@shrkcrft/inspector 0.1.0-alpha.29 → 0.1.0-alpha.31

package/dist/self-config-doctor-v2.js

@@ -17,16 +17,32 @@
  */
 import { existsSync } from 'node:fs';
 import * as nodePath from 'node:path';
+import { coverageShortfall, DEAD_SELECTOR_CAUSES, formatCoverage, RejectionCause, settleUnitLiveness, UnitDeadCause, UnitDeadWeight, UnitLivenessState, } from '@shrkcrft/core';
+import { searchTuningKeyProbes } from "./search-tuning-key-probes.js";
+import { ContributionKind } from "./contribution-kind.js";
+import { resolveEntryFile } from "./contribution-load-failures.js";
+import { UnresolvableReason } from "./unresolvable-reason.js";
+import { listTaskRoutingHintIssues, loadTaskRoutingHints, listTaskRoutingHints, routingHintCanMatch, } from "./task-routing-hint-registry.js";
+import { buildRegistrationHintDoctorReport, listRegistrationHints } from "./registration-hint-registry.js";
+import { listDecisions, loadTsDecisions } from "./decision-records.js";
+import { COMMAND_INDEX_NOT_INJECTED, emptyReferenceKinds, hasCommandResolver, referenceIdExists, referenceIdsFor, referenceKindsOf, resolveCommandReference, resolveShrkCommandReference, warmReferenceRegistries, } from "./reference-registry.js";
+import { nearestIds } from "./nearest-id.js";
+import { formatReferenceKindDeclaration, isReferenceKindDeclarable, referenceKindListVerb, } from "./reference-kind-declarations.js";
+import { PROBED_ID_FIELDS } from "./probed-id-fields.js";
+import { ProbedIdSource } from "./probed-id-source.js";
 import { listConventions } from "./convention-registry.js";
-import { loadAllContractTemplates } from "./contract-template-registry.js";
-import { listMigrationProfilesFromPacks } from "./migration-profile-registry.js";
-import { listPackHelpers } from "./pack-helper-registry.js";
-import { HELPERS } from "./helper-registry.js";
-import { listTaskRoutingHints } from "./task-routing-hint-registry.js";
-import { listRegistrationHints } from "./registration-hint-registry.js";
-import { listDecisions } from "./decision-records.js";
-import { listPlaybooks } from "./playbook-registry.js";
-import { buildPackContributionsInventory } from "./pack-contributions-inventory.js";
+import { ROUTING_RECOMMENDS_CHANNEL_KEYS, ROUTING_RECOMMENDS_CHANNELS, } from "./routing-recommends-channels.js";
+import { doctorScaffoldPatterns, enumerateScaffoldPatternCandidates, loadScaffoldPatternsFromInspection, scaffoldPatternCoverage, } from "./scaffold-patterns.js";
+import { lintSearchTuning } from "./search-tuning-lint.js";
+import { listSearchTuningIssues, loadSearchTuning } from "./search-tuning-registry.js";
+import { resolveSearchTuningKey } from "./search-tuning-key-resolver.js";
+import { SearchTuningKeyStatus } from "./search-tuning-key-status.js";
+import { CommandResolutionStatus } from "./command-resolution-status.js";
+import { collectDeclaredXrefs, declaredXrefCoverage, declaredXrefSummaryLine, } from "./declared-cross-references.js";
+import { DeclaredXrefStatus } from "./declared-xref-status.js";
+import { listConstructs } from "./construct-registry.js";
+import { listPlaybooks, loadPlaybooksWithIssues } from "./playbook-registry.js";
+import { buildPackContributionsInventoryAsync, } from "./pack-contributions-inventory.js";
 export const SELF_CONFIG_DOCTOR_V2_SCHEMA = 'sharkcraft.self-config-doctor/v2';
 export var SelfConfigSeverityV2;
 (function (SelfConfigSeverityV2) {
@@ -35,86 +51,61 @@ export var SelfConfigSeverityV2;
     SelfConfigSeverityV2["Error"] = "error";
 })(SelfConfigSeverityV2 || (SelfConfigSeverityV2 = {}));
 async function buildLookupsV2(inspection) {
-    const knowledge = new Set(inspection.knowledgeEntries.map((k) => k.id));
-    const rules = new Set((inspection.ruleService?.list?.() ?? []).map((r) => r.id));
-    const paths = new Set((inspection.pathService?.list?.() ?? []).map((p) => p.id));
-    const templates = new Set(inspection.templateRegistry?.list?.().map((t) => t.id) ?? []);
-    const pipelines = new Set(inspection.pipelineRegistry?.list?.().map((p) => p.id) ?? []);
-    const conventions = new Set((await listConventions(inspection)).map((e) => e.convention.id));
-    const contractTemplatesPair = await loadAllContractTemplates(inspection);
-    const contractTemplates = new Set(contractTemplatesPair.entries.map((e) => e.template.id));
-    const migrationProfiles = new Set((await listMigrationProfilesFromPacks(inspection)).map((p) => p.id));
-    const helpers = new Set([
-        ...HELPERS.map((h) => h.id),
-        ...(await listPackHelpers(inspection)).map((e) => e.helper.id),
-    ]);
-    const routingHints = new Set((await listTaskRoutingHints(inspection)).map((e) => e.hint.id));
-    const registrationHints = new Set((await listRegistrationHints(inspection)).map((e) => e.hint.id));
-    let playbooks;
-    try {
-        const pb = await listPlaybooks(inspection);
-        playbooks = new Set(pb.map((p) => p.id));
-    }
-    catch {
-        playbooks = new Set();
-    }
-    // Policies surface through the pack contributions inventory; the policy
-    // engine itself runs side-effects we want to avoid here.
-    const policies = new Set();
-    try {
-        const inv = buildPackContributionsInventory(inspection);
-        for (const entry of inv.entriesByKind['policy'] ?? [])
-            policies.add(entry.id);
-    }
-    catch {
-        // ignore
-    }
-    const decisions = new Set();
-    try {
-        for (const d of listDecisions(inspection))
-            decisions.add(d.id);
-    }
-    catch {
-        // ignore
-    }
-    // Commands & MCP tools — taken from the catalog / repository commands
-    // surface. Best-effort; if registries are absent the sets stay empty and
-    // the corresponding checks degrade to info-level.
-    const commands = new Set();
-    const mcpTools = new Set();
-    try {
-        const repoCmds = inspection.repositoryCommands;
-        for (const c of repoCmds ?? [])
-            commands.add(c.id);
-    }
-    catch {
-        // ignore
-    }
+    // Every set is a projection of the SHARED reference registry — the same
+    // module the prose linter and the structured-`references[]` validator use.
+    //
+    // These sets used to be built here from their own sources, and the doc claim
+    // "there is one definition of does-this-id-exist, not two" was true only by
+    // coincidence. It was not always true: `policies` came from the pack
+    // contributions inventory alone, so every LOCALLY declared policy read as
+    // unknown; `scaffoldPatterns` had no set at all; `commands` read a
+    // `repositoryCommands` property nothing assigns. Seven of shrk's own
+    // correctly-registered ids were reported missing.
+    await warmReferenceRegistries(inspection);
+    const ids = (kind) => new Set(referenceIdsFor(inspection, kind));
     return {
-        knowledge,
-        rules,
-        paths,
-        templates,
-        pipelines,
-        policies,
-        playbooks,
-        conventions,
-        contractTemplates,
-        migrationProfiles,
-        helpers,
-        routingHints,
-        registrationHints,
-        decisions,
-        commands,
-        mcpTools,
+        knowledge: ids('knowledge'),
+        rules: ids('rule'),
+        paths: ids('path-convention'),
+        templates: ids('template'),
+        pipelines: ids('pipeline'),
+        policies: ids('policy'),
+        playbooks: ids('playbook'),
+        conventions: ids('convention'),
+        contractTemplates: ids('contract-template'),
+        helpers: ids('helper'),
+        routingHints: ids('routing-hint'),
+        registrationHints: ids('registration-hint'),
+        decisions: ids('decision'),
+        scaffoldPatterns: ids('scaffold-pattern'),
+        // No `commands` set: it was initialised EMPTY (the command index lives in
+        // the CLI, above this layer), so every command in every hint and agent test
+        // was reported missing — correct ones included, and an agent test's correct
+        // `expectedCommands` failed the doctor at error severity. Commands resolve
+        // through the injected resolver instead — see `checkCommandStrings`.
     };
 }
 function findingId(parts) {
     return `${parts.sourceKind}:${parts.sourceId}|${parts.relation}|${parts.targetKind}:${parts.targetId}`;
 }
+/**
+ * Append a finding — or MERGE it into an existing one with the same id and
+ * code (bumping `occurrences`), so the documented unique id is unique for
+ * every check. The same tuning key in three task hints used to be three
+ * identical warnings sharing one id. A same-id finding with a DIFFERENT code
+ * keeps its own entry, its id suffixed with `|<code>`.
+ */
 function pushFinding(out, input) {
+    const baseId = findingId(input);
+    const codedId = `${baseId}|${input.code}`;
+    const same = out.findIndex((f) => (f.id === baseId || f.id === codedId) && f.code === input.code);
+    if (same >= 0) {
+        const prev = out[same];
+        out[same] = { ...prev, occurrences: (prev.occurrences ?? 1) + (input.occurrences ?? 1) };
+        return;
+    }
     const entry = {
-        id: findingId(input),
+        id: out.some((f) => f.id === baseId) ? codedId : baseId,
         severity: input.severity,
         code: input.code,
         sourceKind: input.sourceKind,
@@ -127,9 +118,231 @@ function pushFinding(out, input) {
         ...(input.file !== undefined ? { file: input.file } : {}),
         ...(input.suggestedFix !== undefined ? { suggestedFix: input.suggestedFix } : {}),
         ...(input.nextCommand !== undefined ? { nextCommand: input.nextCommand } : {}),
+        ...(input.occurrences !== undefined && input.occurrences > 1 ? { occurrences: input.occurrences } : {}),
     };
     out.push(entry);
 }
+function severityV2(s) {
+    return s === 'error'
+        ? SelfConfigSeverityV2.Error
+        : s === 'warning'
+            ? SelfConfigSeverityV2.Warning
+            : SelfConfigSeverityV2.Info;
+}
+/**
+ * THE reference-kind → finding-kind table: every kind maps onto ITSELF. The
+ * mapped type makes a kind added to `ReferenceKind` without a row here a
+ * compile error, and a row naming a kind `SelfConfigKind` lacks a compile error
+ * in `selfKindOf`. This was a `switch` whose default was `'unknown'`, so any
+ * kind it forgot rendered every resolvable id of that kind `unknown:`.
