@doidor/agentrig 0.9.0 → 0.11.0

package/dist/commands/update.js

@@ -1,7 +1,8 @@
 import { readFileSync, existsSync } from "node:fs";
 import { createHash } from "node:crypto";
 import { spawnSync } from "node:child_process";
-import { writeState, readState } from "../core/state.js";
+import { dirname } from "node:path";
+import { writeState, readState, lastReconciliationFor, } from "../core/state.js";
 import { loadManifest, refreshPolicy } from "../core/knowledge.js";
 import { install, baseVars, addOnlyCopy } from "../core/install.js";
 import { linkSurfaces } from "../core/surfaces.js";
@@ -14,34 +15,115 @@ import { getProvider } from "../agent/index.js";
 import { buildUpdatePrompt, SYSTEM_MESSAGE } from "../prompts/index.js";
 import { renderAudit } from "./eval.js";
 import { join } from "../core/fsutil.js";
+import { populateAgentsMarkers } from "../core/markers.js";
+import { runValidation } from "../core/validate.js";
+import { autoFix } from "../core/fix.js";
 import pkg from "../version.js";
 function hashFile(path) {
     if (!existsSync(path))
         return null;
     return createHash("sha256").update(readFileSync(path)).digest("hex");
 }
+function classifyDrift(repoFile, canonicalFile, brokenPaths, relPath) {
+    if (brokenPaths.has(relPath)) {
+        return { path: relPath, severity: "broken", reason: "fails YAML/syntax validation" };
+    }
+    const local = readFileSync(repoFile, "utf8");
+    const canonical = readFileSync(canonicalFile, "utf8");
+    if (local.includes(canonical.trim())) {
+        return { path: relPath, severity: "enhancement", reason: "local is a strict superset of canonical" };
+    }
+    if (canonical.includes(local.trim())) {
+        return { path: relPath, severity: "stale", reason: "canonical is a strict superset of local" };
+    }
+    return { path: relPath, severity: "mixed", reason: "both diverged independently" };
+}
+function severityBadge(s) {
+    switch (s) {
+        case "broken": return color.red("🔴 broken");
+        case "stale": return color.yellow("🟡 stale");
+        case "enhancement": return color.green("🟢 enhancement");
+        case "mixed": return color.dim("⚪ mixed");
+    }
+}
 /** Read-only: show how preserved (tailorable) files differ from the latest canonical version. */
 function diffPreserved(repoRoot) {
     const manifest = loadManifest();
+    const validation = runValidation(repoRoot);
+    const brokenPaths = new Set([...validation.yaml.map((y) => y.path)]);
     const preserved = manifest.artifacts.filter((a) => a.kind !== "template" && refreshPolicy(a) === "preserve");
-    let any = false;
+    const classified = [];
+    const driftInfos = [];
     for (const a of preserved) {
         const { drifted } = addOnlyCopy(repoRoot, resolveSrc(a.src), join(repoRoot, a.dest), a.mode, false);
         for (const relPath of drifted) {
-            any = true;
-            const repoFile = join(repoRoot, relPath);
-            // Map the drifted repo-relative path back to its canonical source file.
             const sub = relPath.slice(a.dest.length).replace(/^\//, "");
             const canonical = sub ? join(resolveSrc(a.src), sub) : resolveSrc(a.src);
-            log.info(color.bold(`\n• ${relPath}`) + color.dim("  (preserved; canonical drifted)"));
-            const res = spawnSync("diff", ["-u", "--label", "canonical", canonical, "--label", relPath, repoFile], { encoding: "utf8" });
-            log.info(res.stdout ? res.stdout.trimEnd() : color.dim("  (binary or unreadable diff)"));
+            driftInfos.push({ rel: relPath, canonical });
+            classified.push(classifyDrift(join(repoRoot, relPath), canonical, brokenPaths, relPath));
         }
     }
-    if (!any)
+    if (classified.length === 0) {
         log.ok("no preserved files have drifted from canonical.");
+        return 0;
+    }
+    // Summary first: counts per severity, then the unified diffs grouped by severity.
