@devflow-tools/cli 0.16.11 → 0.16.13

package/dist/commands/doctor.d.ts

@@ -1,4 +1,5 @@
 import type { DoctorReportV1 } from "@devflow-tools/sdk";
+import type { EmbeddingModelStatus } from "@devflow-tools/memory-engine";
 export type { DoctorMetric, DoctorReportV1, DoctorSection, DoctorSeverity, DoctorStatus, } from "@devflow-tools/sdk";
 export type DoctorResult = DoctorReportV1;
 export interface DoctorOptions {
@@ -31,6 +32,10 @@ export interface DoctorDependencies {
     httpGet?: (url: string) => Promise<{
         status: number;
     }>;
+    inspectEmbeddingModel?: (options: {
+        homeDir?: string;
+        env?: NodeJS.ProcessEnv;
+    }) => Promise<EmbeddingModelStatus>;
 }
 export interface DoctorCommandIO {
     stdout(output: string): void;

package/dist/commands/doctor.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/commands/doctor.ts"],"names":[],"mappings":"AA8BA,OAAO,KAAK,EAEV,cAAc,EAIf,MAAM,oBAAoB,CAAC;AAM5B,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,8BAA8B,CAAC;AAEzE,YAAY,EACV,YAAY,EACZ,cAAc,EACd,aAAa,EACb,cAAc,EACd,YAAY,GACb,MAAM,oBAAoB,CAAC;AAoC5B,MAAM,MAAM,YAAY,GAAG,cAAc,CAAC;AAE1C,MAAM,WAAW,aAAa;IAC5B,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,UAAU,eAAe;IACvB,GAAG,CAAC,GAAG,MAAM,EAAE,OAAO,EAAE,GAAG,OAAO,EAAE,CAAC;IACrC,GAAG,CAAC,GAAG,MAAM,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC;IACnC,cAAc,CAAC,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAAC;CACzC;AAED,UAAU,cAAc;IACtB,OAAO,CAAC,GAAG,EAAE,MAAM,GAAG,eAAe,CAAC;IACtC,KAAK,IAAI,IAAI,CAAC;CACf;AAED,MAAM,WAAW,kBAAkB;IACjC,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,mBAAmB,CAAC,EAAE,SAAS,MAAM,EAAE,CAAC;IACxC,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,kBAAkB,CAAC,EAAE,MAAM,CAAC;IAC5B,oBAAoB,CAAC,EAAE,MAAM,CAAC;IAC9B,qBAAqB,CAAC,EAAE,MAAM,CAAC;IAC/B,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,GAAG,CAAC,EAAE,MAAM,CAAC,UAAU,CAAC;IACxB,GAAG,CAAC,EAAE,MAAM,MAAM,CAAC;IACnB,YAAY,CAAC,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,cAAc,CAAC;IAChD,sBAAsB,CAAC,EAAE,MAAM,CAAC;IAChC,OAAO,CAAC,EAAE,CAAC,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC;QAAE,MAAM,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IACvD,qBAAqB,CAAC,EAAE,CAAC,OAAO,EAAE;QAChC,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,GAAG,CAAC,EAAE,MAAM,CAAC,UAAU,CAAC;KACzB,KAAK,OAAO,CAAC,oBAAoB,CAAC,CAAC;CACrC;AAED,MAAM,WAAW,eAAe;IAC9B,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IAC7B,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;CAC9B;AAwmKD,wBAAsB,mBAAmB,CACvC,OAAO,GAAE,aAAkB,EAC3B,YAAY,GAAE,kBAAuB,GACpC,OAAO,CAAC,YAAY,CAAC,CA4BvB;AAED,wBAAgB,SAAS,IAAI,OAAO,CAAC,YAAY,CAAC,CAAC;AACnD,wBAAgB,SAAS,CACvB,OAAO,EAAE,aAAa,EACtB,YAAY,CAAC,EAAE,kBAAkB,GAChC,OAAO,CAAC,YAAY,CAAC,CAAC;AAezB,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,YAAY,GAAG,MAAM,CAoB7D;AAED,wBAAsB,gBAAgB,CACpC,OAAO,GAAE,aAAkB,EAC3B,EAAE,GAAE,eAGH,EACD,YAAY,GAAE,kBAAuB,GACpC,OAAO,CAAC,MAAM,CAAC,CAIjB;AAED,MAAM,WAAW,YAAY;IAC3B,KAAK,EAAE;QAAE,UAAU,EAAE,MAAM,CAAC;QAAC,YAAY,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,OAAO,CAAA;KAAE,CAAC;IACvE,KAAK,EAAE;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;IACxC,MAAM,EAAE;QAAE,YAAY,EAAE,OAAO,CAAC;QAAC,SAAS,EAAE,MAAM,CAAA;KAAE,CAAC;IACrD,SAAS,EAAE;QAAE,OAAO,EAAE,MAAM,CAAA;KAAE,CAAC;IAC/B,OAAO,EAAE;QAAE,SAAS,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,EAAE,CAAA;KAAE,CAAC;IAChD,SAAS,EAAE;QAAE,UAAU,EAAE,MAAM,CAAA;KAAE,CAAC;IAClC,MAAM,EAAE;QAAE,OAAO,EAAE,OAAO,CAAA;KAAE,CAAC;IAC7B,SAAS,EAAE;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAA;KAAE,CAAC;IAC7D,UAAU,EAAE,MAAM,CAAC;CACpB;AAOD,wBAAsB,qBAAqB,CACzC,OAAO,SAAgB,GACtB,OAAO,CAAC,YAAY,CAAC,CA8DvB;AAED,wBAAsB,cAAc,IAAI,OAAO,CAAC;IAC9C,KAAK,EAAE,OAAO,CAAC;IACf,QAAQ,EAAE,MAAM,GAAG,IAAI,CAAC;IACxB,UAAU,EAAE,MAAM,CAAC;CACpB,CAAC,CAiBD;AAED,wBAAsB,iBAAiB,IAAI,OAAO,CAAC;IAAE,OAAO,EAAE,OAAO,CAAA;CAAE,CAAC,CAevE;AAED,wBAAsB,mBAAmB,CAAC,IAAI,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAChE,UAAU,EAAE,KAAK,CAAC;QAChB,IAAI,EAAE,MAAM,CAAC;QACb,QAAQ,EAAE,MAAM,CAAC;QACjB,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;QACtB,EAAE,EAAE,MAAM,CAAC;QACX,SAAS,EAAE,MAAM,CAAC;KACnB,CAAC,CAAC;CACJ,CAAC,CAsBD;AAED,wBAAgB,iBAAiB,IAAI;IAAE,SAAS,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,OAAO,CAAA;CAAE,CASxE"}

package/dist/commands/doctor.js

@@ -6,11 +6,12 @@ import { basename, dirname, extname, isAbsolute, join, relative, resolve, sep }
 import { spawnSync } from "node:child_process";
 import { fileURLToPath } from "node:url";
 import chalk from "chalk";
-import { DOCTOR_SCHEMA_VERSION, checkMcpHealth, loadPluginsWithDiagnostics, readMcpInventory, redactMcpInventory, selectHostAdapter, } from "@devflow-tools/sdk";
+import { DOCTOR_SCHEMA_VERSION, checkMcpHealth, loadPluginsWithDiagnostics, readMcpInventory, redactMcpInventory, readRuntimeEndpointState, listRuntimeHttpCircuits, selectHostAdapter, } from "@devflow-tools/sdk";
 import { resolveActivePlugin, scanClaudeSkillShadowing } from "../lib/plugin-setup.js";
 import { serverStatus } from "./server.js";
 import { inspectSkillHealth } from "./skill-health.js";
 import { getGlobalDevFlowDbPath } from "@devflow-tools/database";
+import { inspectEmbeddingModel } from "@devflow-tools/memory-engine";
 function getProjectHash(rootPath) {
     return createHash("sha256").update(rootPath).digest("hex").slice(0, 16);
 }
@@ -131,6 +132,24 @@ async function checkRuntimeControlPlane(project, dependencies) {
             severity: "warning",
         });
     }
+    const endpoint = readRuntimeEndpointState(home);
+    metrics.push({
+        key: 'runtime_endpoint_registry',
+        value: endpoint ?? 'not registered',
+        target: 'healthy while active, stopped or absent while idle',
+        ok: !endpoint || endpoint.status === 'healthy' || endpoint.status === 'stopped',
+        severity: endpoint?.status === 'degraded' ? 'error' : 'warning',
+    });
+    const now = (dependencies.now ?? Date.now)();
+    const openCircuits = listRuntimeHttpCircuits(home)
+        .filter(circuit => circuit.status === 'open' && (circuit.openUntil ?? 0) > now);
+    metrics.push({
+        key: 'runtime_http_circuits',
+        value: openCircuits,
+        target: [],
+        ok: openCircuits.length === 0,
+        severity: openCircuits.some(circuit => circuit.failures >= 2) ? 'error' : 'warning',
+    });
     return { name: "Contract", status: sectionStatus(metrics), metrics };
 }
 function canonicalizeProject(project) {
@@ -574,7 +593,10 @@ function semanticToolOutcome(row) {
     const data = doctorRecord(output?.data);
     const status = typeof output?.status === "string" ? output.status : undefined;
     const metricStatus = typeof row.metric_status === "string" ? row.metric_status : undefined;
-    const failed = Boolean(row.error)
+    const expectedPolicyBlock = Boolean(row.blocked)
+        && typeof row.block_reason === "string"
+        && row.block_reason.startsWith("DEVFLOW_");
+    const failed = !expectedPolicyBlock && (Boolean(row.error)
         || Boolean(row.failure_category)
         || output?.ok === false
         || output?.success === false
@@ -582,7 +604,7 @@ function semanticToolOutcome(row) {
         || Boolean(output?.error)
         || status === "failed"
         || status === "rejected"