+ */
+const SELF_KIND_OF_REFERENCE_KIND = Object.freeze({
+    file: 'file',
+    directory: 'directory',
+    symbol: 'symbol',
+    command: 'command',
+    package: 'package',
+    url: 'url',
+    template: 'template',
+    pipeline: 'pipeline',
+    playbook: 'playbook',
+    policy: 'policy',
+    construct: 'construct',
+    helper: 'helper',
+    'boundary-rule': 'boundary-rule',
+    'path-convention': 'path-convention',
+    rule: 'rule',
+    knowledge: 'knowledge',
+    decision: 'decision',
+    convention: 'convention',
+    'contract-template': 'contract-template',
+    'migration-profile': 'migration-profile',
+    'workspace-profile': 'workspace-profile',
+    'routing-hint': 'routing-hint',
+    'registration-hint': 'registration-hint',
+    'scaffold-pattern': 'scaffold-pattern',
+});
+/** The ONE place a finding's `unknown` kind comes from: a target THE resolvers placed in no registry. */
+const RESOLVED_NOWHERE = 'unknown';
+/**
+ * A reference kind's finding kind. `undefined` — the caller's resolver placed
+ * the id in NO registry — is `unknown`, and nothing else is: a caller holding a
+ * resolvable id must pass the kind it resolved in (round 12, 12.4).
+ */
+function selfKindOf(kind) {
+    return kind === undefined ? RESOLVED_NOWHERE : SELF_KIND_OF_REFERENCE_KIND[kind];
+}
+/** The `<field>` a validator issue message (`<field>: <message>`) names. */
+function validatorField(message) {
+    const at = message.indexOf(':');
+    return at > 0 ? message.slice(0, at) : message;
+}
+/**
+ * THE contribution kind → rejection-finding table (round 12, 12.1): the
+ * finding kind a rejected entry is labelled with (also its code prefix,
+ * `<kind>-invalid` / `<kind>-duplicate-id`) and the doctor that shows the
+ * loader's own view of it. A mapped type over the enum: a contribution kind
+ * without a row is a compile error, so a new kind can never fall to a borrowed
+ * label (the `unknown:` alarm of 12.4). The routing / registration hint codes
+ * (`routing-hint-invalid`, `registration-hint-duplicate-id`, …) are the ones
+ * those families always emitted.
+ */
+const REJECTION_FINDING = Object.freeze({
+    [ContributionKind.Knowledge]: { kind: 'knowledge', doctor: 'shrk doctor' },
+    [ContributionKind.Rule]: { kind: 'rule', doctor: 'shrk doctor' },
+    [ContributionKind.Path]: { kind: 'path-convention', doctor: 'shrk doctor' },
+    [ContributionKind.PathConvention]: { kind: 'path-convention', doctor: 'shrk doctor' },
+    [ContributionKind.Docs]: { kind: 'docs', doctor: 'shrk doctor' },
+    [ContributionKind.Template]: { kind: 'template', doctor: 'shrk templates doctor' },
+    [ContributionKind.Pipeline]: { kind: 'pipeline', doctor: 'shrk pipelines list' },
+    [ContributionKind.Preset]: { kind: 'preset', doctor: 'shrk presets list' },
+    [ContributionKind.Boundary]: { kind: 'boundary-rule', doctor: 'shrk check boundaries' },
+    [ContributionKind.ScaffoldPattern]: { kind: 'scaffold-pattern', doctor: 'shrk scaffolds doctor' },
+    [ContributionKind.Policy]: { kind: 'policy', doctor: 'shrk policy list' },
+    [ContributionKind.Construct]: { kind: 'construct', doctor: 'shrk constructs list' },
+    [ContributionKind.ConstructFacet]: { kind: 'construct-facet', doctor: 'shrk constructs list' },
+    [ContributionKind.Playbook]: { kind: 'playbook', doctor: 'shrk playbooks list' },
+    [ContributionKind.SearchTuning]: { kind: 'search-tuning', doctor: 'shrk search tuning doctor' },
+    [ContributionKind.FeedbackRule]: { kind: 'feedback-rule', doctor: 'shrk packs contributions' },
+    [ContributionKind.Decision]: { kind: 'decision', doctor: 'shrk packs contributions' },
+    [ContributionKind.ContractTemplate]: { kind: 'contract-template', doctor: 'shrk contract template list' },
+    [ContributionKind.MigrationProfile]: { kind: 'migration-profile', doctor: 'shrk profiles doctor' },
+    [ContributionKind.ContextTest]: { kind: 'context-test', doctor: 'shrk test context' },
+    [ContributionKind.AgentTest]: { kind: 'agent-test', doctor: 'shrk test agent' },
+    [ContributionKind.Helper]: { kind: 'helper', doctor: 'shrk helper doctor' },
+    [ContributionKind.TaskRoutingHint]: { kind: 'routing-hint', doctor: 'shrk packs contributions' },
+    [ContributionKind.RegistrationHint]: { kind: 'registration-hint', doctor: 'shrk registrations doctor' },
+    [ContributionKind.Convention]: { kind: 'convention', doctor: 'shrk conventions doctor' },
+    [ContributionKind.DelegateRecipe]: { kind: 'delegate-recipe', doctor: 'shrk packs contributions' },
+    [ContributionKind.FrameworkExtractor]: { kind: 'framework-extractor', doctor: 'shrk packs contributions' },
+    [ContributionKind.WiringRule]: { kind: 'wiring-rule', doctor: 'shrk gates coverage' },
+    [ContributionKind.Registry]: { kind: 'registry', doctor: 'shrk gates coverage' },
+    [ContributionKind.RegistrationIdiom]: { kind: 'registration-idiom', doctor: 'shrk gates coverage' },
+    [ContributionKind.PolicyRule]: { kind: 'policy-rule', doctor: 'shrk gates coverage' },
+    [ContributionKind.ReusePrimitive]: { kind: 'reuse-primitive', doctor: 'shrk reuse coverage' },
+    [ContributionKind.Baseline]: { kind: 'baseline', doctor: 'shrk gates coverage' },
+    [ContributionKind.GeneratedArtifact]: { kind: 'generated-artifact', doctor: 'shrk gates coverage' },
+    [ContributionKind.DocReference]: { kind: 'doc-reference', doctor: 'shrk docs references check' },
+});
+/** A rejected entry's finding kind and code — THE table above, never a fallback. */
+export function rejectionFindingOf(kind, cause) {
+    const row = REJECTION_FINDING[kind];
+    return {
+        kind: row.kind,
+        code: `${row.kind}-${cause === RejectionCause.DuplicateId ? 'duplicate-id' : 'invalid'}`,
+        doctor: row.doctor,
+    };
+}
+function newIdProbe() {
+    return {
+        probed: 0,
+        resolved: 0,
+        missing: 0,
+        unverified: 0,
+        unverifiedLabels: [],
+        unverifiedRefs: [],
+        emptyKinds: [],
+    };
+}
+/**
+ * The loud-skip reason. It names how to fill each empty kind, from THE
+ * declaration table (`REFERENCE_KIND_DECLARATIONS`), so a NOT VERIFIED unit is
+ * actionable instead of a dead end: `… — declare migration-profile via pack
+ * key migrationProfileFiles · sharkcraft/migration-profiles.ts …`.
+ */
+function emptyRegistryReason(probe) {
+    const base = "could not be checked (their kind's registry is empty in this workspace";
+    if (probe.emptyKinds.length === 0)
+        return `${base})`;
+    const how = probe.emptyKinds.map((k) => `${k} via ${formatReferenceKindDeclaration(k)}`).join('; ');
+    return `${base} — declare ${how})`;
+}
+/** Read a dotted id-list field (`discovery.profileIds`) off an asset; anything but an array reads as absent. */
+function readIdList(asset, field) {
+    let cur = asset;
+    for (const part of field.split('.')) {
+        if (!cur || typeof cur !== 'object')
+            return undefined;
+        cur = cur[part];
+    }
+    return Array.isArray(cur) ? cur : undefined;
+}
+/** How a `*-missing` message ends: a workspace profile id is a vocabulary word, not a registration. */
+function notResolvedTail(kind) {
+    return kind === 'workspace-profile' ? ', which is not a WorkspaceProfile id' : ' but it is not registered';
+}
+/**
+ * THE "this finding reports a reference that resolved nowhere" predicate: a
+ * `*-missing` code (an id, or a referenced file), any severity — the family
+ * r73 reads as "unknown id". The CLI's exit-0 line counts the INFO-severity
+ * ones instead of certifying "every checked probe resolved" over them.
+ */
+export function isUnresolvedReferenceFinding(finding) {
+    return finding.code.endsWith('-missing');
+}
+/**
+ * THE "this reference resolved, but only as a kind its field does not accept"
+ * predicate: a `*-wrong-kind` code (`xref-wrong-kind`, a pipeline step naming a
+ * construct). Not unresolved — `unknown:` is reserved for that — and not a
+ * clean resolution either, so the CLI's exit-0 line counts an info-severity one
+ * instead of certifying "every checked probe resolved".
+ */
+export function isWrongKindReferenceFinding(finding) {
+    return finding.code.endsWith('-wrong-kind');
+}
+function probeIds(inspection, kind, ids, probe, label, onMissing, site) {
+    if (!Array.isArray(ids) || ids.length === 0)
+        return;
+    const empty = emptyReferenceKinds(inspection, [kind]).length > 0;
+    for (const raw of ids) {
+        if (typeof raw !== 'string' || raw.length === 0)
+            continue;
+        probe.probed += 1;
+        if (empty) {
+            probe.unverified += 1;
+            probe.unverifiedLabels.push(label(raw));
+            if (site) {
+                probe.unverifiedRefs.push({
+                    ...(site.file ? { file: resolveEntryFile(inspection, site.file, site.packageName) } : {}),
+                    ...(site.packageName ? { packageName: site.packageName } : {}),
+                    sourceKind: site.sourceKind,
+                    sourceId: site.sourceId,
+                    field: site.field,
+                    kind,
+                    id: raw,
+                    // THE declarability authority: an empty registry nothing can EVER
+                    // fill is a different fact from one this workspace has not filled.