+    const counts = { broken: 0, stale: 0, enhancement: 0, mixed: 0 };
+    for (const c of classified)
+        counts[c.severity]++;
+    log.info(color.bold("Drift summary"));
+    log.info(`  ${severityBadge("broken")}: ${counts.broken}   ${severityBadge("stale")}: ${counts.stale}   ${severityBadge("enhancement")}: ${counts.enhancement}   ${severityBadge("mixed")}: ${counts.mixed}`);
+    log.info(color.dim("  🔴 fails validation — run `agentrig fix` to restore from canonical."));
+    log.info(color.dim("  🟡 canonical has new content your file lacks — review for merge."));
+    log.info(color.dim("  🟢 your file is a superset of canonical — likely safe to keep."));
+    log.info(color.dim("  ⚪ both diverged independently — needs reconciliation."));
+    const order = ["broken", "stale", "mixed", "enhancement"];
+    for (const sev of order) {
+        const group = classified.filter((c) => c.severity === sev);
+        if (!group.length)
+            continue;
+        log.info("");
+        log.info(color.bold(`${severityBadge(sev)} (${group.length})`));
+        for (const c of group) {
+            const info = driftInfos.find((d) => d.rel === c.path);
+            const repoFile = join(repoRoot, c.path);
+            log.info(color.bold(`\n• ${c.path}`) + color.dim(`  — ${c.reason}`));
+            const res = spawnSync("diff", ["-u", "--label", "canonical", info.canonical, "--label", c.path, repoFile], { encoding: "utf8" });
+            log.info(res.stdout ? res.stdout.trimEnd() : color.dim("  (binary or unreadable diff)"));
+        }
+    }
     return 0;
 }
+/** Group a list of repo-relative paths by parent directory for readable enumeration. */
+function groupByDir(paths) {
+    const out = new Map();
+    for (const p of paths.sort()) {
+        const dir = dirname(p) || ".";
+        const list = out.get(dir) ?? [];
+        list.push(p);
+        out.set(dir, list);
+    }
+    return out;
+}
+/** Print `count file(s)` with parent-dir grouping when there are more than a handful. */
+function logFileList(label, paths) {
+    if (paths.length === 0)
+        return;
+    if (paths.length <= 6) {
+        log.info(color.dim(`  ${label}:`));
+        for (const p of paths)
+            log.info(color.dim(`    · ${p}`));
+        return;
+    }
+    log.info(color.dim(`  ${label} (grouped):`));
+    for (const [dir, list] of groupByDir(paths)) {
+        log.info(color.dim(`    · ${dir}/  (${list.length})`));
+        for (const p of list.slice(0, 3))
+            log.info(color.dim(`        ${p}`));
+        if (list.length > 3)
+            log.info(color.dim(`        … and ${list.length - 3} more`));
+    }
+}
 /**
  * Re-sync the latest canonical best practices into a repo. Machinery files are overwritten;
  * tailorable artifacts are refreshed add-only (new files added, existing ones preserved) with any
@@ -94,13 +176,11 @@ export async function updateCommand(repoRoot, options) {
         }
         if (added.length) {
             log.step("dry run — would add new files:");
-            for (const f of added)
-                log.info(`  ${f}`);
+            logFileList("new", added);
         }
         if (drifted.length) {
             log.step("dry run — preserved (local edits kept); agent would reconcile canonical drift:");
-            for (const f of drifted)
-                log.info(color.dim(`  ${f}`));
+            logFileList("preserved", drifted);
         }
         log.step("dry run — agent would reconcile templates:");
         for (const t of templates)
@@ -112,15 +192,32 @@ export async function updateCommand(repoRoot, options) {
     const onlyOverwrite = { ...manifest, artifacts: toOverwrite };
     const { installed } = install(repoRoot, onlyOverwrite, { vars: baseVars(repoRoot), preserve: false });
     log.ok(`overwrote ${installed.length} owned file(s); added ${added.length} new file(s); preserved ${drifted.length} edited file(s)`);
+    logFileList("added", added);
+    if (drifted.length)
+        logFileList("preserved (canonical drifted)", drifted);
     // Ensure vendor-surface symlinks exist (added in later knowledge versions).
     const surfaces = linkSurfaces(repoRoot);
     if (surfaces.created.length)
         log.ok(`linked surfaces: ${surfaces.created.join(", ")} → .agents`);
+    // Repopulate deterministic marker blocks in AGENTS.md BEFORE compile — `compile` does this too
+    // but reading from a fresh skills inventory here guarantees the downstream projections see it
+    // even when AGENTS.md was a preserved (drifted) file and compile's projection picks up the
+    // marker-refreshed body.
