcement using invariant engine.</item>
-  <item>RFC-0660: added legacy-section count reporting for structured knowledge files.</item>
-  <item>RFC-0661: added knowledge-budgets check — validates override shape, computes per-skill budget reports, reports summary with headroom %.</item>
-  <item>RFC-0663: added knowledge-duplicates check (cross-skill L2 duplicate detection) and shared-knowledge-file check (schema/id uniqueness for the shared layer).</item>
-  <item>RFC-0664: added memory-layer health check (budget usage, gitignore coverage, daily-file leak risk).</item>
-  <item>RFC-0704: added independent-version-packages check — validates that paths in independentVersionPackages exist and contain package.json.</item>
-</CHANGE_SUMMARY>
-*/
-import { readFile, readdir, stat } from "node:fs/promises";
-import { readFileSync } from "node:fs";
-import { join, relative, dirname } from "node:path";
-import { parse as parseYaml } from "yaml";
-import { resolveForgeRoot, loadForgeConfig, resolveBinding, resolveTerminology, FORGE_CLI_BINDING_DEFAULTS, resolvePmRunner } from "../config/forge-config.js";
-import { FORGE_SKILLS, discoverPackSkills } from "../registry.js";
-import { discoverWorkspaces } from "./workspace-discovery.js";
-import { buildNestedAgentsMd, selectNestedTemplate } from "./nested-agents-templates.js";
-import { readPackageInfo } from "./nested-agents-generate.js";
-import { listStackProfiles } from "../profiles/stack-profile.js";
-import { resolveAllTerminology } from "../profiles/terminology-utils.js";
-import { TERMINOLOGY_DEFAULTS } from "../profiles/profile-schema.js";
-import { runProfileValidate } from "./profile-validate.js";
-import { parseKnowledgeFile } from "../knowledge/index.js";
-import { computeLayerBudgets, resolveKnowledgeBudgets, DEFAULT_KNOWLEDGE_BUDGETS } from "../knowledge/budgets.js";
-import { detectDuplicatePrinciples } from "../knowledge/index.js";
-import { checkMemoryLayerHealth } from "./memory-scaffold.js";
-import { checkInvariants } from "./invariant-engine.js";
-import { execSync } from "node:child_process";
-async function pathExists(target) {
-    try {
-        await stat(target);
-        return true;
-    }
-    catch {
-        return false;
-    }
-}
-const FORBIDDEN_IMPORT_PATTERN = /(?:^|\n)\s*(?:import\s+[^;]+?\s+from\s+|require\s*\(\s*)["'`](@warpgogol\/[^"'`]+)["'`]/g;
-async function scanForForbiddenImports(dir, workspaceRoot) {
-    const violations = [];
-    const entries = await readdir(dir, { withFileTypes: true }).catch(() => []);
-    for (const entry of entries) {
-        const fullPath = join(dir, entry.name);
-        if (entry.isDirectory()) {
-            if (entry.name === "node_modules" || entry.name === "tests")
-                continue;
-            const sub = await scanForForbiddenImports(fullPath, workspaceRoot);
-            violations.push(...sub);
-        }
-        else if (entry.name.endsWith(".ts")) {
-            const content = await readFile(fullPath, "utf8").catch(() => "");
-            let match;
-            const pattern = new RegExp(FORBIDDEN_IMPORT_PATTERN.source, "g");
-            while ((match = pattern.exec(content)) !== null) {
-                violations.push({
-                    file: relative(workspaceRoot, fullPath),
-                    specifier: match[1],
-                });
-            }
-        }
-    }
-    return violations;
-}
-// ---------------------------------------------------------------------------
-// Bindings validation (RFC-0393)
-// ---------------------------------------------------------------------------
-const BINDING_PATH_KEYS = [
-    "paths.invariantsFile",
-    "paths.reviewsDir",
-    "paths.handoffsDir",
-    "paths.sessionsDir",
-];
-const BINDING_COMMAND_KEYS = [
-    "commands.validateRfc",
-    "commands.validateAdr",
-    "commands.implementStamp",
-    "commands.typecheck",
-    "commands.test",
-    "commands.scopedBuild",
-    "commands.specValidate",
-    "commands.sessionSave",
-];
-async function validateBindings(workspaceRoot) {
-    const result = { resolved: [], absent: [], invalid: [], notices: [] };
-    let config;
-    try {
-        config = loadForgeConfig(workspaceRoot);
-    }
-    catch {
-        return result;
-    }
-    if (!config.bindings) {
-        return result;
-    }
-    for (const key of BINDING_PATH_KEYS) {
-        const value = resolveBinding(config, key);
-        if (value === null) {
-            result.absent.push(key);
-        }
-        else if (typeof value === "string") {
-            const exists = await pathExists(join(workspaceRoot, value));
-            if (exists) {
-                result.resolved.push(key);
-            }
-            else {
-                result.invalid.push(`${key} (path not found: ${value})`);
-            }
-        }
-    }
-    const compassDocs = resolveBinding(config, "paths.compassDocs");
-    if (Array.isArray(compassDocs) && compassDocs.length > 0) {
-        for (const docPath of compassDocs) {
-            const exists = await pathExists(join(workspaceRoot, docPath));
-            if (exists) {
-                result.resolved.push(`paths.compassDocs[${docPath}]`);
-            }
-            else {
-                result.invalid.push(`paths.compassDocs[${docPath}] (path not found)`);
-            }
-        }
-    }
-    else {
-        result.absent.push("paths.compassDocs");
-    }
-    for (const key of BINDING_COMMAND_KEYS) {
-        const value = resolveBinding(config, key);
-        if (value === null) {
-            result.absent.push(key);
-        }
-        else if (typeof value === "string") {
-            result.resolved.push(key);
-        }
-    }
-    // RFC-0540: Emit defaultable-binding-null notices for forge-CLI-backed bindings
-    const pm = config.project.packageManager;
-    const runner = resolvePmRunner(pm);
-    for (const entry of FORGE_CLI_BINDING_DEFAULTS) {