-        || metricStatus === "error";
+        || metricStatus === "error");
     const degraded = !failed && (output?.degraded === true
         || Boolean(output?.degradation)
         || data?.degraded === true
@@ -611,7 +633,7 @@ function rate(count, total) {
 function coverage(total, vectors) {
     return total === 0 ? 1 : vectors / total;
 }
-function checkVectors(project, dependencies) {
+async function checkVectors(project, dependencies) {
     const metrics = [];
     let codegraphNodes = null;
     let symbolVectors = null;
@@ -690,8 +712,21 @@ function checkVectors(project, dependencies) {
                 metrics.push({ key: "knowledge_vector_schema", value: missing, target: [], ok: false, severity: "warning" });
             }
             else {
-                const chunks = doctorCount(db, "SELECT COUNT(*) count FROM knowledge_chunks");
-                const vectors = doctorCount(db, "SELECT COUNT(*) count FROM knowledge_vec_rowids");
+                const docColumns = doctorTableColumns(db, "knowledge_docs");
+                const activeClause = docColumns.has("status") ? "AND d.status = 'active'" : "";
+                const chunks = doctorCount(db, `
+          SELECT COUNT(*) count
+          FROM knowledge_chunks c
+          JOIN knowledge_docs d ON d.id = c.doc_id
+          WHERE 1 = 1 ${activeClause}
+        `);
+                const vectors = doctorCount(db, `
+          SELECT COUNT(*) count
+          FROM knowledge_vec_rowids v
+          JOIN knowledge_chunks c ON c.id = v.id
+          JOIN knowledge_docs d ON d.id = c.doc_id
+          WHERE 1 = 1 ${activeClause}
+        `);
                 const value = coverage(chunks, vectors);
                 const rows = db.prepare(`
           SELECT d.source source, COUNT(c.id) chunks,
@@ -699,6 +734,7 @@ function checkVectors(project, dependencies) {
           FROM knowledge_docs d
           LEFT JOIN knowledge_chunks c ON c.doc_id = d.id
           LEFT JOIN knowledge_vec_rowids v ON v.id = c.id
+          WHERE 1 = 1 ${activeClause}
           GROUP BY d.source ORDER BY d.source
         `).all();
                 const bySource = rows.map(row => {
@@ -737,11 +773,18 @@ function checkVectors(project, dependencies) {
                 metrics.push({ key: "observation_vector_schema", value: "observations/embeddings missing", target: "Batch 2 vector schema", ok: false, severity: "warning" });
             }
             else {
-                const observations = doctorCount(db, "SELECT COUNT(*) count FROM observations");
+                const observationColumns = doctorTableColumns(db, "observations");
+                const hasEligibilityColumns = observationColumns.has("quality_status")
+                    && observationColumns.has("resolution_state");
+                const eligibilityClause = hasEligibilityColumns
+                    ? "WHERE quality_status = 'accepted' AND resolution_state <> 'superseded'"
+                    : "";
+                const observations = doctorCount(db, `SELECT COUNT(*) count FROM observations ${eligibilityClause}`);
                 const vectors = doctorCount(db, `
           SELECT COUNT(DISTINCT e.source_id) count
           FROM embeddings e JOIN observations o ON o.id = e.source_id
           WHERE e.source_type = 'observation'
+          ${hasEligibilityColumns ? "AND o.quality_status = 'accepted' AND o.resolution_state <> 'superseded'" : ""}
         `);
                 const missing = Math.max(0, observations - vectors);
                 metrics.push({ key: "observations", value: observations, ok: true, severity: "info" });