+                    reason: isReferenceKindDeclarable(kind) ? UnresolvableReason.RegistryEmpty : UnresolvableReason.UndeclarableKind,
+                });
+            }
+            if (!probe.emptyKinds.includes(kind))
+                probe.emptyKinds.push(kind);
+            continue;
+        }
+        if (referenceIdExists(inspection, kind, raw)) {
+            probe.resolved += 1;
+            continue;
+        }
+        probe.missing += 1;
+        onMissing(raw, nearestIds(raw, referenceIdsFor(inspection, kind), 1)[0]?.id);
+    }
+}
+function idProbeCoverage(subject, unit, probe) {
+    if (probe.probed === 0)
+        return [];
+    return [
+        {
+            subject,
+            unit,
+            expected: probe.probed,
+            examined: probe.probed - probe.unverified,
+            ...(probe.unverified > 0
+                ? { unexamined: probe.unverifiedLabels.slice(0, 20), unexaminedTotal: probe.unverified }
+                : {}),
+            reason: emptyRegistryReason(probe),
+        },
+    ];
+}
 // ─── 1. Knowledge → file references ───────────────────────────────────────
 function checkKnowledgeFileRefs(inspection, findings) {
     for (const k of inspection.knowledgeEntries) {
@@ -159,41 +372,182 @@ function checkKnowledgeFileRefs(inspection, findings) {
         }
     }
 }
-// ─── 2. Search-tuning targets ─────────────────────────────────────────────
-async function checkSearchTuning(inspection, lookups, findings) {
-    const { listSearchTuning } = await import("./search-tuning-registry.js");
-    const entries = listSearchTuning(inspection);
-    for (const entry of entries) {
-        const boostMaps = [entry.boostIds, ...(entry.taskHints ?? []).map((h) => h.boostIds)];
-        for (const idMap of boostMaps) {
-            if (!idMap)
-                continue;
-            for (const targetId of Object.keys(idMap)) {
-                const found = lookups.knowledge.has(targetId) ||
-                    lookups.rules.has(targetId) ||
-                    lookups.templates.has(targetId) ||
-                    lookups.pipelines.has(targetId) ||
-                    lookups.contractTemplates.has(targetId) ||
-                    lookups.conventions.has(targetId) ||
-                    lookups.playbooks.has(targetId) ||
-                    lookups.helpers.has(targetId) ||
-                    lookups.commands.has(targetId);
-                if (found)
-                    continue;
-                pushFinding(findings, {
-                    severity: SelfConfigSeverityV2.Warning,
-                    code: 'search-tuning-target-missing',
-                    sourceKind: 'unknown',
-                    sourceId: entry.id,
-                    targetKind: 'unknown',
-                    targetId,
-                    relation: 'tunes',
-                    file: entry.sourceFile,
-                    message: `Search tuning "${entry.id}" boosts unknown id "${targetId}".`,
-                    suggestedFix: 'Register the target id or remove the boost entry.',
-                });
-            }
+/**
+ * The search-tuning boost keys as a REFERENCE probe (round 13): the key probes
+ * THE lint judged (`searchTuningKeyProbes`), one per (entry, key), and every
+ * one THE key resolver could not check — its kind's registry is empty here
+ * (`registry-empty`), or its document kind has no id registry at all
+ * (`undeclarable-kind`, kind `search-document`). `packs contributions` reads
+ * this, so it and `search tuning doctor` can no longer disagree about the same
+ * contributed boost.
+ */
+function tuningReferenceProbe(inspection, probes) {
+    const probe = newIdProbe();
+    for (const p of probes) {
+        const r = p.resolution;
+        probe.probed += 1;
+        if (r.status === SearchTuningKeyStatus.Resolved)
+            probe.resolved += 1;
+        else if (r.status === SearchTuningKeyStatus.Missing)
+            probe.missing += 1;
+        if (r.status !== SearchTuningKeyStatus.Unverified)
+            continue;
+        const kind = r.referenceKind;
+        probe.unverified += 1;
+        probe.unverifiedLabels.push(`${p.tuningId} → ${kind ?? 'search-document'} ${kind !== undefined ? r.id : p.key}`);
+        probe.unverifiedRefs.push({
+            ...(p.sourceFile ? { file: resolveEntryFile(inspection, p.sourceFile, p.packageName) } : {}),
+            ...(p.packageName ? { packageName: p.packageName } : {}),
+            sourceKind: 'search-tuning',
+            sourceId: p.tuningId,
+            field: p.lists[0] ?? 'boostIds',
+            kind: kind ?? 'search-document',
+            id: kind !== undefined ? r.id : p.key,
+            reason: kind !== undefined && isReferenceKindDeclarable(kind)
+                ? UnresolvableReason.RegistryEmpty
+                : UnresolvableReason.UndeclarableKind,
+        });
+        if (kind !== undefined && !probe.emptyKinds.includes(kind))
+            probe.emptyKinds.push(kind);
+    }
+    return probe;
+}
+/**
+ * THE search-tuning lint (`lintSearchTuning`, shared with `shrk search tuning
+ * doctor`), each issue prefixed `search-tuning-`.
+ *
+ * A boost key is a search-document id, `<kind>:<id>`. This used to look the
+ * WHOLE prefixed key up in bare-id registries, so every correctly prefixed key
+ * (which fires) was reported missing and a bare key (which never fires)
+ * passed — the exact inverse of the truth. The key is now split on its first
+ * `:` and resolved within the named kind; a bare key is `key-unprefixed`.
+ */
+async function checkSearchTuning(inspection, findings) {
+    const lint = await lintSearchTuning(inspection);
+    for (const issue of lint.issues) {
+        const fix = issue.code === 'target-missing'
+            ? issue.suggestion
+                ? `Use "${issue.suggestion}", or register ${issue.referenceKind} "${issue.targetId}", or remove the boost.`
+                : `Register ${issue.referenceKind} "${issue.targetId}" or remove the boost.`
+            : issue.code === 'key-unprefixed' || issue.code === 'key-unknown-kind'
+                ? issue.suggestion
+                    ? `Rewrite the key as "${issue.suggestion}".`
+                    : 'Prefix the key with its document kind (`knowledge:`, `rule:`, `template:`, …) or remove it.'
+                : issue.suggestion
+                    ? `Did you mean "${issue.suggestion}"?`
+                    : undefined;
+        const target = searchTuningTarget(issue);
+        pushFinding(findings, {
+            severity: severityV2(issue.severity),
+            code: `search-tuning-${issue.code}`,
+            sourceKind: 'search-tuning',
+            sourceId: issue.tuningId,
+            targetKind: target.targetKind,
+            targetId: target.targetId,
+            relation: target.relation,
+            file: issue.source,
+            message: issue.message,
+            suggestedFix: fix,
+            nextCommand: 'shrk search tuning doctor',
+            occurrences: issue.occurrences,
+        });
+    }
+    return {
+        probes: lint.probes,
+        coverage: lint.coverage,
+        deadUnits: lint.deadUnits,
+        liveness: lint.liveness,
+        refProbe: tuningReferenceProbe(inspection, lint.keyProbes),
+    };
+}
+/**
+ * THE label of a search-tuning finding's target, in order:
+ *
+ *   1. a kind THE key resolver (or the index) placed it in → `<kind>:<id>`
+ *      (a missing / excluded / resolvable bare key, a capped document);
+ *   2. a document with no id registry, or the cap summary → `search-document`;
+ *   3. a key no registry can be asked about (`doc:`, `preset:`, …) →
+ *      `search-document`;
+ *   4. a key that resolves NOWHERE (a bare id no registry lists, an unknown
+ *      `<kind>:` prefix) → `unknown:<the whole key>` — the genuine case;
+ *   5. a declaration-shape finding (triggers, vocabulary) → `schema:<field>`.
+ *
+ * Everything without a `referenceKind` used to fall to `unknown`, so a capped
+ * document (`unknown:knowledge:gamma.entry`), a resolvable bare key, a tag, a
+ * doc id and the finding CODE itself rendered `unknown:` — while the one really
+ * missing id did not (round 12, 12.4).
+ */
+function searchTuningTarget(t) {
+    if (t.referenceKind !== undefined) {
+        return {
+            targetKind: selfKindOf(t.referenceKind),
+            targetId: t.targetId ?? t.key ?? t.docId ?? t.code,
+            relation: 'tunes',
+        };
+    }
+    if (t.docId !== undefined)
+        return { targetKind: 'search-document', targetId: t.docId, relation: 'tunes' };
+    if (t.moreDocuments !== undefined) {
+        return { targetKind: 'search-document', targetId: `${t.moreDocuments} more document(s)`, relation: 'tunes' };
+    }
+    if (t.key !== undefined) {
+        if (t.status === SearchTuningKeyStatus.Unverified) {
+            return { targetKind: 'search-document', targetId: t.key, relation: 'tunes' };
         }
+        // The WHOLE key: an unknown prefix's right-hand id may well exist.
+        return { targetKind: selfKindOf(undefined), targetId: t.key, relation: 'tunes' };
+    }
+    return { targetKind: 'schema', targetId: t.field ?? t.code, relation: 'validates' };
+}
+/**
+ * A loader issue's target. A file-level issue (load-failed, missing-file, an
+ * entry with no id) is about the file. A clamped `boostIds` key is a
+ * search-document id, labelled through THE key resolver exactly like the lint's
+ * keys (the registries are warm: `buildLookupsV2` and the lint both warmed
+ * them); a clamped tag / source / kind name is no id at all — it is the
+ * declaration `schema:<map>.<name>`. Every clamped key used to read
+ * `unknown:<key>`: a resolvable id, or a tag labelled an unknown id.
+ */
+function searchTuningLoadTarget(inspection, i) {
+    if (i.key === undefined)
+        return { targetKind: 'file', targetId: i.source ?? i.code };
+    if (i.field === 'boostIds' || i.field?.endsWith('.boostIds') === true) {
+        const r = resolveSearchTuningKey(inspection, i.key);
+        const t = searchTuningTarget({
+            code: i.code,
+            key: i.key,
+            status: r.status,
+            referenceKind: r.referenceKind,
+            targetId: r.id,
+        });
+        return { targetKind: t.targetKind, targetId: t.targetId };
+    }
+    return { targetKind: 'schema', targetId: i.field !== undefined ? `${i.field}.${i.key}` : i.key };
+}
+/**
+ * The tuning loader's own issues (a file that failed to import, a clamped
+ * boost). A `missing-id` entry is a REJECTED entry: THE rejection family
+ * reports it (error, `search-tuning-invalid`) — never a second time here.
+ */
+function checkSearchTuningLoadIssues(inspection, findings) {
+    for (const i of listSearchTuningIssues(inspection)) {
+        // A refused entry (no id; round 13: a malformed boost value or marker) is
+        // THE rejection family's to report — once, as an error.