-        const value = resolveBinding(config, entry.key);
-        if (value === null) {
-            result.notices.push({
-                key: entry.key,
-                rule: "defaultable-binding-null",
-                suggestion: `${runner} ${entry.template}`,
-            });
-        }
-    }
-    return result;
-}
-// ---------------------------------------------------------------------------
-// Stale knowledge file detection (RFC-0524)
-// ---------------------------------------------------------------------------
-async function checkStaleKnowledgeFiles(workspaceRoot, forgeRoot) {
-    const stale = [];
-    let config;
-    try {
-        config = loadForgeConfig(workspaceRoot);
-    }
-    catch {
-        return { name: "knowledge-files", status: "pass", message: "No forge.yaml — knowledge file check skipped" };
-    }
-    const agentsSkillsDir = join(workspaceRoot, config.paths.skillsDir);
-    for (const skill of FORGE_SKILLS) {
-        if (!skill.knowledge || skill.knowledge.length === 0)
-            continue;
-        const skillSrcDir = dirname(join(forgeRoot, skill.path));
-        for (const kf of skill.knowledge) {
-            const srcPath = join(skillSrcDir, kf);
-            const destPath = join(agentsSkillsDir, skill.name, kf);
-            const srcExists = await pathExists(srcPath);
-            const destExists = await pathExists(destPath);
-            if (srcExists && destExists) {
-                const srcContent = await readFile(srcPath, "utf8").catch(() => "");
-                const destContent = await readFile(destPath, "utf8").catch(() => "");
-                if (srcContent !== destContent) {
-                    stale.push(`${skill.name}/${kf}`);
-                }
-            }
-            // If source exists but dest doesn't, skip — expected on first install
-            // If source doesn't exist, SKILL-13 in forge.skill.validate catches it
-        }
-    }
-    // RFC-0539: Check pack skill knowledge files
-    const packSkills = discoverPackSkills(workspaceRoot, config);
-    for (const skill of packSkills) {
-        if (!skill.knowledge || skill.knowledge.length === 0)
-            continue;
-        const skillSrcDir = dirname(join(workspaceRoot, skill.dir, skill.path));
-        for (const kf of skill.knowledge) {
-            const srcPath = join(skillSrcDir, kf);
-            const destPath = join(agentsSkillsDir, skill.name, kf);
-            const srcExists = await pathExists(srcPath);
-            const destExists = await pathExists(destPath);
-            if (srcExists && destExists) {
-                const srcContent = await readFile(srcPath, "utf8").catch(() => "");
-                const destContent = await readFile(destPath, "utf8").catch(() => "");
-                if (srcContent !== destContent) {
-                    stale.push(`${skill.name}/${kf}`);
-                }
-            }
-        }
-    }
-    return {
-        name: "knowledge-files",
-        status: stale.length === 0 ? "pass" : "warn",
-        message: stale.length === 0
-            ? "All knowledge files in sync"
-            : `${stale.length} stale knowledge file(s): ${stale.join(", ")} — run 'forge create' to sync`,
-    };
-}
-// ---------------------------------------------------------------------------
-// Legacy section detection (RFC-0660)
-// ---------------------------------------------------------------------------
-function checkLegacyKnowledgeSections(workspaceRoot, forgeRoot) {
-    let config;
-    try {
-        config = loadForgeConfig(workspaceRoot);
-    }
-    catch {
-        return { name: "knowledge-legacy", status: "pass", message: "No forge.yaml — legacy section check skipped" };
-    }
-    let totalLegacy = 0;
-    let filesWithLegacy = 0;
-    // Check forge skills
-    for (const skill of FORGE_SKILLS) {
-        if (!skill.knowledge || skill.knowledge.length === 0)
-            continue;
-        const skillDir = join(forgeRoot, dirname(skill.path));
-        for (const kf of skill.knowledge) {
-            const kfPath = join(skillDir, kf);
-            try {
-                const parsed = parseKnowledgeFile(kfPath);
-                if (parsed.isKnowledgeAdjacent)
-                    continue;
-                if (parsed.legacySections.length > 0) {
-                    totalLegacy += parsed.legacySections.length;
-                    filesWithLegacy++;
-                }
-            }
-            catch {
-                // File read errors are handled by stale knowledge check
-            }
-        }
-    }
-    // Check pack skills
-    const packSkills = discoverPackSkills(workspaceRoot, config);
-    for (const skill of packSkills) {
-        if (!skill.knowledge || skill.knowledge.length === 0)
-            continue;
-        const skillDir = join(workspaceRoot, skill.dir, dirname(skill.path));
-        for (const kf of skill.knowledge) {
-            const kfPath = join(skillDir, kf);
-            try {
-                const parsed = parseKnowledgeFile(kfPath);
-                if (parsed.isKnowledgeAdjacent)
-                    continue;
-                if (parsed.legacySections.length > 0) {
-                    totalLegacy += parsed.legacySections.length;
-                    filesWithLegacy++;
-                }
-            }
-            catch {
-                // File read errors are handled by stale knowledge check
-            }
-        }
-    }
-    return {
-        name: "knowledge-legacy",
-        status: totalLegacy === 0 ? "pass" : "warn",
-        message: totalLegacy === 0
-            ? "No legacy knowledge sections"
-            : `${totalLegacy} legacy section${totalLegacy === 1 ? "" : "s"} across ${filesWithLegacy} knowledge file${filesWithLegacy === 1 ? "" : "s"} — run the knowledge compaction command to migrate`,
-    };
-}
-// ---------------------------------------------------------------------------