@@ -771,7 +814,56 @@ function checkVectors(project, dependencies) {
             metrics.push({ key: "embedder_error_log_read", value: error.message, target: "readable error log", ok: false, severity: "error" });
         }
     }
-    metrics.push({ key: "embedder_errors_24h", value: recentErrors, target: 0, ok: recentErrors === 0, severity: "warning" });
+    metrics.push({
+        key: "embedder_errors_24h",
+        value: recentErrors,
+        target: "trend; current readiness is gated by model state and integrity",
+        ok: true,
+        severity: "info",
+    });
+    try {
+        const model = await (dependencies.inspectEmbeddingModel ?? inspectEmbeddingModel)({
+            homeDir: dependencies.homePath,
+            env: dependencies.env ?? process.env,
+        });
+        metrics.push({
+            key: "embedding_model_state",
+            value: {
+                state: model.state,
+                modelId: model.modelId,
+                revision: model.revision,
+            },
+            target: { state: "ready" },
+            ok: model.ready,
+            severity: "warning",
+        });
+        metrics.push({
+            key: "embedding_model_cache_root",
+            value: model.cacheRoot,
+            target: "stable shared DevFlow cache",
+            ok: true,
+            severity: "info",
+        });
+        metrics.push({
+            key: "embedding_model_integrity",
+            value: {
+                missingFiles: model.missingFiles,
+                corruptFiles: model.corruptFiles,
+            },
+            target: { missingFiles: [], corruptFiles: [] },
+            ok: model.missingFiles.length === 0 && model.corruptFiles.length === 0,
+            severity: "warning",
+        });
+    }
+    catch (error) {
+        metrics.push({
+            key: "embedding_model_inspection",
+            value: error.message,
+            target: "readable verified shared model cache",
+            ok: false,
+            severity: "warning",
+        });
+    }
     return { name: "Vectors", status: sectionStatus(metrics), metrics };
 }
 function checkTelemetry(project, strict, dependencies) {
@@ -1054,6 +1146,9 @@ function checkTelemetry(project, strict, dependencies) {
                     toolEventColumns.has("error") ? "event.error" : "NULL error",
                     toolEventColumns.has("failure_category") ? "event.failure_category" : "NULL failure_category",
                     toolEventColumns.has("output") ? "event.output" : "NULL output",
+                    toolEventColumns.has("blocked") ? "event.blocked" : "0 blocked",
+                    toolEventColumns.has("block_reason") ? "event.block_reason" : "NULL block_reason",
+                    canProjectFilterEvents ? "event_session.status session_status" : "NULL session_status",
                     canJoinMetrics ? "metric.status metric_status" : "NULL metric_status",
                 ].join(", ");
                 const eventRows = db.prepare(`
@@ -1066,11 +1161,20 @@ function checkTelemetry(project, strict, dependencies) {
         `).all(...(canProjectFilterEvents ? [cutoff, project] : [cutoff]));
                 const semantic = eventRows.map(semanticToolOutcome);
                 const semanticFailures = semantic.filter(outcome => outcome.failed).length;
+                const unresolvedSemanticFailures = semantic.filter((outcome, index) => outcome.failed
+                    && eventRows[index]?.session_status !== "completed").length;
                 const semanticDegradations = semantic.filter(outcome => outcome.degraded).length;
                 metrics.push({ key: "semantic_tool_calls_24h", value: eventRows.length, ok: true, severity: "info" });