+    const markerReport = populateAgentsMarkers(repoRoot);
+    if (markerReport.updated.length) {
+        log.ok(`AGENTS.md: refreshed marker block${markerReport.updated.length === 1 ? "" : "s"} — ${markerReport.updated.join(", ")}`);
+    }
     // Re-project the canonical source into every agent surface (local + remote).
     const compiled = compileSurfaces(repoRoot);
     log.ok(`compiled ${compiled.generated.length} agent-surface file(s)`);
-    // The agent reconciles templates plus any preserved files whose canonical version drifted.
-    const reconcileList = [...drifted, ...templates];
+    // The agent reconciles templates plus any preserved files whose canonical version drifted —
+    // but skip files the user has already consciously diverged on AGAINST the same canonical hash.
+    const reconcileNeeded = drifted.filter((rel) => !alreadyDivergedOn(repoRoot, state, rel, refreshable));
+    const skippedFromReconcile = drifted.filter((rel) => alreadyDivergedOn(repoRoot, state, rel, refreshable));
+    if (skippedFromReconcile.length) {
+        log.info(color.dim(`  skipping ${skippedFromReconcile.length} file(s) you previously chose to keep local; canonical hasn't changed since then.`));
+    }
+    const reconcileList = [...reconcileNeeded, ...templates];
     if (!options.skipAgent) {
         const provider = getProvider();
         const pre = await provider.preflight();
@@ -151,21 +248,60 @@ export async function updateCommand(repoRoot, options) {
         }
     }
     else if (drifted.length) {
-        log.warn(`--skip-agent: ${drifted.length} edited file(s) were preserved; canonical updates to them were NOT applied.`);
+        log.warn(`--skip-agent: ${drifted.length} edited file(s) were preserved; canonical updates to them were NOT applied:`);
+        logFileList("not reconciled", drifted);
         log.warn("Run `agentrig update` (with the agent) to reconcile them, or diff against the templates manually.");
     }
+    // Validate the refreshed install. Hard failures (broken YAML, unknown model id) are fatal
+    // unless --auto-fix was passed, in which case we self-heal here.
+    const validation = runValidation(repoRoot);
+    if (validation.hasBlockers) {
+        log.info("");
+        if (options.autoFix) {
+            log.step("validation found blockers; --auto-fix applying deterministic repairs…");
+            const fix = autoFix(repoRoot, { yamlFindings: validation.yaml, modelFindings: validation.models });
+            for (const a of fix.actions)
+                log.ok(`${a.path}: ${a.description}`);
+            for (const u of fix.unresolved)
+                log.warn(`unresolved: ${u.path} — ${u.reason}`);
+            if (fix.unresolved.length) {
+                log.error("auto-fix could not resolve every blocker; aborting.");
+                return 1;
+            }
+        }
+        else {
+            for (const y of validation.yaml)
+                log.error(`${y.path}: invalid YAML — ${y.error.split("\n")[0]}`);
+            for (const m of validation.models) {
+                const hint = m.suggestions.length ? `; did you mean ${m.suggestions.join(", ")}?` : "";
+                log.error(`${m.path}: unknown model "${m.value}"${hint}`);
+            }
+            log.error("Refusing to leave a broken install in place. Re-run with --auto-fix to repair from canonical, or `agentrig fix`.");
+            return 1;
+        }
+    }
     // Merge installed records: every refreshable artifact is present/current after update.