-// Knowledge budget check (RFC-0661)
-// ---------------------------------------------------------------------------
-function checkKnowledgeBudgets(workspaceRoot, forgeRoot) {
-    let config;
-    try {
-        config = loadForgeConfig(workspaceRoot);
-    }
-    catch {
-        return { name: "knowledge-budgets", status: "pass", message: "No forge.yaml — budget check skipped" };
-    }
-    // Validate override shape if present
-    const overrideWarnings = [];
-    const effectiveBudgets = resolveKnowledgeBudgets(workspaceRoot);
-    let usingDefaults = true;
-    try {
-        const forgeYamlPath = join(workspaceRoot, "forge.yaml");
-        const content = readFileSync(forgeYamlPath, "utf8");
-        const parsed = parseYaml(content);
-        const bindings = parsed?.bindings;
-        const knowledge = bindings?.knowledge;
-        const budgets = knowledge?.budgets;
-        if (budgets) {
-            usingDefaults = false;
-            if (typeof budgets.hot !== "number" || budgets.hot <= 0 || !Number.isInteger(budgets.hot)) {
-                overrideWarnings.push(`bindings.knowledge.budgets.hot invalid (got ${String(budgets.hot)}), using default ${DEFAULT_KNOWLEDGE_BUDGETS.hot}`);
-            }
-            if (typeof budgets.warm !== "number" || budgets.warm <= 0 || !Number.isInteger(budgets.warm)) {
-                overrideWarnings.push(`bindings.knowledge.budgets.warm invalid (got ${String(budgets.warm)}), using default ${DEFAULT_KNOWLEDGE_BUDGETS.warm}`);
-            }
-        }
-    }
-    catch {
-        // forge.yaml not readable — defaults already applied
-    }
-    // Collect all parsed knowledge files from forge skills and pack skills
-    const parsedFiles = [];
-    for (const skill of FORGE_SKILLS) {
-        if (!skill.knowledge || skill.knowledge.length === 0)
-            continue;
-        const skillDir = join(forgeRoot, dirname(skill.path));
-        for (const kf of skill.knowledge) {
-            const kfPath = join(skillDir, kf);
-            try {
-                const parsed = parseKnowledgeFile(kfPath);
-                if (parsed.layer !== null && parsed.layer !== "L0" && !parsed.isKnowledgeAdjacent && parsed.parseIssues.length === 0) {
-                    parsedFiles.push({ file: parsed, skillName: skill.name });
-                }
-            }
-            catch {
-                // File read errors are handled by stale knowledge check
-            }
-        }
-    }
-    const packSkills = discoverPackSkills(workspaceRoot, config);
-    for (const skill of packSkills) {
-        if (!skill.knowledge || skill.knowledge.length === 0)
-            continue;
-        const skillDir = join(workspaceRoot, skill.dir, dirname(skill.path));
-        for (const kf of skill.knowledge) {
-            const kfPath = join(skillDir, kf);
-            try {
-                const parsed = parseKnowledgeFile(kfPath);
-                if (parsed.layer !== null && parsed.layer !== "L0" && !parsed.isKnowledgeAdjacent && parsed.parseIssues.length === 0) {
-                    parsedFiles.push({ file: parsed, skillName: skill.name, pack: skill.pack });
-                }
-            }
-            catch {
-                // File read errors are handled by stale knowledge check
-            }
-        }
-    }
-    // Compute budget reports
-    const filesForBudget = parsedFiles.map((p) => p.file);
-    const skillNames = new Map();
-    for (const p of parsedFiles) {
-        skillNames.set(p.file.path, p.skillName);
-    }
-    const reports = computeLayerBudgets(filesForBudget, effectiveBudgets, skillNames);
-    // Build summary
-    const budgetSource = usingDefaults ? "defaults" : "override";
-    const parts = [`budgets: hot=${effectiveBudgets.hot} warm=${effectiveBudgets.warm} (${budgetSource})`];
-    if (reports.length > 0) {
-        const summary = reports.map((r) => {
-            const pct = Math.round((r.activeChars / r.budget) * 100);
-            return `${r.skill}/${r.file}[${r.layer}]: ${r.activeChars}/${r.budget} (${pct}%)`;
-        });
-        parts.push(`${reports.length} file${reports.length === 1 ? "" : "s"}: ${summary.join(", ")}`);
-    }
-    else {
-        parts.push("no hot/warm knowledge files to check");
-    }
-    if (overrideWarnings.length > 0) {
-        parts.push(overrideWarnings.join("; "));
-    }
-    const status = overrideWarnings.length > 0 ? "warn" : "pass";
-    return {
-        name: "knowledge-budgets",
-        status,
-        message: parts.join(" | "),
-    };
-}
-// ---------------------------------------------------------------------------
-// Knowledge duplicate detection (RFC-0663)
-// ---------------------------------------------------------------------------
-function collectL2Files(workspaceRoot, forgeRoot) {
-    let config;
-    try {
-        config = loadForgeConfig(workspaceRoot);
-    }
-    catch {
-        return [];
-    }
-    const files = [];
-    for (const skill of FORGE_SKILLS) {
-        if (!skill.knowledge || skill.knowledge.length === 0)
-            continue;
-        const skillDir = join(forgeRoot, dirname(skill.path));
-        for (const kf of skill.knowledge) {
-            if (kf !== "learned-principles.md")
-                continue;
-            const kfPath = join(skillDir, kf);
-            try {
-                const parsed = parseKnowledgeFile(kfPath);
-                if (parsed.isKnowledgeAdjacent)
-                    continue;
-                if (parsed.parseIssues.length > 0)
-                    continue;
-                files.push({ skill: skill.name, parsed });
-            }
-            catch {
-                // File read errors are handled by stale knowledge check
-            }
-        }
-    }
-    const packSkills = discoverPackSkills(workspaceRoot, config);
-    for (const skill of packSkills) {
-        if (!skill.knowledge || skill.knowledge.length === 0)