-                metrics.push({ key: "semantic_tool_failures_24h", value: semanticFailures, target: 0, ok: semanticFailures === 0, severity: strictSeverity });
+                metrics.push({ key: "semantic_tool_failures_24h", value: semanticFailures, target: "trend", ok: true, severity: "info" });
+                metrics.push({
+                    key: "unresolved_semantic_tool_failures_24h",
+                    value: unresolvedSemanticFailures,
+                    target: 0,
+                    ok: unresolvedSemanticFailures === 0,
+                    severity: strictSeverity,
+                });
                 metrics.push({ key: "semantic_tool_degradations_24h", value: semanticDegradations, target: 0, ok: semanticDegradations === 0, severity: strictSeverity });
-                metrics.push({ key: "semantic_tool_failure_rate_24h", value: rate(semanticFailures, eventRows.length), target: 0, ok: semanticFailures === 0, severity: strictSeverity });
+                metrics.push({ key: "semantic_tool_failure_rate_24h", value: rate(semanticFailures, eventRows.length), target: "trend", ok: true, severity: "info" });
                 metrics.push({ key: "semantic_tool_degradation_rate_24h", value: rate(semanticDegradations, eventRows.length), target: 0, ok: semanticDegradations === 0, severity: strictSeverity });
                 metrics.push({
                     key: "semantic_tool_project_scope",
@@ -1086,8 +1190,11 @@ function checkTelemetry(project, strict, dependencies) {
                             continue;
                         distribution[row.failure_category] = (distribution[row.failure_category] ?? 0) + 1;
                     }
-                    const classifiedEvents = Object.values(distribution).reduce((sum, count) => sum + count, 0);
-                    const classificationCoverage = semanticFailures === 0 ? 1 : classifiedEvents / semanticFailures;
+                    const unresolvedRows = eventRows.filter((row, index) => semantic[index]?.failed
+                        && row.session_status !== "completed");
+                    const classifiedEvents = unresolvedRows.filter(row => typeof row.failure_category === "string"
+                        && row.failure_category.trim().length > 0).length;
+                    const classificationCoverage = unresolvedRows.length === 0 ? 1 : classifiedEvents / unresolvedRows.length;
                     metrics.push({
                         key: "failure_categories_24h",
                         value: distribution,
@@ -1454,6 +1561,75 @@ function checkBenchmark(dependencies) {
     }
     return { name: "Benchmark", status: sectionStatus(metrics), metrics };
 }
+function checkRetrievalQuality(project, dependencies) {
+    const metrics = [];
+    const home = dependencies.homePath ?? homedir();
+    const path = getGlobalDevFlowDbPath(home);
+    if (!existsSync(path)) {
+        metrics.push({
+            key: 'retrieval_quality_report',
+            value: 'missing global database',
+            target: 'passing retrieval-quality report',
+            ok: false,
+            severity: 'warning',
+        });
+        return { name: 'Retrieval quality', status: sectionStatus(metrics), metrics };
+    }
+    let db;
+    try {
+        db = doctorOpenDatabase(path, dependencies);
+        if (!doctorTableExists(db, 'benchmark_reports'))
+            throw new Error('benchmark_reports table missing');
+        const row = db.prepare(`
+      SELECT report_json, created_at
+      FROM benchmark_reports
+      WHERE suite_id = 'retrieval-quality' AND project_root = ?