+    // Also append reconciliation records for every drifted file so a future update can know
+    // the user consciously chose to keep this version.
     const now = new Date().toISOString();
     const byId = new Map(state.installed.map((i) => [i.id, i]));
     for (const a of refreshable) {
         byId.set(a.id, { id: a.id, dest: a.dest, knowledgeVersion: manifest.knowledgeVersion, installedAt: now });
     }
+    const newReconciliations = drifted.map((rel) => ({
+        dest: rel,
+        knowledgeVersion: manifest.knowledgeVersion,
+        decision: "kept-local",
+        canonicalHash: canonicalHashFor(rel, refreshable) ?? "",
+        decidedAt: now,
+    }));
     const newState = {
         ...state,
         agentrigVersion: pkg.version,
         knowledgeVersion: manifest.knowledgeVersion,
         updatedAt: now,
         installed: [...byId.values()],
+        reconciled: [...(state.reconciled ?? []), ...newReconciliations],
     };
     writeState(repoRoot, newState);
     log.ok("updated .agentrig/state.json");
@@ -173,4 +309,34 @@ export async function updateCommand(repoRoot, options) {
     renderAudit(auditHarness(repoRoot));
     return 0;
 }
+/**
+ * Resolve the canonical source path for a repo-relative drifted file by scanning the manifest.
+ * Returns null when no canonical match exists (e.g. user-added file under a managed dir).
+ */
+function canonicalPathFor(rel, artifacts) {
+    for (const a of artifacts) {
+        if (a.dest === rel)
+            return resolveSrc(a.src);
+        if (a.kind === "dir" && rel.startsWith(`${a.dest}/`)) {
+            const sub = rel.slice(a.dest.length).replace(/^\//, "");
+            return join(resolveSrc(a.src), sub);
+        }
+    }
+    return null;
+}
+function canonicalHashFor(rel, artifacts) {
+    const p = canonicalPathFor(rel, artifacts);
+    return p ? hashFile(p) : null;
+}
+/**
+ * True when the user has previously chosen to keep their local copy of this file AND canonical
+ * hasn't changed since that decision. In that case we skip re-prompting on the next update.
+ */
+function alreadyDivergedOn(_repoRoot, state, rel, artifacts) {
+    const record = lastReconciliationFor(state, rel);
+    if (!record || record.decision !== "kept-local")
+        return false;
+    const currentCanonical = canonicalHashFor(rel, artifacts);
+    return Boolean(currentCanonical) && currentCanonical === record.canonicalHash;
+}
 //# sourceMappingURL=update.js.map

package/dist/commands/update.js.map

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package/dist/core/audit.js

@@ -1,7 +1,9 @@
 import { existsSync, statSync, readdirSync } from "node:fs";
 import { join, resolve } from "node:path";
+import YAML from "yaml";
 import { readText } from "./fsutil.js";
 import { loadCanonicalChecks } from "./knowledge.js";
+import { sameFamily } from "./model-family.js";
 function frontmatter(text) {
     if (!text || !text.startsWith("---"))
         return null;
@@ -53,7 +55,43 @@ function scoreCheck(repoRoot, c) {
                 ? { score: 1, evidence: "" }
                 : { score: 0.5, evidence: `missing keys: ${missing.join(", ")}` };
         }
+        case "frontmatter-keys-all": {
+            // Walk every <dir>/<entry>/<file> and assert each has the required frontmatter keys.
+            // Catches the gap where today only one skill (self-verify) is spot-checked.
+            const dir = String(c.path);
+            const fileName = String(c.file ?? "SKILL.md");
+            const abs = rel(dir);
+            if (!existsSync(abs) || !statSync(abs).isDirectory()) {
+                return { score: 0, evidence: `missing dir ${dir}` };
+            }
+            const keys = c.keys ?? [];
+            const offenders = [];
+            for (const entry of readdirSync(abs)) {
+                if (entry.startsWith(".") || entry.startsWith("_"))
+                    continue;
+                const subAbs = join(abs, entry);
+                if (!statSync(subAbs).isDirectory())
+                    continue;
+                const filePath = join(subAbs, fileName);
+                if (!existsSync(filePath)) {
+                    offenders.push(`${entry}/${fileName} missing`);
+                    continue;
+                }
+                const fm = frontmatter(readText(filePath));
+                if (fm == null) {
+                    offenders.push(`${entry} no frontmatter`);
+                    continue;
+                }
+                const missing = keys.filter((k) => !new RegExp("^\\s*" + k + "\\s*:", "m").test(fm));
+                if (missing.length)
+                    offenders.push(`${entry} missing ${missing.join("/")}`);
+            }
+            if (offenders.length === 0)
+                return { score: 1, evidence: "" };
+            return { score: 0.5, evidence: offenders.join("; ") };
+        }
         case "roles-distinct-models": {
+            // Legacy: kept for back-compat. Prefer roles-distinct-families.