-            continue;
-        const skillDir = join(workspaceRoot, skill.dir, dirname(skill.path));
-        for (const kf of skill.knowledge) {
-            if (kf !== "learned-principles.md")
-                continue;
-            const kfPath = join(skillDir, kf);
-            try {
-                const parsed = parseKnowledgeFile(kfPath);
-                if (parsed.isKnowledgeAdjacent)
-                    continue;
-                if (parsed.parseIssues.length > 0)
-                    continue;
-                files.push({ skill: skill.name, parsed });
-            }
-            catch {
-                // File read errors are handled by stale knowledge check
-            }
-        }
-    }
-    const sharedPath = join(forgeRoot, "skills", "shared", "knowledge", "learned-principles.md");
-    try {
-        const parsed = parseKnowledgeFile(sharedPath);
-        if (!parsed.isKnowledgeAdjacent && parsed.parseIssues.length === 0 && parsed.entries.length > 0) {
-            files.push({ skill: "shared", parsed });
-        }
-    }
-    catch {
-        // Shared layer not initialized — not an error
-    }
-    return files;
-}
-function checkKnowledgeDuplicates(workspaceRoot, forgeRoot) {
-    const l2Files = collectL2Files(workspaceRoot, forgeRoot);
-    if (l2Files.length === 0) {
-        return { name: "knowledge-duplicates", status: "pass", message: "No L2 knowledge files to check" };
-    }
-    const pairs = detectDuplicatePrinciples(l2Files);
-    if (pairs.length === 0) {
-        return { name: "knowledge-duplicates", status: "pass", message: "No cross-skill duplicate principles detected" };
-    }
-    const pairSummaries = pairs.map((p) => `${p.a.skill}/${p.a.entryId} ↔ ${p.b.skill}/${p.b.entryId} (${p.kind})`);
-    return {
-        name: "knowledge-duplicates",
-        status: "warn",
-        message: `${pairs.length} duplicate pair${pairs.length === 1 ? "" : "s"} detected — run fo-knowledge-distill to promote: ${pairSummaries.join("; ")}`,
-    };
-}
-// ---------------------------------------------------------------------------
-// Shared knowledge file validation (RFC-0663)
-// ---------------------------------------------------------------------------
-function checkSharedKnowledgeFile(workspaceRoot, forgeRoot) {
-    const sharedPath = join(forgeRoot, "skills", "shared", "knowledge", "learned-principles.md");
-    let parsed;
-    try {
-        parsed = parseKnowledgeFile(sharedPath);
-    }
-    catch {
-        return { name: "shared-knowledge-file", status: "pass", message: "Shared knowledge layer not initialized — created on first promotion" };
-    }
-    if (parsed.isKnowledgeAdjacent) {
-        return { name: "shared-knowledge-file", status: "pass", message: "Shared knowledge layer is empty (no structured entries)" };
-    }
-    const issues = [];
-    for (const issue of parsed.parseIssues) {
-        issues.push(`line ${issue.line}: ${issue.message}`);
-    }
-    const seenIds = new Set();
-    for (const entry of parsed.entries) {
-        if (seenIds.has(entry.meta.id)) {
-            issues.push(`duplicate entry id: ${entry.meta.id}`);
-        }
-        seenIds.add(entry.meta.id);
-    }
-    if (issues.length > 0) {
-        return {
-            name: "shared-knowledge-file",
-            status: "fail",
-            message: `${issues.length} issue${issues.length === 1 ? "" : "s"}: ${issues.join("; ")}`,
-        };
-    }
-    return {
-        name: "shared-knowledge-file",
-        status: "pass",
-        message: `Shared knowledge layer: ${parsed.entries.length} entr${parsed.entries.length === 1 ? "y" : "ies"}`,
-    };
-}
-// ---------------------------------------------------------------------------
-// Independent version packages diagnostics (RFC-0704)
-// ---------------------------------------------------------------------------
-async function checkIndependentVersionPackages(workspaceRoot) {
-    let config;
-    try {
-        config = loadForgeConfig(workspaceRoot);
-    }
-    catch {
-        return { name: "independent-version-packages", status: "pass", message: "No forge.yaml — independent version packages check skipped" };
-    }
-    if (!config.independentVersionPackages || config.independentVersionPackages.length === 0) {
-        return { name: "independent-version-packages", status: "pass", message: "No independent version packages declared" };
-    }
-    const issues = [];
-    let validCount = 0;
-    for (const pkgPath of config.independentVersionPackages) {
-        const dirExists = await pathExists(join(workspaceRoot, pkgPath));
-        const pkgJsonExists = await pathExists(join(workspaceRoot, pkgPath, "package.json"));
-        if (!dirExists) {
-            issues.push(`path '${pkgPath}' does not exist`);
-        }
-        else if (!pkgJsonExists) {
-            issues.push(`path '${pkgPath}' has no package.json`);
-        }
-        else {
-            validCount++;
-        }
-    }
-    if (issues.length === 0) {
-        return {
-            name: "independent-version-packages",
-            status: "pass",
-            message: `${validCount} independent version package${validCount === 1 ? "" : "s"} declared`,
-        };
-    }
-    return {
-        name: "independent-version-packages",
-        status: "warn",
-        message: `${issues.length} issue${issues.length === 1 ? "" : "s"}: ${issues.join(", ")}`,
-    };
-}
-// ---------------------------------------------------------------------------
-// Pack skill diagnostics (RFC-0539)
-// ---------------------------------------------------------------------------
-async function checkPackSkills(workspaceRoot) {
-    let config;
-    try {
-        config = loadForgeConfig(workspaceRoot);
-    }
-    catch {
-        return { name: "pack-skills", status: "pass", message: "No forge.yaml — pack skill check skipped" };
-    }