+        if (i.code === 'missing-id' || i.code === 'invalid-entry')
+            continue;
+        const target = searchTuningLoadTarget(inspection, i);
+        pushFinding(findings, {
+            severity: severityV2(i.severity),
+            code: `search-tuning-${i.code}`,
+            sourceKind: 'search-tuning',
+            sourceId: i.tuningId ?? i.source ?? 'search-tuning',
+            targetKind: target.targetKind,
+            targetId: target.targetId,
+            relation: 'validates',
+            file: i.source,
+            message: i.message,
+            nextCommand: 'shrk search tuning doctor',
+        });
     }
 }
 // ─── 3. Agent-tests → helpers / commands / playbooks / policies ───────────
@@ -231,108 +585,160 @@ async function checkAgentTests(inspection, lookups, findings) {
         probe(t, t.expectedHelpers, 'helper', lookups.helpers, 'expects');
         probe(t, t.expectedPlaybooks, 'playbook', lookups.playbooks, 'expects');
         probe(t, t.expectedPolicies, 'policy', lookups.policies, 'expects');
-        probe(t, t.expectedCommands, 'command', lookups.commands, 'expects');
+        // `expectedCommands` go through `checkCommandStrings` (the injected resolver).
     }
 }
 // ─── 4. Templates → conventions / helpers / profiles / registration hints ─
-function checkTemplateMetadata(inspection, lookups, findings) {
+/**
+ * Template `metadata` id fields, each probed through THE id resolver per THE
+ * binding table (`PROBED_ID_FIELDS`): `requiredProfileIds` → workspace-profile,
+ * `requiredConventionIds` → convention, `requiredHelperIds` → helper,
+ * `registrationHintIds` → registration-hint.
+ *
+ * This used bare `lookups.X.has(id)` loops: `requiredProfileIds` resolved
+ * against the MIGRATION registry, and every field warned "not registered"
+ * over an EMPTY registry — while the same id in a registration hint was a loud
+ * skip. One question, two answers (round 12, 12.3b). An id checked against an
+ * empty registry is now an unexamined unit (NOT VERIFIED), never a warning.
+ */
+function checkTemplateMetadata(inspection, findings) {
     const templates = (inspection.templates ?? []);
+    const rows = PROBED_ID_FIELDS.filter((r) => r.source === ProbedIdSource.Template);
+    const probe = newIdProbe();
     for (const t of templates) {
-        const m = t.metadata;
-        if (!m)
+        if (!t.metadata)
             continue;
-        for (const id of m.requiredConventionIds ?? []) {
-            if (lookups.conventions.has(id))
-                continue;
-            pushFinding(findings, {
-                severity: SelfConfigSeverityV2.Warning,
-                code: 'template-convention-missing',
-                sourceKind: 'template',
-                sourceId: t.id,
-                targetKind: 'convention',
-                targetId: id,
-                relation: 'requires',
-                message: `Template "${t.id}" requires convention "${id}" but it is not registered.`,
-                nextCommand: 'shrk conventions list --source pack',
-            });
-        }
-        for (const id of m.requiredHelperIds ?? []) {
-            if (lookups.helpers.has(id))
-                continue;
-            pushFinding(findings, {
+        const src = inspection.templateSources?.get(t.id);
+        for (const row of rows) {
+            probeIds(inspection, row.kind, readIdList(t, row.field), probe, 
+            // The unexamined label names the KIND resolved against (the report's
+            // `kind`), never the code label — `profile` was ambiguous once
+            // `workspace-profile` existed (round 12 review, T4).
+            (id) => `${t.id} → ${row.kind} ${id}`, (id, nearest) => pushFinding(findings, {
                 severity: SelfConfigSeverityV2.Warning,
-                code: 'template-helper-missing',
+                code: `template-${row.label}-missing`,
                 sourceKind: 'template',
                 sourceId: t.id,
-                targetKind: 'helper',
+                targetKind: selfKindOf(row.kind),
                 targetId: id,
                 relation: 'requires',
-                message: `Template "${t.id}" requires helper "${id}" but it is not registered.`,
-                nextCommand: 'shrk helper list --source pack',
-            });
+                message: `Template "${t.id}" ${row.field} names ${row.label} "${id}"${notResolvedTail(row.kind)}.`,
+                ...(nearest ? { suggestedFix: `Did you mean "${nearest}"?` } : {}),
+                nextCommand: referenceKindListVerb(row.kind),
+            }), { sourceKind: 'template', sourceId: t.id, field: row.field, file: src?.file, packageName: src?.packageName });
         }
-        for (const id of m.requiredProfileIds ?? []) {
-            if (lookups.migrationProfiles.has(id))
-                continue;
-            pushFinding(findings, {
-                severity: SelfConfigSeverityV2.Warning,
-                code: 'template-profile-missing',
-                sourceKind: 'template',
-                sourceId: t.id,
-                targetKind: 'profile',
-                targetId: id,
-                relation: 'requires',
-                message: `Template "${t.id}" requires profile "${id}" but it is not registered.`,
-                nextCommand: 'shrk profiles list',
-            });
-        }
-        for (const id of m.registrationHintIds ?? []) {
-            if (lookups.registrationHints.has(id))
+    }
+    return { coverage: idProbeCoverage('templates', 'required ids', probe), deadUnits: [], refProbe: probe };
+}
+// ─── 5. Routing hints → commands / templates / helpers / playbooks / profiles ───
+/**
+ * Routing hints: the loader's issues (which had NO consumer), whether each
+ * hint can match at all, and every `recommends` id through THE channel table
+ * and THE id resolver. The old probe list skipped the declared `knowledge` and
+ * `policies` channels entirely. An invalid hint or a duplicate id is a
+ * REJECTED entry: THE rejection family reports it (`routing-hint-invalid` /
+ * `routing-hint-duplicate-id`, one reporter) — this pass skips those codes.
+ */
+async function checkRoutingHints(inspection, findings) {
+    const loaded = await loadTaskRoutingHints(inspection);
+    const entries = loaded.entries;
+    for (const i of await listTaskRoutingHintIssues(inspection)) {
+        if (i.code === 'invalid-hint' || i.code === 'duplicate-id')
+            continue;
+        pushFinding(findings, {
+            severity: severityV2(i.severity),
+            code: `routing-hint-${i.code}`,
+            sourceKind: 'routing-hint',
+            sourceId: i.hintId ?? i.source ?? 'routing-hints',
+            targetKind: i.code === 'load-failed' || i.code === 'missing-file' ? 'file' : 'schema',
+            targetId: i.code,
+            relation: 'validates',
+            file: i.source,
+            message: i.message,
+        });
+    }
+    const probe = newIdProbe();
+    // A hint that can never match is dead by SHAPE (out of expectEmpty scope — no
+    // target can ever make it match); it still settles through THE liveness
+    // authority, unmarked, so this file's dead list has one derivation.
+    const hintObservations = [];
+    for (const e of entries) {
+        const canMatch = routingHintCanMatch(e.hint);
+        hintObservations.push({
+            list: 'routing hints',
+            unit: e.hint.id,
+            exists: canMatch,
+            live: canMatch,
+            ...(canMatch
+                ? {}
+                : { cause: UnitDeadCause.Defect, deadReason: 'declares no criterion the matcher scores, so it can never match' }),
+        });
+        const rec = (e.hint.recommends ?? {});
+        for (const channel of ROUTING_RECOMMENDS_CHANNEL_KEYS) {
+            const spec = ROUTING_RECOMMENDS_CHANNELS[channel];
+            // `recommends.commands` go through `checkCommandStrings` (the injected resolver).
+            if (spec.kind === 'command')
                 continue;
-            pushFinding(findings, {
-                severity: SelfConfigSeverityV2.Warning,
-                code: 'template-registration-hint-missing',
-                sourceKind: 'template',
-                sourceId: t.id,
-                targetKind: 'registration-hint',
+            const kind = spec.kind;
+            probeIds(inspection, kind, rec[channel], probe, (id) => `${e.hint.id} → ${kind} ${id}`, (id, nearest) => pushFinding(findings, {
+                severity: SelfConfigSeverityV2.Info,
+                code: `routing-hint-${spec.label}-missing`,
+                sourceKind: 'routing-hint',
+                sourceId: e.hint.id,
+                // THE kind the id was resolved against — no relabel. (`profile` was a
+                // display alias no registry or list verb has; round 12, 12.3.)
+                targetKind: selfKindOf(kind),
                 targetId: id,
-                relation: 'requires',
-                message: `Template "${t.id}" references registration hint "${id}" but it is not registered.`,
-                nextCommand: 'shrk registrations list',
+                relation: 'routes-to',
+                file: e.sourceFile,
+                message: `Routing hint "${e.hint.id}" recommends ${kind === 'migration-profile' ? 'migration profile' : spec.label} "${id}" (recommends.${channel}) but it is not registered.`,
+                ...(nearest ? { suggestedFix: `Did you mean "${nearest}"?` } : {}),
+                nextCommand: referenceKindListVerb(kind),
+            }), {
+                sourceKind: 'routing-hint',
+                sourceId: e.hint.id,
+                field: `recommends.${channel}`,
+                file: e.sourceFile,
+                packageName: e.packageName,
             });
         }
     }
-}
-// ─── 5. Routing hints → commands / templates / helpers / playbooks / profiles ───
-async function checkRoutingHints(inspection, lookups, findings) {
-    const entries = await listTaskRoutingHints(inspection);
-    for (const e of entries) {
-        const rec = e.hint.recommends;
-        const probe = (ids, kind, lookup) => {
-            if (!ids)
-                return;
-            for (const id of ids) {
-                if (lookup.has(id))
-                    continue;
-                pushFinding(findings, {
-                    severity: SelfConfigSeverityV2.Info,
-                    code: `routing-hint-${kind}-missing`,
-                    sourceKind: 'routing-hint',
-                    sourceId: e.hint.id,
-                    targetKind: kind,
-                    targetId: id,
-                    relation: 'routes-to',
-                    message: `Routing hint "${e.hint.id}" recommends ${kind} "${id}" but it is not registered.`,
-                });
-            }
-        };
-        probe(rec.templates, 'template', lookups.templates);
-        probe(rec.helpers, 'helper', lookups.helpers);
-        probe(rec.conventions, 'convention', lookups.conventions);
-        probe(rec.profiles, 'profile', lookups.migrationProfiles);
-        probe(rec.commands, 'command', lookups.commands);
-        probe(rec.playbooks, 'playbook', lookups.playbooks);
+    const hints = settleUnitLiveness({
+        subject: 'routing hints',
+        unitLabel: 'hints',
+        weight: UnitDeadWeight.Coverage,
+        observations: hintObservations,
+        marks: [],
+        deadSummary: 'declare no criterion the matcher scores (keyword, phrase, compiling regex), so they can never match',
+    });
+    const coverage = [...hints.coverage];
+    // A hint file that failed to import (or a pack-declared one that is absent)
+    // hides every hint in it: the file is unexamined, never a healthy registry.