             const key = String(c.key ?? "model");
             const dev = extractValue(read(String(c.developer)), key);
             const rev = extractValue(read(String(c.reviewer)), key);
@@ -63,10 +101,220 @@ function scoreCheck(repoRoot, c) {
                 ? { score: 1, evidence: "" }
                 : { score: 0.5, evidence: `developer and reviewer share model "${dev}"` };
         }
+        case "roles-distinct-families": {
+            // The single-model-bias mitigation principle is about model FAMILIES, not exact ids.
+            // claude-sonnet-4.5 vs claude-sonnet-4.6 must FAIL here.
+            const key = String(c.key ?? "model");
+            const dev = extractValue(read(String(c.developer)), key);
+            const rev = extractValue(read(String(c.reviewer)), key);
+            if (!dev || !rev)
+                return { score: 0, evidence: "developer/reviewer model not declared" };
+            if (!sameFamily(dev, rev))
+                return { score: 1, evidence: "" };
+            return { score: 0, evidence: `developer "${dev}" and reviewer "${rev}" share a model family` };
+        }
+        case "state-machine-dag": {
+            // Structural: parse the state machine YAML and assert it actually IS a DAG with
+            // the minimum lifecycle present, instead of just substring-matching "states:".
+            const p = String(c.path);
+            const text = read(p);
+            if (text == null)
+                return { score: 0, evidence: `missing ${p}` };
+            let parsed;
+            try {
+                parsed = YAML.parse(text);
+            }
+            catch (e) {
+                return { score: 0, evidence: `${p} is not valid YAML: ${e.message}` };
+            }
+            const states = Array.isArray(parsed?.states) ? parsed.states : [];
+            const transitions = Array.isArray(parsed?.transitions) ? parsed.transitions : [];
+            const minStates = Number(c.minStates ?? 6);
+            const requirePath = String(c.requirePath ?? "queued->merged");
+            const problems = [];
+            if (states.length < minStates)
+                problems.push(`${states.length} states, need ≥${minStates}`);
+            const stateNames = new Set(states.map((s) => String(s?.name ?? "")).filter(Boolean));
+            const badTransitions = transitions.filter((t) => !t?.from || !t?.to || !t?.trigger);
+            if (badTransitions.length)
+                problems.push(`${badTransitions.length} transitions missing from/to/trigger`);
+            // BFS for the required path. The 'any' wildcard from-state acts as a universal source.
+            const [src, dst] = requirePath.split("->");
+            if (src && dst) {
+                const adj = new Map();
+                for (const t of transitions) {
+                    const from = String(t?.from ?? "");
+                    const to = String(t?.to ?? "");
+                    if (!from || !to)
+                        continue;
+                    if (from === "any") {
+                        for (const s of stateNames) {
+                            if (!adj.has(s))
+                                adj.set(s, new Set());
+                            adj.get(s).add(to);
+                        }
+                    }
+                    else {
+                        if (!adj.has(from))
+                            adj.set(from, new Set());
+                        adj.get(from).add(to);
+                    }
+                }
+                if (!hasPath(adj, src, dst))
+                    problems.push(`no path ${src}→${dst}`);
+            }
+            if (problems.length === 0)
+                return { score: 1, evidence: "" };
+            return { score: 0.5, evidence: problems.join("; ") };
+        }
+        case "quality-probe": {
+            // A handful of cheap content sanity checks (P1.4). Each probe has a `probe` kind.
+            const probe = String(c.probe ?? "");
+            const p = String(c.path ?? "");
+            switch (probe) {
+                case "no-unfilled-placeholders": {
+                    const text = read(p);
+                    if (text == null)
+                        return { score: 0, evidence: `missing ${p}` };
+                    // Strip ```code blocks``` and `inline code` before scanning, so the probe doesn't
+                    // false-positive on docs that *describe* placeholder syntax (e.g. "{{VAR}} substitution").