+      ORDER BY created_at DESC
+      LIMIT 1
+    `).get(project);
+        if (!row?.report_json) {
+            metrics.push({
+                key: 'retrieval_quality_report',
+                value: 'no project report',
+                target: 'run retrieval-quality benchmark for this project',
+                ok: false,
+                severity: 'warning',
+            });
+            return { name: 'Retrieval quality', status: sectionStatus(metrics), metrics };
+        }
+        const report = JSON.parse(row.report_json);
+        const ageMs = (dependencies.now ?? Date.now)() - Number(row.created_at ?? 0);
+        metrics.push({
+            key: 'retrieval_quality_report',
+            value: { status: report.qualityStatus, ageMs, diagnostics: report.diagnostics ?? [] },
+            target: { status: 'passed', maxAgeMs: BENCHMARK_MAX_AGE_MS },
+            ok: report.qualityStatus === 'passed' && ageMs <= BENCHMARK_MAX_AGE_MS,
+            severity: report.qualityStatus === 'failed' ? 'error' : 'warning',
+        });
+        for (const [key, passed] of Object.entries(report.gates ?? {})) {
+            metrics.push({
+                key: `retrieval_${key}`,
+                value: report.metrics?.[key],
+                target: report.thresholds?.[key],
+                ok: passed,
+                severity: 'error',
+            });
+        }
+    }
+    catch (error) {
+        metrics.push({
+            key: 'retrieval_quality_read',
+            value: error.message,
+            target: 'readable retrieval quality report',
+            ok: false,
+            severity: 'error',
+        });
+    }
+    finally {
+        db?.close();
+    }
+    return { name: 'Retrieval quality', status: sectionStatus(metrics), metrics };
+}
 function hookDebugFootprint(root) {
     if (!existsSync(root))
         return { bytes: 0, files: 0 };
@@ -4454,6 +4630,50 @@ function checkMemoryQuality(project, dependencies) {
                 ok: true,
                 severity: "info",
             });
+            if (doctorTableExists(db, 'retrieval_access_log')) {
+                const attribution = db.prepare(`
+          SELECT access_type, COUNT(*) count
+          FROM retrieval_access_log
+          GROUP BY access_type
+        `).all();
+                metrics.push({
+                    key: 'memory_retrieval_attribution',
+                    value: Object.fromEntries(attribution.map(row => [row.access_type, Number(row.count)])),
+                    target: 'selected/exposed are distinct from adopted',
+                    ok: true,
+                    severity: 'info',
+                });
+            }
+            if (doctorTableExists(db, 'observations')) {
+                const observationColumns = doctorTableColumns(db, 'observations');
+                if (!observationColumns.has('evidence_status')) {
+                    metrics.push({
+                        key: 'explicit_memory_evidence_schema',
+                        value: 'evidence_status missing',
+                        target: 'memory schema v8+',
+                        ok: false,
+                        severity: 'error',
+                    });
+                }
+                else {
+                    const evidence = db.prepare(`
+            SELECT
+              COUNT(*) total,
+              SUM(CASE WHEN evidence_status = 'verified' THEN 1 ELSE 0 END) verified
+            FROM observations
+            WHERE source = 'explicit_intent' AND quality_status = 'accepted'
+          `).get();
+                    const total = Number(evidence?.total ?? 0);
+                    const verified = Number(evidence?.verified ?? 0);
+                    metrics.push({
+                        key: 'explicit_memory_evidence_coverage',
+                        value: total > 0 ? verified / total : 1,
+                        target: 1,
+                        ok: total === 0 || verified === total,
+                        severity: 'warning',
+                    });
+                }
+            }
             metrics.push({
                 key: "memory_access_distribution",
                 value: {
@@ -4487,13 +4707,41 @@ function checkKnowledgeQuality(project, dependencies) {
             metrics.push({ key: "knowledge_schema", value: "knowledge_chunks missing", target: "Batch 3 knowledge schema", ok: false, severity: "warning" });
         }
         else {
-            const lengths = db.prepare("SELECT length(content) length FROM knowledge_chunks ORDER BY length(content)").all().map(row => Number(row.length));
+            const chunkColumns = doctorTableColumns(db, 'knowledge_chunks');
+            const tokenExpression = chunkColumns.has('token_count')
+                ? 'COALESCE(token_count, CAST((length(content) + 3) / 4 AS INTEGER))'
+                : 'CAST((length(content) + 3) / 4 AS INTEGER)';
+            const lengths = db.prepare(`SELECT ${tokenExpression} length FROM knowledge_chunks ORDER BY ${tokenExpression}`).all().map(row => Number(row.length));