-    if (!config.skillPacks || config.skillPacks.length === 0) {
-        return { name: "pack-skills", status: "pass", message: "No skill packs declared" };
-    }
-    const issues = [];
-    // Validate skillPacks config: unique prefixes, unique dirs, no 'fo' prefix, dir exists
-    const prefixes = new Set();
-    const dirs = new Set();
-    for (const pack of config.skillPacks) {
-        if (prefixes.has(pack.prefix)) {
-            issues.push(`duplicate prefix '${pack.prefix}'`);
-        }
-        prefixes.add(pack.prefix);
-        if (pack.prefix === "fo") {
-            issues.push(`prefix 'fo' is reserved for forge`);
-        }
-        if (dirs.has(pack.dir)) {
-            issues.push(`duplicate dir '${pack.dir}'`);
-        }
-        dirs.add(pack.dir);
-        const packDirExists = await pathExists(join(workspaceRoot, pack.dir));
-        if (!packDirExists) {
-            issues.push(`pack dir '${pack.dir}' does not exist`);
-        }
-    }
-    // Check for stale/missing pack skill copies
-    const packSkills = discoverPackSkills(workspaceRoot, config);
-    const agentsSkillsDir = join(workspaceRoot, config.paths.skillsDir);
-    for (const skill of packSkills) {
-        const srcPath = join(workspaceRoot, skill.dir, skill.path);
-        const destPath = join(agentsSkillsDir, skill.name, "SKILL.md");
-        const srcExists = await pathExists(srcPath);
-        const destExists = await pathExists(destPath);
-        if (srcExists && destExists) {
-            const srcContent = await readFile(srcPath, "utf8").catch(() => "");
-            const destContent = await readFile(destPath, "utf8").catch(() => "");
-            if (srcContent !== destContent) {
-                issues.push(`stale copy of '${skill.name}'`);
-            }
-        }
-        else if (srcExists && !destExists) {
-            issues.push(`missing copy of '${skill.name}'`);
-        }
-    }
-    return {
-        name: "pack-skills",
-        status: issues.length === 0 ? "pass" : "warn",
-        message: issues.length === 0
-            ? `${packSkills.length} pack skill(s) in sync`
-            : `${issues.length} issue(s): ${issues.join(", ")} — run 'forge create' to sync`,
-    };
-}
-// ---------------------------------------------------------------------------
-// Nested AGENTS.md diagnostics (RFC-0611)
-// ---------------------------------------------------------------------------
-async function checkNestedAgentsMd(workspaceRoot, workspaceTypes) {
-    let config;
-    try {
-        config = loadForgeConfig(workspaceRoot);
-    }
-    catch {
-        return {
-            name: "nested-AGENTS.md",
-            status: "pass",
-            message: "forge.yaml not loadable — nested AGENTS.md check skipped",
-        };
-    }
-    const workspaces = discoverWorkspaces(workspaceRoot, workspaceTypes);
-    if (workspaces.length === 0) {
-        return {
-            name: "nested-AGENTS.md",
-            status: "pass",
-            message: "no workspace directories found",
-        };
-    }
-    const issues = [];
-    let missing = 0;
-    let stale = 0;
-    let handwritten = 0;
-    for (const ws of workspaces) {
-        if (!ws.hasAgentsMd) {
-            missing++;
-            issues.push(`${ws.path}/AGENTS.md missing`);
-            continue;
-        }
-        if (!ws.isGenerated) {
-            handwritten++;
-            const suggestions = [];
-            try {
-                const content = await readFile(join(workspaceRoot, ws.path, "AGENTS.md"), "utf8");
-                if (!content.includes("AGENTS.md")) {
-                    suggestions.push("reference root AGENTS.md");
-                }
-            }
-            catch {
-                // unreadable — skip
-            }
-            if (suggestions.length > 0) {
-                issues.push(`${ws.path}/AGENTS.md hand-written — consider: ${suggestions.join(", ")}`);
-            }
-            continue;
-        }
-        // Stale check: compare in-memory render to committed file
-        // Must match the generate pipeline: readPackageInfo + buildNestedAgentsMd + selectNestedTemplate
-        try {
-            const packageInfo = readPackageInfo(workspaceRoot, ws.path);
-            const fallback = buildNestedAgentsMd(ws, config, packageInfo);
-            const profile = config.profile;
-            const terminology = resolveAllTerminology(config, profile);
-            const wsType = workspaceTypes?.find((wt) => wt.id === ws.type);
-            const expected = selectNestedTemplate(wsType, profile, terminology, fallback);
-            const actual = await readFile(join(workspaceRoot, ws.path, "AGENTS.md"), "utf8");
-            if (expected !== actual) {
-                stale++;
-                issues.push(`${ws.path}/AGENTS.md stale — run 'forge agents generate'`);
-            }
-        }
-        catch {
-            // unreadable — skip
-        }
-    }
-    if (issues.length === 0) {
-        return {
-            name: "nested-AGENTS.md",
-            status: "pass",
-            message: `${workspaces.length} workspace(s) — all AGENTS.md in sync`,
-        };
-    }
-    const parts = [];
-    if (missing > 0)
-        parts.push(`${missing} missing`);
-    if (stale > 0)
-        parts.push(`${stale} stale`);
-    if (handwritten > 0)
-        parts.push(`${handwritten} hand-written`);
-    return {
-        name: "nested-AGENTS.md",
-        status: stale > 0 ? "warn" : "pass",
-        message: `${parts.join(", ")} — ${issues.slice(0, 3).join("; ")}${issues.length > 3 ? ` (+${issues.length - 3} more)` : ""}`,
-    };
-}
-function buildTerminologyMap(config, profileTerminology) {
-    const result = {};
-    for (const key of Object.keys(TERMINOLOGY_DEFAULTS)) {
-        result[key] = resolveTerminology(config, profileTerminology, key);
-    }
-    // Also include any custom keys from bindings.terminology