+                    const stripped = text
+                        .replace(/```[\s\S]*?```/g, "")
+                        .replace(/`[^`\n]*`/g, "");
+                    const tokens = stripped.match(/\{\{[A-Z_]+\}\}/g) ?? [];
+                    return tokens.length === 0
+                        ? { score: 1, evidence: "" }
+                        : { score: 0, evidence: `unfilled tokens in ${p}: ${[...new Set(tokens)].join(", ")}` };
+                }
+                case "axes-json-coherent": {
+                    const text = read(p);
+                    if (text == null)
+                        return { score: 0, evidence: `missing ${p}` };
+                    let j;
+                    try {
+                        j = JSON.parse(text);
+                    }
+                    catch (e) {
+                        return { score: 0, evidence: `${p} not valid JSON: ${e.message}` };
+                    }
+                    if (!j?.types)
+                        return { score: 0, evidence: `${p} missing "types"` };
+                    const issues = [];
+                    for (const [tname, t] of Object.entries(j.types)) {
+                        if (!t?.categories) {
+                            issues.push(`${tname}: no categories`);
+                            continue;
+                        }
+                        for (const [cname, cat] of Object.entries(t.categories)) {
+                            for (const [axis, spec] of Object.entries(cat)) {
+                                // Both shapes: v1 = ["CODE",...]; v2 = { codes: [...], weight, veto }
+                                const codes = Array.isArray(spec) ? spec : spec?.codes;
+                                if (!Array.isArray(codes) || codes.length === 0) {
+                                    issues.push(`${tname}/${cname}/${axis}: no issue codes`);
+                                }
+                            }
+                        }
+                    }
+                    return issues.length === 0
+                        ? { score: 1, evidence: "" }
+                        : { score: 0.5, evidence: issues.join("; ") };
+                }
+                case "checks-json-coherent": {
+                    const text = read(p);
+                    if (text == null)
+                        return { score: 0, evidence: `missing ${p}` };
+                    let j;
+                    try {
+                        j = JSON.parse(text);
+                    }
+                    catch (e) {
+                        return { score: 0, evidence: `${p} not valid JSON: ${e.message}` };
+                    }
+                    const checks = j?.checks ?? [];
+                    const knownTypes = new Set([
+                        "path-exists", "file-contains", "dir-min", "frontmatter-keys",
+                        "frontmatter-keys-all", "roles-distinct-models", "roles-distinct-families",
+                        "state-machine-dag", "quality-probe", "marker-populated",
+                    ]);
+                    const ids = checks.map((x) => x?.id ?? "");
+                    const dupIds = ids.filter((id, i) => id && ids.indexOf(id) !== i);
+                    const badTypes = checks.filter((x) => !knownTypes.has(String(x?.type ?? "")));
+                    const issues = [];
+                    if (dupIds.length)
+                        issues.push(`duplicate ids: ${[...new Set(dupIds)].join(", ")}`);
+                    if (badTypes.length)
+                        issues.push(`unknown check types: ${badTypes.map((x) => x?.type).join(", ")}`);
+                    return issues.length === 0
+                        ? { score: 1, evidence: "" }
+                        : { score: 0.5, evidence: issues.join("; ") };
+                }
+                case "context-md-present": {
+                    return existsSync(rel(p))
+                        ? { score: 1, evidence: "" }
+                        : { score: 0.5, evidence: `${p} missing — run \`agentrig init\` to investigate the repo` };
+                }
+                default:
+                    return { score: 0, evidence: `unknown quality probe "${probe}"` };
+            }
+        }
+        case "marker-populated": {
+            // Assert that an AGENTRIG:<name>:start/end block in AGENTS.md is non-empty AND, when a
+            // `enumerateDir` is supplied, mentions every entry under that directory. Catches the
+            // failure mode where the marker pair exists but nothing populates the body.