+    const brokenHintFiles = [
+        ...new Set(loaded.issues
+            .filter((i) => i.code === 'load-failed' || i.code === 'missing-file')
+            .map((i) => nodePath.relative(inspection.projectRoot, i.source ?? '') || (i.source ?? '?'))),
+    ];
+    if (loaded.files > 0) {
+        coverage.push({
+            subject: 'routing hints',
+            unit: 'hint files',
+            expected: loaded.files,
+            examined: Math.max(0, loaded.files - brokenHintFiles.length),
+            ...(brokenHintFiles.length > 0
+                ? { unexamined: brokenHintFiles.slice(0, 20), unexaminedTotal: brokenHintFiles.length }
+                : {}),
+            reason: 'failed to load or are missing, so none of their hints are known',
+        });
     }
+    coverage.push(...idProbeCoverage('routing hints', 'recommended ids', probe));
+    return {
+        probes: { probed: probe.probed, resolved: probe.resolved, missing: probe.missing, unverified: probe.unverified },
+        coverage,
+        deadUnits: hints.dead.map((u) => `routing hint ${u.unit} (can never match)`),
+        refProbe: probe,
+        liveness: [hints],
+    };
 }
 // ─── 6. Pipelines → templates / commands (via cliCommands) ────────────────
 function checkPipelines(inspection, lookups, findings) {
@@ -340,7 +746,8 @@ function checkPipelines(inspection, lookups, findings) {
         (inspection.pipelines ?? []);
     for (const p of pipelines) {
         for (const step of p.steps ?? []) {
-            // Templates referenced by id should resolve.
+            // A step reference names a knowledge entry / template / path convention
+            // (`IPipelineStep.references`), or a convention / helper.
             for (const ref of step.references ?? []) {
                 if (lookups.templates.has(ref) ||
                     lookups.knowledge.has(ref) ||
@@ -348,16 +755,24 @@ function checkPipelines(inspection, lookups, findings) {
                     lookups.paths.has(ref) ||
                     lookups.helpers.has(ref))
                     continue;
+                // Not an accepted kind — but THE resolver may still place it (a
+                // construct id): that is the wrong kind, never "unknown". It used to
+                // read `references unknown:<id>` for an id `self-config resolve` finds.
+                const kinds = referenceKindsOf(inspection, ref);
+                const resolvedAs = kinds[0];
                 pushFinding(findings, {
                     severity: SelfConfigSeverityV2.Info,
-                    code: 'pipeline-reference-missing',
+                    code: resolvedAs === undefined ? 'pipeline-reference-missing' : 'pipeline-reference-wrong-kind',
                     sourceKind: 'pipeline',
                     sourceId: p.id,
-                    targetKind: 'unknown',
+                    targetKind: selfKindOf(resolvedAs),
                     targetId: ref,
                     relation: 'references',
                     file: p.source?.origin ?? undefined,
-                    message: `Pipeline "${p.id}" step "${step.id}" references unknown id "${ref}".`,
+                    message: resolvedAs === undefined
+                        ? `Pipeline "${p.id}" step "${step.id}" references unknown id "${ref}".`
+                        : `Pipeline "${p.id}" step "${step.id}" references "${ref}", which is a ${kinds.join(' | ')} — a step reference names a knowledge entry, template, path convention, convention or helper.`,
+                    nextCommand: `shrk self-config resolve ${ref}`,
                     confidence: 'medium',
                 });
             }
@@ -365,13 +780,31 @@ function checkPipelines(inspection, lookups, findings) {
     }
 }
 // ─── 7. Playbooks → templates / helpers / commands / profiles ─────────────
+/**
+ * Playbooks: the loader's issues (an import failure used to be swallowed, so a
+ * broken `playbooks.ts` reported a healthy, merely smaller registry), file
+ * coverage, and each playbook's template / pipeline ids. Reads the LOADER —
+ * the cache-only `listPlaybooks` answered "no playbooks" whenever nothing had
+ * warmed it.
+ */
 async function checkPlaybooks(inspection, lookups, findings) {
-    let playbooks;
-    try {
-        playbooks = (await listPlaybooks(inspection));
-    }
-    catch {
-        return;
+    const { playbooks, issues, files } = await loadPlaybooksWithIssues(inspection);
+    const brokenFiles = [];
+    for (const i of issues) {
+        const rel = nodePath.relative(inspection.projectRoot, i.source) || i.source;
+        if (!brokenFiles.includes(rel))
+            brokenFiles.push(rel);
+        pushFinding(findings, {
+            severity: severityV2(i.severity),
+            code: `playbook-${i.code}`,
+            sourceKind: 'playbook',
+            sourceId: i.packageName ? `${i.packageName}:${rel}` : rel,
+            targetKind: 'file',
+            targetId: i.code,
+            relation: 'validates',
+            file: i.source,
+            message: i.message,
+        });
     }
     for (const p of playbooks) {
         for (const id of p.recommendedTemplateIds ?? []) {
@@ -405,36 +838,178 @@ async function checkPlaybooks(inspection, lookups, findings) {
             });
         }
     }
+    const coverage = files > 0
+        ? [
+            {
+                subject: 'playbooks',
+                unit: 'playbook files',
+                expected: files,
+                examined: Math.max(0, files - brokenFiles.length),
+                ...(brokenFiles.length > 0
+                    ? { unexamined: brokenFiles.slice(0, 20), unexaminedTotal: brokenFiles.length }
+                    : {}),
+                reason: 'failed to load or are missing, so none of their playbooks are known',
+            },
+        ]
+        : [];
+    return { coverage, deadUnits: [] };
 }
 // ─── 8. Registration hints → templates / conventions / profiles ───────────
-async function checkRegistrationHints(inspection, lookups, findings) {
-    const entries = await listRegistrationHints(inspection);
+/**
+ * Registration hints, through THE discovery authority
+ * (`buildRegistrationHintDoctorReport` — the one `registrations doctor` and
+ * `preview` read): load issues, dead / ambiguous / capped discovery, missing
+ * anchors. Plus the hint's real cross-references, `discovery.conventionIds` /
+ * `discovery.profileIds`. This used to read `relatedTemplateIds` & co. through
+ * a cast to fields `IRegistrationHint` does not declare — a probe that could
+ * never fire.
+ */
+async function checkRegistrationHints(inspection, findings) {
+    const report = await buildRegistrationHintDoctorReport(inspection);
+    for (const i of report.issues) {
+        // An invalid hint / a duplicate id is a REJECTED entry — THE rejection
+        // family reports it (`registration-hint-invalid` / `-duplicate-id`).
+        if (i.code === 'invalid-hint' || i.code === 'duplicate-id')
+            continue;
+        pushFinding(findings, {
+            severity: severityV2(i.severity),
+            code: `registration-hint-${i.code}`,
+            sourceKind: 'registration-hint',
+            sourceId: i.hintId ?? i.source ?? 'registration-hints',
+            targetKind: 'file',
+            targetId: i.target ?? i.code,
+            relation: 'validates',
+            file: i.source,
+            message: i.message,
+            nextCommand: 'shrk registrations doctor',
+        });
+    }
+    const ids = await probeRegistrationHintIds(inspection, findings);
+    return {
+        coverage: [...report.coverage, ...ids.coverage],
+        deadUnits: report.deadUnits,
+        ...(ids.refProbe ? { refProbe: ids.refProbe } : {}),
+        liveness: [report.liveness],
+    };
+}
+/**
+ * A registration hint's cross-references — THE reference-probe half of the
+ * family, with no discovery walk, so `collectUnresolvableReferences` runs
+ * exactly what the doctor runs.
+ */
+async function probeRegistrationHintIds(inspection, findings) {
+    // `discovery.conventionIds` / `discovery.profileIds`, per THE binding table:
+    // profileIds are WorkspaceProfile ids (`workspace-profile`). They were bound
+    // to `migration-profile` and relabelled `profile` — NOT VERIFIED forever with
+    // no migration profiles, a false "not registered" with any (round 12, 12.3).
+    const probe = newIdProbe();
+    const rows = PROBED_ID_FIELDS.filter((r) => r.source === ProbedIdSource.RegistrationHint);
+    for (const e of await listRegistrationHints(inspection)) {
+        for (const row of rows) {
+            probeIds(inspection, row.kind, readIdList(e.hint, row.field), probe, (id) => `${e.hint.id} → ${row.kind} ${id}`, (id, nearest) => pushFinding(findings, {
+                severity: SelfConfigSeverityV2.Info,
+                code: `registration-hint-${row.label}-missing`,
+                sourceKind: 'registration-hint',
+                sourceId: e.hint.id,
+                targetKind: selfKindOf(row.kind),
+                targetId: id,
+                relation: 'related',
+                file: e.sourceFile,
+                message: `Registration hint "${e.hint.id}" ${row.field} references ${row.label} "${id}"${notResolvedTail(row.kind)}.`,
+                ...(nearest ? { suggestedFix: `Did you mean "${nearest}"?` } : {}),
+                nextCommand: referenceKindListVerb(row.kind),
+            }), {
+                sourceKind: 'registration-hint',
+                sourceId: e.hint.id,
+                field: row.field,
+                file: e.sourceFile,
+                packageName: e.packageName,
+            });
+        }
+    }
+    return { coverage: idProbeCoverage('registration hints', 'related ids', probe), deadUnits: [], refProbe: probe };
+}
+// ─── 8b. Conventions → applicability profile ids ──────────────────────────
+/**
+ * A convention's `appliesTo` id fields, per THE binding table — today
+ * `appliesTo.profileIds` → `workspace-profile`. It was never probed at all, so
+ * a typo'd profile id could never surface. Resolution only: `conventions
+ * check` does not yet FILTER on profileIds (making a firing gate fire less is
+ * not strictly more honest), which the field's JSDoc says.
+ */
+async function checkConventionApplicability(inspection, findings) {
+    let entries;
+    try {
+        entries = await listConventions(inspection);
+    }
+    catch {
+        // A convention file that will not load is `conventions doctor`'s to report.