-    if (config.bindings?.terminology) {
-        for (const key of Object.keys(config.bindings.terminology)) {
-            if (!(key in result)) {
-                result[key] = resolveTerminology(config, profileTerminology, key);
-            }
-        }
-    }
-    return result;
-}
-function resolveDomainReport(workspaceRoot, forgeRoot) {
-    // 1. Try forge.yaml domain field
-    try {
-        const config = loadForgeConfig(workspaceRoot);
-        if (config.project.domain) {
-            const terminology = buildTerminologyMap(config);
-            const register = readRegisterFromPrefs(workspaceRoot);
-            return {
-                domain: config.project.domain,
-                register,
-                terminology,
-                invariants: [],
-                source: "forge.yaml",
-            };
-        }
-    }
-    catch {
-        // forge.yaml not loadable
-    }
-    // 2. Try to find domain from stack profile matching config.project.stack
-    try {
-        const config = loadForgeConfig(workspaceRoot);
-        const profiles = listStackProfiles(forgeRoot);
-        for (const stackId of config.project.stack) {
-            const profile = profiles.find((p) => p.id === stackId);
-            if (profile?.domain) {
-                const terminology = buildTerminologyMap(config, profile.terminology);
-                const register = profile.register ?? readRegisterFromPrefs(workspaceRoot);
-                return {
-                    domain: profile.domain,
-                    register,
-                    terminology,
-                    invariants: profile.invariants ?? [],
-                    source: "profile",
-                    profileId: profile.id,
-                };
-            }
-        }
-    }
-    catch {
-        // config or profiles not loadable
-    }
-    // 3. Default: software domain
-    return {
-        domain: "software",
-        register: null,
-        terminology: {},
-        invariants: [],
-        source: "default",
-    };
-}
-function readRegisterFromPrefs(workspaceRoot) {
-    try {
-        const prefsPath = join(workspaceRoot, "PREFERENCES.md");
-        const content = readFileSync(prefsPath, "utf8");
-        const fmMatch = content.match(/^---\r?\n([\s\S]*?)\r?\n---/);
-        if (fmMatch) {
-            const fm = parseYaml(fmMatch[1]);
-            if (fm["register"] === "creative")
-                return "creative";
-            if (fm["register"] === "business")
-                return "business";
-        }
-    }
-    catch {
-        // PREFERENCES.md missing or unreadable
-    }
-    return null;
-}
-function checkDomainInfo(domainReport) {
-    const parts = [`domain: ${domainReport.domain}`, `source: ${domainReport.source}`];
-    if (domainReport.register) {
-        parts.push(`register: ${domainReport.register}`);
-    }
-    if (Object.keys(domainReport.terminology).length > 0) {
-        const terms = Object.entries(domainReport.terminology)
-            .map(([k, v]) => `${k}=${v}`)
-            .join(", ");
-        parts.push(`terminology: ${terms}`);
-    }
-    if (domainReport.invariants.length > 0) {
-        parts.push(`invariants: ${domainReport.invariants.length} declared`);
-    }
-    return {
-        name: "domain-info",
-        status: "pass",
-        message: parts.join(", "),
-    };
-}
-// RFC-0664: Memory layer health check
-function checkMemoryLayer(workspaceRoot) {
-    const health = checkMemoryLayerHealth(workspaceRoot);
-    if (!health.memoryMdExists) {
-        return {
-            name: "memory-layer",
-            status: "pass",
-            message: "Memory layer not initialized — run 'forge create' or 'forge upgrade' to scaffold .agents/memory/",
-        };
-    }
-    const overBudget = health.memoryMdChars > health.budget;
-    const leakRisk = !health.gitignoreCoversDaily && health.dailyFileCount > 0;
-    if (overBudget && leakRisk) {
-        return {
-            name: "memory-layer",
-            status: "warn",
-            message: `MEMORY.md over budget (${health.memoryMdChars}/${health.budget} chars); ${health.dailyFileCount} daily file(s) untracked by .gitignore — add forge-agent-memory block`,
-        };
-    }
-    if (overBudget) {
-        return {
-            name: "memory-layer",
-            status: "warn",
-            message: `MEMORY.md over budget (${health.memoryMdChars}/${health.budget} chars) — compact or promote to skill knowledge`,
-        };
-    }
-    if (leakRisk) {
-        return {
-            name: "memory-layer",
-            status: "warn",
-            message: `${health.dailyFileCount} daily file(s) not covered by .gitignore — add forge-agent-memory block to prevent committing ephemeral logs`,
-        };
-    }
-    return {
-        name: "memory-layer",
-        status: "pass",
-        message: `MEMORY.md ${health.memoryMdChars}/${health.budget} chars; ${health.dailyFileCount} daily file(s); gitignore ${health.gitignoreCoversDaily ? "covers" : "absent (no daily files)"}`,
-    };
-}
-// ---------------------------------------------------------------------------
-// Prerequisite checks (profile-declared system dependencies)
-// ---------------------------------------------------------------------------
-function checkPrerequisites(prerequisites) {
-    if (prerequisites.length === 0) {
-        return { name: "prerequisites", status: "pass", message: "No prerequisites declared" };
-    }
-    const results = [];
-    for (const prereq of prerequisites) {
-        try {
-            execSync(prereq.check, { stdio: "pipe", timeout: 10000 });
-            results.push({ id: prereq.id, name: prereq.name, status: "pass", message: `${prereq.name} found` });
-        }
-        catch {
-            const hint = prereq.installHint ? ` — install: ${prereq.installHint}` : "";
-            results.push({ id: prereq.id, name: prereq.name, status: "fail", message: `${prereq.name} not found${hint}` });