             const p95Index = Math.max(0, Math.ceil(lengths.length * 0.95) - 1);
             const p95 = lengths.length === 0 ? 0 : lengths[p95Index];
-            metrics.push({ key: "knowledge_chunk_length_p95", value: p95, target: "<= 3000", ok: p95 <= 3000, severity: "warning" });
+            metrics.push({ key: "knowledge_chunk_length_p95", value: p95, target: "<= 3000 tokens", ok: p95 <= 3000, severity: "error" });
             const fts = db.prepare("SELECT sql FROM sqlite_master WHERE type = 'table' AND name = 'knowledge_fts'").get();
             const trigram = /tokenize\s*=\s*['\"]?trigram/i.test(fts?.sql ?? "");
             metrics.push({ key: "knowledge_fts_tokenizer", value: trigram ? "trigram" : "missing/non-trigram", target: "trigram", ok: trigram, severity: "warning" });
+            if (doctorTableExists(db, 'knowledge_source_readiness')) {
+                const readiness = db.prepare(`
+          SELECT source, expected_version, documents, chunks, vectors, coverage, status, failure_category
+          FROM knowledge_source_readiness ORDER BY source
+        `).all();
+                const active = readiness.filter(row => Number(row.documents ?? 0) > 0 || Number(row.chunks ?? 0) > 0);
+                const minimumCoverage = active.length > 0
+                    ? Math.min(...active.map(row => Number(row.coverage ?? 0)))
+                    : 0;
+                metrics.push({
+                    key: 'knowledge_source_readiness',
+                    value: readiness,
+                    target: 'all active sources current with >=95% vector coverage',
+                    ok: active.length > 0 && active.every(row => row.status === 'ready' && Number(row.coverage ?? 0) >= 0.95),
+                    severity: 'error',
+                });
+                metrics.push({
+                    key: 'knowledge_vector_coverage',
+                    value: minimumCoverage,
+                    target: '>= 0.95',
+                    ok: active.length > 0 && minimumCoverage >= 0.95,
+                    severity: 'error',
+                });
+            }
         }
     }
     catch (error) {
@@ -4545,8 +4793,19 @@ async function checkUiReachability(dependencies) {
     const { manifest, metrics } = acceptanceManifestMetrics(dependencies);
     const routes = manifest?.ui?.routes ?? [];
     metrics.push({ key: "dashboard_routes", value: routes.length, target: ">= 13", ok: manifest?.ui?.status === "green" && routes.length >= 13, severity: "warning" });
+    const endpoint = readRuntimeEndpointState(dependencies.homePath ?? homedir());
+    if ((!endpoint || endpoint.status === "stopped") && !dependencies.httpGet) {
+        metrics.push({
+            key: "dashboard_server_health",
+            value: "inactive",
+            target: "HTTP 200 when the runtime endpoint is active",
+            ok: true,
+            severity: "info",
+        });
+        return { name: "UI reachability", status: sectionStatus(metrics), metrics };
+    }
     const port = dependencies.env?.PORT ?? process.env.PORT ?? "13337";
-    const healthUrl = `http://127.0.0.1:${port}/api/health`;
+    const healthUrl = `${endpoint?.url ?? `http://127.0.0.1:${port}`}/api/health`;
     try {
         const response = await (dependencies.httpGet ?? defaultHttpGet)(healthUrl);
         metrics.push({ key: "dashboard_server_health", value: { url: healthUrl, status: response.status }, target: "HTTP 200", ok: response.status === 200, severity: "warning" });
@@ -4567,7 +4826,7 @@ export async function runStructuredDoctor(options = {}, dependencies = {}) {
         checkIsolation(requestedProject, dependencies),
         checkDistill(canonical.path, dependencies),
         checkLegacyPaths(canonical.path, dependencies),
-        checkVectors(canonical.path, dependencies),
+        await checkVectors(canonical.path, dependencies),
         checkTelemetry(canonical.path, Boolean(options.strict), dependencies),
         checkInjection(canonical.path, dependencies),
         checkMemoryQuality(canonical.path, dependencies),
@@ -4575,14 +4834,14 @@ export async function runStructuredDoctor(options = {}, dependencies = {}) {
         contract,
         checkDeadcode(dependencies),
         checkBenchmark(dependencies),
+        checkRetrievalQuality(canonical.path, dependencies),
         checkDataFace(dependencies),
         checkRuntimeSecurity(dependencies),
         await checkUiReachability(dependencies),
         checkHookPathHealth(dependencies),
     ];
-    const exitCode = options.strict && sections.some((section) => section.status !== "green")
-        ? 1
-        : 0;
+    const exitCode = sections.some(section => section.status === 'red'
+        || (options.strict && section.status === 'yellow')) ? 1 : 0;
     return { schemaVersion: DOCTOR_SCHEMA_VERSION, sections, exitCode };
 }
 export function runDoctor(options, dependencies = {}) {