+        return { coverage: [], deadUnits: [] };
+    }
+    const rows = PROBED_ID_FIELDS.filter((r) => r.source === ProbedIdSource.Convention);
+    const probe = newIdProbe();
     for (const e of entries) {
-        const h = e.hint;
-        const probe = (ids, kind, lookup) => {
-            if (!ids)
-                return;
-            for (const id of ids) {
-                if (lookup.has(id))
-                    continue;
-                pushFinding(findings, {
-                    severity: SelfConfigSeverityV2.Info,
-                    code: `registration-hint-${kind}-missing`,
-                    sourceKind: 'registration-hint',
-                    sourceId: h.id,
-                    targetKind: kind,
-                    targetId: id,
-                    relation: 'related',
-                    file: e.sourceFile,
-                    message: `Registration hint "${h.id}" references ${kind} "${id}" but it is not registered.`,
-                    confidence: 'medium',
-                });
-            }
-        };
-        probe(h.relatedTemplateIds, 'template', lookups.templates);
-        probe(h.relatedConventionIds, 'convention', lookups.conventions);
-        probe(h.relatedProfileIds, 'profile', lookups.migrationProfiles);
+        for (const row of rows) {
+            probeIds(inspection, row.kind, readIdList(e.convention, row.field), probe, (id) => `${e.convention.id} → ${row.kind} ${id}`, (id, nearest) => pushFinding(findings, {
+                severity: SelfConfigSeverityV2.Info,
+                code: `convention-${row.label}-missing`,
+                sourceKind: 'convention',
+                sourceId: e.convention.id,
+                targetKind: selfKindOf(row.kind),
+                targetId: id,
+                relation: 'related',
+                file: e.sourceFile,
+                message: `Convention "${e.convention.id}" ${row.field} names ${row.label} "${id}"${notResolvedTail(row.kind)}.`,
+                ...(nearest ? { suggestedFix: `Did you mean "${nearest}"?` } : {}),
+                nextCommand: referenceKindListVerb(row.kind),
+            }), {
+                sourceKind: 'convention',
+                sourceId: e.convention.id,
+                field: row.field,
+                file: e.sourceFile,
+                packageName: e.packageName,
+            });
+        }
     }
+    return {
+        coverage: idProbeCoverage('conventions', 'applicability profile ids', probe),
+        deadUnits: [],
+        refProbe: probe,
+    };
+}
+/**
+ * Scaffold patterns' dead selectors: a `matchPaths` glob matching no file, a
+ * pattern matching none after `excludePaths` — counted by THE enumeration
+ * `infer templates` attributes candidates with. (The definition checks stay
+ * `shrk scaffolds doctor`'s.)
+ */
+async function checkScaffoldPatterns(inspection, findings) {
+    let patterns;
+    try {
+        patterns = (await loadScaffoldPatternsFromInspection(inspection)).patterns;
+    }
+    catch {
+        return { coverage: [], deadUnits: [] };
+    }
+    if (patterns.length === 0)
+        return { coverage: [], deadUnits: [] };
+    const enumeration = enumerateScaffoldPatternCandidates(inspection.projectRoot, patterns);
+    for (const i of doctorScaffoldPatterns(patterns, inspection, enumeration)) {
+        if (!i.code)
+            continue;
+        pushFinding(findings, {
+            severity: severityV2(i.severity),
+            code: `scaffold-pattern-${i.code}`,
+            sourceKind: 'scaffold-pattern',
+            sourceId: i.patternId,
+            targetKind: 'file',
+            targetId: i.target ?? '(any file)',
+            relation: 'references',
+            message: `Scaffold pattern "${i.patternId}" ${i.message}.`,
+            nextCommand: 'shrk scaffolds doctor',
+        });
+    }
+    return scaffoldPatternCoverage(patterns, enumeration);
 }
 /**
  * Decision records are parsed from Markdown via the heading text; the
@@ -513,51 +1088,451 @@ function checkDecisions(inspection, lookups, findings) {
         }
     }
 }
-// ─── 10. Stale pack signatures (surface as warning) ───────────────────────
-function checkStaleSignatures(inspection, findings) {
+// ─── 9b. Declared cross-references (knowledge / construct / boundary / template) ─
+/**
+ * Every id in a declared `related`-style field (knowledge `related` / `seeAlso`
+ * / `supersededBy` / `actionHints.related*`, construct `related*` + facets that
+ * declare `resolvesAs`, boundary `related*`, template `related`), read from THE
+ * collector — this pass never walks a field itself. `buildLookupsV2` already
+ * warmed the registries, so the collector's sync half is enough.
+ *
+ * A dangling id is a warning (it shrinks a result, it does not misroute —
+ * `--strict` fails on it); a dangling `supersededBy`, a supersession cycle and
+ * a facet naming an unknown kind are errors. An id that could not be looked up
+ * is `xref-unverified` (info) AND an unexamined unit in the coverage record,
+ * so the doctor cannot settle to a pass over it.
+ */
+function checkDeclaredCrossReferences(inspection, findings) {
+    const report = collectDeclaredXrefs(inspection);
+    for (const row of report.rows) {
+        if (row.status === DeclaredXrefStatus.Ok)
+            continue;
+        const firstAccepted = row.accepts === 'any' ? undefined : row.accepts[0];
+        const wrongKindAs = row.status === DeclaredXrefStatus.WrongKind ? row.resolvedAs[0] : undefined;
+        pushFinding(findings, {
+            severity: severityV2(row.severity),
+            code: row.status === DeclaredXrefStatus.Dangling
+                ? 'xref-dangling'
+                : row.status === DeclaredXrefStatus.WrongKind
+                    ? 'xref-wrong-kind'
+                    : 'xref-unverified',
+            sourceKind: selfKindOf(row.sourceKind),
+            sourceId: row.sourceId,
+            targetKind: selfKindOf(wrongKindAs ?? firstAccepted),
+            targetId: row.targetId,
+            relation: row.relation,
+            file: row.file,
+            message: row.message,
+            suggestedFix: row.status === DeclaredXrefStatus.Unverified
+                ? 'Run `shrk self-config doctor` from the CLI (it warms every registry), or fix the empty registry the id resolves against.'
+                : row.didYouMean.length > 0
+                    ? `Did you mean "${row.didYouMean[0]}"? Correct the id, register the target, or remove it from \`${row.field}\`.`
+                    : `Register the target, or remove the id from \`${row.field}\`.`,
+            nextCommand: `shrk self-config resolve ${row.targetId}`,
+            confidence: 'high',
+        });
+    }
+    for (const issue of report.issues) {
+        const superseded = issue.code === 'xref-superseded-cycle' || issue.code === 'xref-superseded-chain';
+        // A supersession issue names the successor (a knowledge id). A declaration
+        // issue (`xref-unknown-kind`, `xref-malformed`) is about the FIELD: the
+        // facet value there may well resolve — its declared KIND is what is wrong.
+        // It used to read `related unknown:<value>` (round 12, 12.4).
+        const target = superseded
+            ? { targetKind: 'knowledge', targetId: issue.targetId ?? issue.field, relation: 'supersedes' }
+            : {
+                targetKind: 'schema',
+                targetId: issue.facetId !== undefined ? `${issue.field}[${issue.facetId}]` : issue.field,
+                relation: 'validates',
+            };
+        pushFinding(findings, {
+            severity: severityV2(issue.severity),
+            code: issue.code,
+            sourceKind: selfKindOf(issue.sourceKind),
+            sourceId: issue.sourceId,
+            targetKind: target.targetKind,
+            targetId: target.targetId,
+            relation: target.relation,
+            file: issue.file,
+            message: issue.message,
+            confidence: 'high',
+        });
+    }
+    // Like every probe family: a workspace that declares no cross-reference ids
+    // contributes no record (it is not "nothing examined" for the whole doctor).
+    const coverage = report.counts.ids > 0 || report.examined.unreadSources.length > 0
+        ? [{ ...declaredXrefCoverage(report), subject: 'declared cross-references' }]
+        : [];
+    return {
+        summary: { examined: report.examined, counts: report.counts, summary: declaredXrefSummaryLine(report) },
+        coverage,
+        report,
+    };
+}
+/** THE declared-xref rows that could not be looked up, as unresolvable references (one per row). */
+function xrefUnresolvableReferences(inspection, report) {
+    return report.rows
+        .filter((r) => r.status === DeclaredXrefStatus.Unverified)
+        .map((r) => {
+        const kind = r.accepts === 'any' ? 'any' : r.accepts[0];
+        const declarable = kind === undefined || kind === 'any' || isReferenceKindDeclarable(kind);
+        return {
+            // The collector records the file project-relative when possible.
+            ...(r.file ? { file: nodePath.resolve(inspection.projectRoot, r.file) } : {}),
+            ...(r.packageName ? { packageName: r.packageName } : {}),
+            sourceKind: r.sourceKind,
+            sourceId: r.sourceId,
+            field: r.field,
+            kind: kind ?? 'any',
+            id: r.targetId,
+            reason: declarable ? UnresolvableReason.RegistryEmpty : UnresolvableReason.UndeclarableKind,
+        };
+    });
+}
+/**
+ * THE unresolvable-reference scan over the reference families' probes and the
+ * declared-xref report: what was probed (`expected` — the reference families'
+ * units plus the xref ids), what could be checked, and each that could not.
+ * The doctor carries it; `collectUnresolvableReferences` returns it.
+ */
+function referenceScanOf(inspection, probes, xrefs) {
+    const present = probes.filter((p) => p !== undefined);
+    const references = [...present.flatMap((p) => p.unverifiedRefs), ...xrefUnresolvableReferences(inspection, xrefs)];
+    const expected = present.reduce((n, p) => n + p.probed, 0) + xrefs.counts.ids;
+    return { expected, examined: expected - references.length, references };
+}
+// ─── 10. Pack contribution conflicts (every kind) ─────────────────────────
+/**
+ * EVERY pack contribution conflict (duplicate id, shadowed, invalid,
+ * missing-loader, stale signature). This used to surface only stale
+ * signatures, so a duplicate-id or shadowed conflict was visible over MCP (v1)
+ * and invisible to `shrk self-config doctor` (v2). Stale signatures keep their
+ * v2 code `pack-signature-stale`; the v1 projection maps it back to
+ * `pack-conflict:stale-signature`.
+ */
+async function checkPackConflicts(inspection, findings) {
     try {
-        const inv = buildPackContributionsInventory(inspection);
+        // The ASYNC inventory (loaders consulted); the stale-signature conflict it
+        // carries is read from the one pack-asset freshness authority.
+        const inv = await buildPackContributionsInventoryAsync(inspection);
+        checkContributionRejections(findings, inv.rejections);
         for (const c of inv.conflicts) {
-            if (c.kind !== 'stale-signature')
-                continue;
+            const stale = c.kind === 'stale-signature';
             pushFinding(findings, {
-                severity: SelfConfigSeverityV2.Warning,
-                code: 'pack-signature-stale',
+                severity: stale ? SelfConfigSeverityV2.Warning : severityV2(c.severity),
+                code: stale ? 'pack-signature-stale' : `pack-conflict:${c.kind}`,
                 sourceKind: 'pack',
                 sourceId: c.id,
-                targetKind: 'schema',
-                targetId: 'sharkcraft.pack-manifest/v1',
+                targetKind: stale ? 'schema' : 'pack',
+                targetId: stale ? 'sharkcraft.pack-manifest/v1' : String(c.contributionKind),
                 relation: 'validates',
                 message: c.message,
                 ...(c.nextCommand ? { nextCommand: c.nextCommand } : {}),
                 confidence: 'high',
             });
         }
+        return inv;
+    }
+    catch {
+        // An inventory that cannot be built is `shrk packs doctor`'s to report.