-        }
-    }
-    const failed = results.filter((r) => r.status === "fail");
-    const hasErrors = failed.some((r) => prerequisites.find((p) => p.id === r.id)?.severity === "error");
-    const hasWarnings = failed.some((r) => prerequisites.find((p) => p.id === r.id)?.severity === "warning");
-    const status = hasErrors ? "fail" : hasWarnings ? "warn" : "pass";
-    const parts = results.map((r) => `${r.name}: ${r.status === "pass" ? "ok" : "missing"}`);
-    return {
-        name: "prerequisites",
-        status,
-        message: `${results.length} prerequisite(s): ${parts.join(", ")}`,
-    };
-}
-export async function runDoctor(input, context) {
-    const { workspaceRoot, logger, outputFormat } = context;
-    const strict = input.flags["strict"] === true;
-    const checks = [];
-    // Check forge.yaml
-    const forgeYamlExists = await pathExists(join(workspaceRoot, "forge.yaml"));
-    checks.push({
-        name: "forge.yaml",
-        status: forgeYamlExists ? "pass" : "warn",
-        message: forgeYamlExists
-            ? "forge.yaml found"
-            : "forge.yaml not found — run 'forge create' to create project configuration",
-    });
-    // Check AGENTS.md
-    const agentsMdExists = await pathExists(join(workspaceRoot, "AGENTS.md"));
-    checks.push({
-        name: "AGENTS.md",
-        status: agentsMdExists ? "pass" : "warn",
-        message: agentsMdExists
-            ? "AGENTS.md found"
-            : "AGENTS.md not found — run 'forge create' to deploy agent instructions",
-    });
-    // Check PREFERENCES.md
-    const preferencesExists = await pathExists(join(workspaceRoot, "PREFERENCES.md"));
-    checks.push({
-        name: "PREFERENCES.md",
-        status: preferencesExists ? "pass" : "warn",
-        message: preferencesExists
-            ? "PREFERENCES.md found"
-            : "PREFERENCES.md not found — run 'forge create' to create preferences file",
-    });
-    // Check .agents/skills/
-    const skillsDirExists = await pathExists(join(workspaceRoot, ".agents", "skills"));
-    checks.push({
-        name: ".agents/skills/",
-        status: skillsDirExists ? "pass" : "fail",
-        message: skillsDirExists
-            ? ".agents/skills/ directory found"
-            : ".agents/skills/ directory not found — run 'forge create' to deploy skills",
-    });
-    // Check docs/rfcs/
-    const rfcsDirExists = await pathExists(join(workspaceRoot, "docs", "rfcs"));
-    checks.push({
-        name: "docs/rfcs/",
-        status: rfcsDirExists ? "pass" : "warn",
-        message: rfcsDirExists
-            ? "docs/rfcs/ directory found"
-            : "docs/rfcs/ directory not found — run 'forge create' to create RFC directory",
-    });
-    // Check docs/adrs/
-    const adrsDirExists = await pathExists(join(workspaceRoot, "docs", "adrs"));
-    checks.push({
-        name: "docs/adrs/",
-        status: adrsDirExists ? "pass" : "warn",
-        message: adrsDirExists
-            ? "docs/adrs/ directory found"
-            : "docs/adrs/ directory not found — run 'forge create' to create ADR directory",
-    });
-    // Check @warpgogol/* forbidden imports (autonomy guard)
-    let forgeRoot;
-    try {
-        forgeRoot = resolveForgeRoot(workspaceRoot);
-    }
-    catch {
-        forgeRoot = join(workspaceRoot, "packages", "forge");
-    }
-    // RFC-0640: Resolve domain report for domain-aware checks
-    const domainReport = resolveDomainReport(workspaceRoot, forgeRoot);
-    // RFC-0640: Domain info check
-    checks.push(checkDomainInfo(domainReport));
-    // RFC-0675: Enforce invariants using the invariant engine
-    if (domainReport.invariants.length > 0) {
-        const profiles = listStackProfiles(forgeRoot);
-        const profile = domainReport.profileId
-            ? profiles.find((p) => p.id === domainReport.profileId)
-            : undefined;
-        const invariantResults = profile
-            ? checkInvariants(profile, workspaceRoot)
-            : [];
-        const allViolations = invariantResults.flatMap((r) => r.violations);
-        const errorViolations = allViolations.filter((v) => v.severity === "error");
-        const warningViolations = allViolations.filter((v) => v.severity === "warning");
-        const checkedCount = invariantResults.filter((r) => r.checked).length;
-        const advisoryCount = invariantResults.filter((r) => !r.checked).length;
-        const status = errorViolations.length > 0 ? "fail" :
-            warningViolations.length > 0 ? "warn" :
-                "pass";
-        const parts = [];
-        if (allViolations.length > 0) {
-            parts.push(`${allViolations.length} violation(s)`);
-            for (const v of allViolations.slice(0, 3)) {
-                parts.push(`${v.invariantId}: ${v.file} — ${v.message}`);
-            }
-            if (allViolations.length > 3)
-                parts.push(`(+${allViolations.length - 3} more)`);
-        }
-        else {
-            parts.push(`${checkedCount} checked, ${advisoryCount} advisory`);
-        }
-        checks.push({
-            name: "domain-invariants",
-            status,
-            message: parts.join("; "),
-            invariantViolations: allViolations.length > 0 ? allViolations : undefined,
-        });
-    }
-    // Prerequisite checks (profile-declared system dependencies)
-    if (domainReport.profileId) {
-        const profiles = listStackProfiles(forgeRoot);
-        const profile = profiles.find((p) => p.id === domainReport.profileId);
-        if (profile?.prerequisites && profile.prerequisites.length > 0) {
-            checks.push(checkPrerequisites(profile.prerequisites));
-        }
-    }
-    // RFC-0640: Run forge.profile.validate as advisory check (warn on failure, not fail)
-    const profileValidateResult = await runProfileValidate({ argv: [], flags: {} }, { ...context, forgeRoot });