+            const p = String(c.path);
+            const name = String(c.marker ?? "");
+            const text = read(p);
+            if (text == null)
+                return { score: 0, evidence: `missing ${p}` };
+            const pair = new RegExp(`<!--\\s*AGENTRIG:${name.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}:start\\s*-->([\\s\\S]*?)<!--\\s*AGENTRIG:${name.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}:end\\s*-->`);
+            const m = text.match(pair);
+            if (!m)
+                return { score: 0, evidence: `marker pair AGENTRIG:${name} missing from ${p}` };
+            const body = m[1].trim();
+            if (!body || /\{\{[A-Z_]+\}\}/.test(body)) {
+                return { score: 0, evidence: `AGENTRIG:${name} block is empty or has unfilled placeholders` };
+            }
+            const enumerateDir = c.enumerateDir ? String(c.enumerateDir) : null;
+            if (enumerateDir) {
+                const abs = rel(enumerateDir);
+                if (!existsSync(abs) || !statSync(abs).isDirectory()) {
+                    // Nothing to enumerate — body just needs to be non-empty, which we already checked.
+                    return { score: 1, evidence: "" };
+                }
+                const required = readdirSync(abs).filter((e) => !e.startsWith(".") && !e.startsWith("_"));
+                const missing = required.filter((entry) => !body.includes(entry));
+                if (missing.length === 0)
+                    return { score: 1, evidence: "" };
+                return { score: 0.5, evidence: `block missing entries from ${enumerateDir}: ${missing.join(", ")}` };
+            }
+            return { score: 1, evidence: "" };
+        }
         default:
             return { score: 0, evidence: `unknown check type ${c.type}` };
     }
 }
+/** BFS path existence. Used by the state-machine-dag check. */
+function hasPath(adj, src, dst) {
+    if (src === dst)
+        return true;
+    const seen = new Set([src]);
+    const queue = [src];
+    while (queue.length) {
+        const cur = queue.shift();
+        const nexts = adj.get(cur);
+        if (!nexts)
+            continue;
+        for (const n of nexts) {
+            if (n === dst)
+                return true;
+            if (!seen.has(n)) {
+                seen.add(n);
+                queue.push(n);
+            }
+        }
+    }
+    return false;
+}
 /** Resolve which checks to use: prefer the repo's installed checks.json, else AgentRig canonical. */
 function resolveChecks(repoRoot) {
     const repoChecks = readText(join(repoRoot, ".agentrig", "eval", "checks.json"));
@@ -84,24 +332,36 @@ export function auditHarness(repoRoot) {
     const { checks, source } = resolveChecks(repoRoot);
     const results = checks.map((c) => {
         const { score, evidence } = scoreCheck(repoRoot, c);
-        return { id: c.id, principle: c.principle, title: c.title, score, evidence };
+        // Default layer is "completeness" so unannotated check files still work.
+        const layer = c.layer === "quality" ? "quality" : "completeness";
+        return { id: c.id, principle: c.principle, title: c.title, score, evidence, layer };
     });
-    let wSum = 0;
-    let wScore = 0;
+    let cwSum = 0, cwScore = 0; // completeness
+    let qwSum = 0, qwScore = 0; // quality
     const principleAcc = new Map();
     for (let i = 0; i < results.length; i++) {
+        const r = results[i];
         const w = Number(checks[i].weight ?? 1);
-        wSum += w;
-        wScore += w * results[i].score;
-        const acc = principleAcc.get(results[i].principle) ?? { sum: 0, n: 0 };
-        acc.sum += results[i].score;
+        if (r.layer === "quality") {
+            qwSum += w;
+            qwScore += w * r.score;
+        }
+        else {
+            cwSum += w;
+            cwScore += w * r.score;
+        }
+        const acc = principleAcc.get(r.principle) ?? { sum: 0, n: 0 };
+        acc.sum += r.score;
         acc.n += 1;
-        principleAcc.set(results[i].principle, acc);
+        principleAcc.set(r.principle, acc);
     }
-    const aggregate = wSum ? wScore / wSum : 0;
+    const aggregate = cwSum ? cwScore / cwSum : 0;
+    const qualityAggregate = qwSum ? qwScore / qwSum : 0;
     return {
         harnessScore: Math.round(aggregate * 1000) / 10,
         aggregate,
+        qualityScore: Math.round(qualityAggregate * 1000) / 10,
+        qualityAggregate,
         results,
         byPrinciple: [...principleAcc.entries()]
             .sort((a, b) => a[0] - b[0])