+        return null;
+    }
+}
+/**
+ * THE rejection family (round 12, 12.1): every declared contribution entry a
+ * loader refused — from THE rejection channel the inventory carries — is an
+ * ERROR, one finding per failing field (`<kind>-invalid`, or
+ * `<kind>-duplicate-id`), local and pack alike: an entry that never takes
+ * effect is a defect, and it used to reach no surface but its kind's doctor
+ * (conventions, helpers) or none at all (knowledge, templates, playbooks, …).
+ * The routing / registration hint families no longer report their own
+ * `invalid-hint` / `duplicate-id` issues, so each rejection has one reporter.
+ */
+function checkContributionRejections(findings, rejections) {
+    for (const r of rejections) {
+        const f = rejectionFindingOf(r.kind, r.cause);
+        const where = r.index >= 0 ? `${r.exportName ?? ''}[${r.index}]` : (r.exportName ?? 'default');
+        const who = r.entryId !== undefined ? `"${r.entryId}"` : `at ${where}`;
+        for (const reason of r.reasons) {
+            pushFinding(findings, {
+                severity: SelfConfigSeverityV2.Error,
+                code: f.code,
+                sourceKind: f.kind,
+                sourceId: r.entryId ?? `${r.file}:${where}`,
+                targetKind: 'schema',
+                targetId: validatorField(reason),
+                relation: 'validates',
+                file: r.file,
+                message: `${f.kind} ${who} in ${r.file} (${where}) was rejected by its loader — ${reason}. It does not take effect.`,
+                nextCommand: r.packageName ? `shrk packs contributions --pack ${r.packageName}` : f.doctor,
+                confidence: 'high',
+            });
+        }
+    }
+}
+/**
+ * A reference that resolves nowhere may name an entry that WAS declared — and
+ * refused by its loader. Its `*-missing` finding then says so instead of
+ * offering a did-you-mean (round 12, 12.1): the id is not a typo.
+ */
+function annotateRejectedTargets(findings, rejections) {
+    const byId = new Map();
+    for (const r of rejections)
+        if (r.entryId !== undefined && !byId.has(r.entryId))
+            byId.set(r.entryId, r);
+    if (byId.size === 0)
+        return;
+    findings.forEach((f, i) => {
+        if (!isUnresolvedReferenceFinding(f))
+            return;
+        const r = byId.get(f.targetId);
+        if (!r)
+            return;
+        const rejectedAs = rejectionFindingOf(r.kind, r.cause).kind;
+        if (f.targetKind !== rejectedAs && f.targetKind !== selfKindOf(undefined))
+            return;
+        findings[i] = {
+            ...f,
+            suggestedFix: `'${f.targetId}' is declared in ${r.file} but was rejected: ${r.reasons.join('; ')}`,
+        };
+    });
+}
+function actionHintCommand(c) {
+    if (typeof c === 'string')
+        return c;
+    if (c && typeof c === 'object' && typeof c.command === 'string') {
+        return c.command;
+    }
+    return undefined;
+}
+/**
+ * Every command string an asset prescribes, with where it came from. A broken
+ * source degrades to "no commands from it" — that asset's own loader reports
+ * the load failure.
+ */
+async function collectCommandSites(inspection) {
+    const sites = [];
+    const add = (sourceKind, sourceId, field, commands, severity, relation, file, assumeShrk = false) => {
+        for (const raw of commands ?? []) {
+            const command = actionHintCommand(raw)?.trim();
+            if (command) {
+                sites.push({
+                    sourceKind,
+                    sourceId,
+                    field,
+                    command,
+                    severity,
+                    relation,
+                    file,
+                    ...(assumeShrk ? { assumeShrk: true } : {}),
+                });
+            }
+        }
+    };
+    const W = SelfConfigSeverityV2.Warning;
+    try {
+        const { loadAgentContractTests } = await import("./test-runner.js");
+        // An agent test's expectation is load-bearing: a dead expected command fails
+        // the test forever, so it is an error here too.
+        for (const t of await loadAgentContractTests(inspection)) {
+            add('agent-test', t.id, 'expectedCommands', t.expectedCommands, SelfConfigSeverityV2.Error, 'expects', undefined, true);
+        }
+    }
+    catch {
+        // agent-test loader failure is reported by `shrk test agent`
+    }
+    try {
+        for (const e of await listTaskRoutingHints(inspection)) {
+            add('routing-hint', e.hint.id, 'recommends.commands', e.hint.recommends?.commands, W, 'routes-to', e.sourceFile);
+        }
     }
     catch {
-        // ignore
+        // reported by the routing-hint loader
     }
+    try {
+        for (const e of await listRegistrationHints(inspection)) {
+            add('registration-hint', e.hint.id, 'validationCommands', e.hint.validationCommands, W, 'validates', e.sourceFile);
+        }
+    }
+    catch {
+        // reported by the registration-hint loader
+    }
+    for (const p of inspection.pipelineRegistry?.list?.() ?? []) {
+        for (const step of p.steps ?? []) {
+            add('pipeline', p.id, `steps.${step.id}.cliCommands`, step.cliCommands, W, 'references');
+        }
+    }
+    for (const p of listPlaybooks(inspection)) {
+        // The loader refuses a playbook without an array `steps` (12.1d: an
+        // accepted one crashed the whole doctor here); guard anyway.
+        (Array.isArray(p.steps) ? p.steps : []).forEach((step, i) => {
+            add('playbook', p.id, `steps[${i}].commands`, step?.commands, W, 'references');
+        });
+    }
+    for (const c of listConstructs(inspection)) {
+        add('construct', c.id, 'commands', c.commands, W, 'references');
+    }
+    for (const p of inspection.presetRegistry?.list?.() ?? []) {
+        add('preset', p.id, 'recommendedNextCommands', p.recommendedNextCommands, W, 'references');
+    }
+    for (const k of inspection.knowledgeEntries) {
+        const origin = k.source?.origin ?? undefined;
+        add('knowledge', k.id, 'actionHints.commands', k.actionHints?.commands, W, 'references', origin);
+        const refCommands = (k.references ?? [])
+            .filter((r) => r.kind === 'command')
+            .map((r) => r.id ?? r.command)
+            .filter((c) => typeof c === 'string' && c.length > 0);
+        add('knowledge', k.id, 'references', refCommands, W, 'references', origin, true);
+    }
+    try {
+        for (const d of await loadTsDecisions(inspection)) {
+            add('decision', d.id, 'relatedCommands', d.relatedCommands, W, 'related', d.sourceFile);
+        }
+    }
+    catch {
+        // reported by the decisions loader
+    }
+    return sites;
+}
+/**
+ * The command-strings pass: every command an asset prescribes, resolved
+ * through THE injected command resolver, deduped per (asset, command).
+ *
+ * Without a resolver (outside the CLI) nothing is checked, and the pass says
+ * so ONCE (`command-probe-unverified`, info) — never a finding per command,
+ * and never an error. The old probes checked against a set initialised empty,
+ * so every command in every hint was "missing", correct ones included.
+ */
+async function checkCommandStrings(inspection, findings) {
+    const seen = new Set();
+    const sites = (await collectCommandSites(inspection)).filter((s) => {
+        // The reading is part of the key: one asset may cite `doctor` both as free
+        // shell text and as a command reference, and the two resolve differently.
+        const key = `${s.sourceKind}:${s.sourceId}|${s.assumeShrk === true ? 'ref' : 'sh'}|${s.command}`;
+        if (seen.has(key))
+            return false;
+        seen.add(key);
+        return true;
+    });
+    const counts = { probed: sites.length, exists: 0, prefixOnly: 0, notShrk: 0, unknown: 0, unverified: 0 };
+    if (sites.length === 0)
+        return counts;
+    if (!hasCommandResolver(inspection)) {
+        counts.unverified = sites.length;
+        pushFinding(findings, {
+            severity: SelfConfigSeverityV2.Info,
+            code: 'command-probe-unverified',
+            // The doctor's own probe summary — it has a kind (it borrowed `unknown`).