-    const invalidProfiles = profileValidateResult.data?.profiles.filter((p) => !p.valid) ?? [];
-    checks.push({
-        name: "profile-validate",
-        status: invalidProfiles.length === 0 ? "pass" : "warn",
-        message: invalidProfiles.length === 0
-            ? `${profileValidateResult.data?.profiles.length ?? 0} profile(s) valid`
-            : `${invalidProfiles.length} profile(s) invalid (advisory): ${invalidProfiles.map((p) => p.id).join(", ")}`,
-    });
-    const forbiddenImports = await scanForForbiddenImports(forgeRoot, workspaceRoot);
-    checks.push({
-        name: "autonomy-guard",
-        status: forbiddenImports.length === 0 ? "pass" : "fail",
-        message: forbiddenImports.length === 0
-            ? "No @warpgogol/* imports in forge source"
-            : `${forbiddenImports.length} @warpgogol/* import(s) found in forge source — remove them`,
-    });
-    // Check bindings contract (RFC-0393)
-    const bindingsResult = await validateBindings(workspaceRoot);
-    checks.push({
-        name: "bindings",
-        status: bindingsResult.invalid.length === 0 ? "pass" : "fail",
-        message: bindingsResult.invalid.length === 0
-            ? `Bindings: ${bindingsResult.resolved.length} resolved, ${bindingsResult.absent.length} absent`
-            : `Bindings: ${bindingsResult.invalid.length} invalid — ${bindingsResult.invalid.join(", ")}`,
-    });
-    // Check stale knowledge files (RFC-0524, RFC-0539)
-    const staleCheck = await checkStaleKnowledgeFiles(workspaceRoot, forgeRoot);
-    checks.push(staleCheck);
-    // RFC-0660: Check legacy sections in knowledge files
-    const legacyCheck = checkLegacyKnowledgeSections(workspaceRoot, forgeRoot);
-    checks.push(legacyCheck);
-    // RFC-0661: Check knowledge layer token budgets
-    const budgetCheck = checkKnowledgeBudgets(workspaceRoot, forgeRoot);
-    checks.push(budgetCheck);
-    // RFC-0663: Check cross-skill duplicate principles
-    const duplicatesCheck = checkKnowledgeDuplicates(workspaceRoot, forgeRoot);
-    checks.push(duplicatesCheck);
-    // RFC-0663: Validate shared knowledge layer file
-    const sharedKnowledgeCheck = checkSharedKnowledgeFile(workspaceRoot, forgeRoot);
-    checks.push(sharedKnowledgeCheck);
-    // RFC-0664: Check memory layer health (budget, gitignore coverage, leak risk)
-    checks.push(checkMemoryLayer(workspaceRoot));
-    // RFC-0539: Check pack skills — stale/missing copies and config validation
-    const packCheck = await checkPackSkills(workspaceRoot);
-    checks.push(packCheck);
-    // RFC-0704: Check independent version packages — paths must exist and contain package.json
-    const independentCheck = await checkIndependentVersionPackages(workspaceRoot);
-    checks.push(independentCheck);
-    // RFC-0611: Check nested AGENTS.md — missing, stale, hand-written
-    // RFC-0640: Use profile-driven workspace types when available (all domains)
-    // RFC-0640 fix: previously gated by isSoftwareDomain, which skipped the check
-    // entirely for non-software domains. Now runs for all domains — profile-driven
-    // wsTypes replace hardcoded detection when present.
-    {
-        let wsTypes;
-        try {
-            const config = loadForgeConfig(workspaceRoot);
-            // RFC-0643: prefer config.profile (loaded by loadForgeConfig)
-            if (config.profile?.workspaceTypes && config.profile.workspaceTypes.length > 0) {
-                wsTypes = config.profile.workspaceTypes;
-            }
-            else {
-                const profiles = listStackProfiles(forgeRoot);
-                for (const stackId of config.project.stack) {
-                    const profile = profiles.find((p) => p.id === stackId);
-                    if (profile?.workspaceTypes && profile.workspaceTypes.length > 0) {
-                        wsTypes = profile.workspaceTypes;
-                        break;
-                    }
-                }
-            }
-        }
-        catch {
-            // profiles not loadable
-        }
-        const nestedCheck = await checkNestedAgentsMd(workspaceRoot, wsTypes);
-        checks.push(nestedCheck);
-    }
-    // RFC-0640: --strict flag elevates warn to fail for domain-related checks
-    const finalChecks = strict
-        ? checks.map((c) => c.status === "warn" &&
-            (c.name === "domain-invariants" || c.name === "profile-validate")
-            ? { ...c, status: "fail" }
-            : c)
-        : checks;
-    const allPass = finalChecks.every((c) => c.status === "pass");
-    const hasFails = finalChecks.some((c) => c.status === "fail");
-    if (outputFormat === "pretty") {
-        logger.section(`Forge Doctor — ${workspaceRoot}`);
-        for (const check of finalChecks) {
-            const icon = check.status === "pass" ? "✓" : check.status === "warn" ? "⚠" : "✖";
-            const fn = check.status === "pass" ? logger.success : check.status === "warn" ? logger.warn : logger.error;
-            fn(`${icon} ${check.name}: ${check.message}`);
-        }
-        if (allPass) {
-            logger.success("All checks passed — forge is properly configured.");
-        }
-        else if (hasFails) {
-            logger.error("Some checks failed — run 'forge create' to fix.");
-        }
-        else {
-            logger.warn("Some checks warn — review above.");
-        }
-    }
-    return {
-        data: { command: "forge.doctor", checks: finalChecks, allPass, forbiddenImports, bindings: bindingsResult, domain: domainReport },
-        exitCode: hasFails ? 1 : 0,
-        summary: allPass
-            ? "forge.doctor: all checks passed"
-            : `forge.doctor: ${finalChecks.filter((c) => c.status === "fail").length} fail(s), ${finalChecks.filter((c) => c.status === "warn").length} warn(s)`,
-    };
-}
-//# sourceMappingURL=doctor.js.map