+            sourceKind: 'self-config',
+            sourceId: 'command-probes',
+            targetKind: 'command',
+            targetId: `${sites.length} command string(s)`,
+            relation: 'references',
+            message: `${sites.length} command string(s) prescribed by assets were NOT checked: ${COMMAND_INDEX_NOT_INJECTED}.`,
+            suggestedFix: 'Run `shrk self-config doctor` from the CLI, which injects the live command index.',
+            confidence: 'high',
+        });
+        return counts;
+    }
+    for (const site of sites) {
+        const resolution = site.assumeShrk
+            ? resolveShrkCommandReference(inspection, site.command)
+            : resolveCommandReference(inspection, site.command);
+        switch (resolution.status) {
+            case CommandResolutionStatus.Ok:
+                counts.exists += 1;
+                break;
+            case CommandResolutionStatus.PrefixOnly:
+                counts.prefixOnly += 1;
+                break;
+            case CommandResolutionStatus.NotShrk:
+                counts.notShrk += 1;
+                break;
+            case CommandResolutionStatus.Unverified:
+                counts.unverified += 1;
+                break;
+            default: {
+                counts.unknown += 1;
+                const closest = resolution.closest ?? [];
+                pushFinding(findings, {
+                    severity: site.severity,
+                    code: 'unknown-command',
+                    sourceKind: site.sourceKind,
+                    sourceId: site.sourceId,
+                    targetKind: 'command',
+                    targetId: site.command,
+                    relation: site.relation,
+                    file: site.file,
+                    message: `${site.sourceKind} "${site.sourceId}" ${site.field} prescribes \`${site.command}\`, which does not resolve (${resolution.status}${resolution.reason ? ` — ${resolution.reason}` : ''}).`,
+                    suggestedFix: closest.length > 0
+                        ? `Did you mean \`${closest[0]}\`? Update or remove the command.`
+                        : 'Update or remove the command.',
+                    nextCommand: 'shrk surface list',
+                    confidence: 'high',
+                });
+            }
+        }
+    }
+    return counts;
 }
 // ─── Public entry ─────────────────────────────────────────────────────────
 export async function buildSelfConfigDoctorReportV2(inspection) {
     const findings = [];
     const lookups = await buildLookupsV2(inspection);
     checkKnowledgeFileRefs(inspection, findings);
-    await checkSearchTuning(inspection, lookups, findings);
+    const tuning = await checkSearchTuning(inspection, findings);
+    checkSearchTuningLoadIssues(inspection, findings);
     await checkAgentTests(inspection, lookups, findings);
-    checkTemplateMetadata(inspection, lookups, findings);
-    await checkRoutingHints(inspection, lookups, findings);
+    const templateFamily = checkTemplateMetadata(inspection, findings);
+    const routing = await checkRoutingHints(inspection, findings);
     checkPipelines(inspection, lookups, findings);
-    await checkPlaybooks(inspection, lookups, findings);
-    await checkRegistrationHints(inspection, lookups, findings);
+    const playbookFamily = await checkPlaybooks(inspection, lookups, findings);
+    const registration = await checkRegistrationHints(inspection, findings);
+    const conventionFamily = await checkConventionApplicability(inspection, findings);
+    const scaffolds = await checkScaffoldPatterns(inspection, findings);
     checkDecisions(inspection, lookups, findings);
-    checkStaleSignatures(inspection, findings);
+    const xrefs = checkDeclaredCrossReferences(inspection, findings);
+    const inventory = await checkPackConflicts(inspection, findings);
+    const commandProbes = await checkCommandStrings(inspection, findings);
+    if (inventory)
+        annotateRejectedTargets(findings, inventory.rejections);
+    const referenceScan = referenceScanOf(inspection, [templateFamily.refProbe, routing.refProbe, registration.refProbe, conventionFamily.refProbe, tuning.refProbe], xrefs.report);
+    const selectorUnits = [
+        ...(tuning.liveness ?? []),
+        ...(routing.liveness ?? []),
+        ...(registration.liveness ?? []),
+        ...(scaffolds.liveness ?? []),
+    ]
+        .flatMap((s) => s.units)
+        .filter((u) => u.state !== UnitLivenessState.Live);
+    const coverage = [
+        ...commandProbeCoverage(commandProbes),
+        ...tuning.coverage,
+        ...routing.coverage,
+        ...playbookFamily.coverage,
+        ...registration.coverage,
+        ...conventionFamily.coverage,
+        ...templateFamily.coverage,
+        ...scaffolds.coverage,
+        ...xrefs.coverage,
+    ];
+    const deadUnits = [
+        ...tuning.deadUnits,
+        ...routing.deadUnits,
+        ...registration.deadUnits,
+        ...scaffolds.deadUnits,
+    ];
     const totals = computeTotalsV2(findings);
-    const verdict = totals.error > 0 ? 'errors' : totals.warning > 0 ? 'warnings' : 'ok';
+    // One derivation: core's `coverageShortfall`, the rule the CLI settles with.
+    const unverified = coverage.some((c) => coverageShortfall(c) !== undefined);
+    const verdict = totals.error > 0 ? 'errors' : unverified ? 'unverified' : totals.warning > 0 ? 'warnings' : 'ok';
     const nextCommands = [];
     if (totals.error > 0) {
         nextCommands.push('Fix the errored ids first — agent-test expectations and template requirements are load-bearing.', 'shrk packs conflicts');
     }
+    else if (unverified) {
+        nextCommands.push(`Some units were NOT verified (see coverage): a dead selector / boost is a ${DEAD_SELECTOR_CAUSES} — fix it, or mark a planned target expectEmpty; and run from the CLI, which injects the command index.`);
+    }
     else if (totals.warning > 0) {
         nextCommands.push('Review warnings — most resolve by registering the missing id or removing the stale link.');
     }
@@ -572,8 +1547,91 @@ export async function buildSelfConfigDoctorReportV2(inspection) {
         totals,
         verdict,
         nextCommands,
+        coverage,
+        deadUnits,
+        selectorUnits,
+        unresolvableReferences: referenceScan.references,
+        probes: {
+            command: commandProbes,
+            'search-tuning-target': tuning.probes,
+            'routing-hint-target': routing.probes,
+        },
+        crossReferences: xrefs.summary,
     };
 }
+/**
+ * Every declared reference that could not be resolved because its kind's
+ * registry is empty here, or can never be filled (round 12, ONE-CHANGE) —
+ * running EXACTLY the doctor's reference probes (template metadata, routing
+ * `recommends`, registration-hint and convention id fields, declared
+ * cross-references) over a warmed inspection, without the rest of the doctor.
+ * `buildSelfConfigDoctorReportV2` carries the same list, so the doctor and
+ * `shrk packs contributions` cannot disagree.
+ */
+export async function collectUnresolvableReferences(inspection) {
+    await warmReferenceRegistries(inspection);
+    const scratch = [];
+    const templateFamily = checkTemplateMetadata(inspection, scratch);
+    const routing = await checkRoutingHints(inspection, scratch);
+    const registration = await probeRegistrationHintIds(inspection, scratch);
+    const conventionFamily = await checkConventionApplicability(inspection, scratch);
+    const xrefs = checkDeclaredCrossReferences(inspection, scratch);
+    // THE key probes the tuning lint judges (round 13) — the same function, so
+    // `packs contributions` and `search tuning doctor` answer from one resolution.
+    const { entries: tunings } = await loadSearchTuning(inspection);
+    const tuning = tuningReferenceProbe(inspection, searchTuningKeyProbes(inspection, tunings));
+    return referenceScanOf(inspection, [templateFamily.refProbe, routing.refProbe, registration.refProbe, conventionFamily.refProbe, tuning], xrefs.report);
+}
+/**
+ * The command-string probes' coverage: every prescribed command string must
+ * have been resolved. Only present when assets prescribe any — a repo with no
+ * command strings is not "nothing examined" for the whole doctor.
+ *
+ * `not-shrk` strings (git, tsc, a script with no package.json to read) are a
+ * DELIBERATE narrowing — not this engine's to judge — so they leave `expected`
+ * rather than counting as examined. A set that is ALL not-shrk narrows to
+ * nothing and carries no record, exactly like a set with no strings at all.
+ * `prefix-only` strings stay in scope (the verb was proven); the clean line
+ * names how many tails went unproven.
+ */
+function commandProbeCoverage(c) {
+    const expected = c.probed - c.notShrk;
+    if (expected <= 0)
+        return [];
+    return [
+        {
+            unit: 'command strings',
+            expected,
+            examined: expected - c.unverified,
+            // `reason` names why a GAP exists. Only the no-resolver path returns
+            // Unverified, so `unverified > 0` means exactly "index not injected";
+            // a fully examined run carries no reason (a verified row labelled
+            // NOT VERIFIED misled JSON readers).
+            ...(c.unverified > 0 ? { reason: COMMAND_INDEX_NOT_INJECTED } : {}),
+        },
+    ];
+}
+/** One-line summary of the command-string probes, shared by the renderers. */
+function commandProbeLine(report) {
+    const c = report.probes.command;
+    return `probed ${c.probed} · unknown ${c.unknown} · prefix-only ${c.prefixOnly} · not-shrk ${c.notShrk} · unverified ${c.unverified}`;
+}
+/**
+ * The tuning-key probes on ONE line — so a 100% failure rate reads as a probe
+ * fault, not as N independent content errors.
+ */
+function tuningProbeLine(report) {
+    const t = report.probes['search-tuning-target'];
+    return `probed ${t.probed} · resolved ${t.resolved} · missing ${t.missing} · unprefixed ${t.unprefixed} · unknown-kind ${t.unknownKind} · unverified ${t.unverified}`;
+}
+function routingProbeLine(report) {
+    const r = report.probes['routing-hint-target'];
+    return `probed ${r.probed} · resolved ${r.resolved} · missing ${r.missing} · unverified ${r.unverified}`;
+}
+/** `<subject>: <formatCoverage>` per record — what each family examined. */
+function coverageLines(report) {
+    return report.coverage.map((c) => `${c.subject ? `${c.subject}: ` : ''}${formatCoverage(c)}`);
+}
 function computeTotalsV2(findings) {
     const byRelation = {};
     const bySourceKind = {};
@@ -603,13 +1661,22 @@ export function renderSelfConfigDoctorV2Text(report) {
     lines.push(`  errors        ${report.totals.error}`);
     lines.push(`  warnings      ${report.totals.warning}`);
     lines.push(`  info          ${report.totals.info}`);
+    lines.push(`  commands      ${commandProbeLine(report)}`);
+    lines.push(`  tuning keys   ${tuningProbeLine(report)}`);
+    lines.push(`  routing ids   ${routingProbeLine(report)}`);
+    if (report.crossReferences)
+        lines.push(`  xrefs         ${report.crossReferences.summary}`);
+    for (const c of coverageLines(report))
+        lines.push(`  coverage      ${c}`);
     lines.push('');
     if (report.findings.length === 0) {
-        lines.push('  No cross-reference issues. ✓');
+        // No ✓ here: whether this is a pass is the settled verdict's call (a dead
+        // or unverified unit is not a finding, and still is not a pass).
+        lines.push('  No findings.');
         return lines.join('\n') + '\n';
     }
     for (const f of report.findings.slice(0, 200)) {
-        lines.push(`  ${f.severity.padEnd(7)} [${f.code}] ${f.sourceKind}:${f.sourceId} ${f.relation} ${f.targetKind}:${f.targetId}`);
+        lines.push(`  ${f.severity.padEnd(7)} [${f.code}] ${f.sourceKind}:${f.sourceId} ${f.relation} ${f.targetKind}:${f.targetId}${f.occurrences && f.occurrences > 1 ? ` (×${f.occurrences})` : ''}`);
         lines.push(`           ${f.message}`);
         if (f.suggestedFix)
             lines.push(`           fix: ${f.suggestedFix}`);
@@ -635,9 +1702,16 @@ export function renderSelfConfigDoctorV2Markdown(report) {
     lines.push(`- errors: ${report.totals.error}`);
     lines.push(`- warnings: ${report.totals.warning}`);
     lines.push(`- info: ${report.totals.info}`);
+    lines.push(`- commands: ${commandProbeLine(report)}`);
+    lines.push(`- tuning keys: ${tuningProbeLine(report)}`);
+    lines.push(`- routing ids: ${routingProbeLine(report)}`);
+    if (report.crossReferences)
+        lines.push(`- xrefs: ${report.crossReferences.summary}`);
+    for (const c of coverageLines(report))
+        lines.push(`- coverage: ${c}`);
     lines.push('');
     if (report.findings.length === 0) {
-        lines.push('No cross-reference issues. ✓');
+        lines.push('No findings.');
         return lines.join('\n') + '\n';
     }
     lines.push('| Severity | Source | Relation | Target | Message | Next |');