fix(mcp-server): audit fixes — 3 bugs + 2 new tools

Bug fixes:
- lysnrai: add lysnrai.sessions.get tool (GET /sessions/:id existed but had no MCP surface)
- nomgap: add nomgap.autophagyConfidence tool (POST /fasting/autophagy-confidence had no tool)
- chronomind: fix syncStatus description 'paused' -> 'pending' (wrong field name)

New client functions: lysnraiSessionGet, nomgapAutophagyConfidence (with typed interfaces)

Root bug fixed in learning_voice_ai_agent commit 42aa931:
GET /transcripts/:id was missing from backend — lysnrai.transcripts.get was always 404-ing

services/mcp-server/src/lib/lysnrai-client.ts

@@ -111,6 +111,13 @@ export interface SessionDoc {
   updatedAt: string;
 }
 
+export function lysnraiSessionGet(
+  sessionId: string,
+  opts: LysnraiClientOptions
+): Promise<SessionDoc> {
+  return lysnraiFetch(`/sessions/${sessionId}`, { method: 'GET' }, opts);
+}
+
 export function lysnraiSessionsList(
   params: { limit?: number; offset?: number; status?: string },
   opts: LysnraiClientOptions

services/mcp-server/src/lib/nomgap-client.ts

@@ -101,6 +101,42 @@ export function nomgapBodyStagesList(
   return nomgapFetch('/fasting/stages', { method: 'GET' }, opts);
 }
 
+// ── Autophagy confidence ──────────────────────────────────────────────────
+
+export interface AutophagyConfidenceInput {
+  durationHours: number;
+  activityLevel: 'sedentary' | 'light' | 'moderate' | 'active' | 'very_active';
+  lastMealCarbs?: number;
+  sleepHours?: number;
+  completionHistory?: { totalFasts: number; completionRate: number };
+  hrvData?: { restingHR?: number; hrv?: number };
+}
+
+export interface AutophagyConfidenceResult {
+  confidence: number;
+  label: 'unlikely' | 'possible' | 'likely' | 'very_likely' | 'near_certain';
+  breakdown: {
+    duration: number;
+    meal: number;
+    activity: number;
+    sleep: number;
+    history: number;
+    hrv: number;
+  };
+  currentStage: string;
+}
+
+export function nomgapAutophagyConfidence(
+  input: AutophagyConfidenceInput,
+  opts: Pick<NomGapClientOptions, 'requestId'>
+): Promise<AutophagyConfidenceResult> {
+  return nomgapFetch(
+    '/fasting/autophagy-confidence',
+    { method: 'POST', body: JSON.stringify(input) },
+    opts
+  );
+}
+
 // ── Push triggers ──────────────────────────────────────────────────────────
 
 export type PushTriggerType =

services/mcp-server/src/modules/chronomind/chronomind-tools.ts

@@ -109,7 +109,7 @@ registerTool({
 registerTool({
   name: 'chronomind.syncStatus',
   description:
-    'Instant sync health check: total timers, active count, paused count, unsynced count, and last sync timestamp. Requires admin role.',
+    'Instant sync health check: total timers, active count, pending count, unsynced count, and last sync timestamp. Requires admin role.',
   requiredRole: 'admin',
   inputSchema: z.object({}),
   async execute(_args, req) {

services/mcp-server/src/modules/lysnrai/lysnrai-tools.ts

@@ -14,6 +14,7 @@ import {
   lysnraiTranscriptGet,
   lysnraiTranscriptRunExtraction,
   lysnraiSttGetBackendStatus,
+  lysnraiSessionGet,
   lysnraiSessionsList,
   lysnraiOrgsList,
   lysnraiOrgGet,
@@ -84,6 +85,21 @@ registerTool({
   },
 });
 
+// ── lysnrai.sessions.get ──────────────────────────────────────────────────
+
+registerTool({
+  name: 'lysnrai.sessions.get',
+  description:
+    'Get a single dictation session by ID including its entries[], composedText, compositionHistory, and status. Requires admin role.',
+  requiredRole: 'admin',
+  inputSchema: z.object({
+    sessionId: z.string().min(1).describe('Session ID (ses_… prefix)'),
+  }),
+  async execute(args, req) {
+    return lysnraiSessionGet(args.sessionId, { token: tokenOf(req), requestId: req.id });
+  },
+});
+
 // ── lysnrai.sessions.list ─────────────────────────────────────────────────
 
 registerTool({

services/mcp-server/src/modules/nomgap/nomgap-tools.ts

@@ -14,6 +14,7 @@ import {
   nomgapFastingGetWeeklyStats,
   nomgapProtocolsList,
   nomgapBodyStagesList,
+  nomgapAutophagyConfidence,
   nomgapPushFire,
   nomgapPushGetStats,
   nomgapPushGetPending,
@@ -158,6 +159,53 @@ registerTool({
   },
 });
 
+// ── nomgap.autophagyConfidence ─────────────────────────────────────────────────
+
+registerTool({
+  name: 'nomgap.autophagyConfidence',
+  description: [
+    'Calculate a personalised autophagy confidence score (0–100) given fasting duration and biometrics.',
+    'Weights: duration 40%, last-meal carbs 20%, activity 15%, sleep 10%, completion history 10%, HRV 5%.',
+    'Returns: confidence (0–100), label (unlikely/possible/likely/very_likely/near_certain), breakdown, currentStage.',
+    'Public endpoint — no auth required on backend.',
+  ].join(' '),
+  requiredRole: 'admin',
+  inputSchema: z.object({
+    durationHours: z.coerce.number().min(0).describe('Hours elapsed since the fast started'),
+    activityLevel: z
+      .enum(['sedentary', 'light', 'moderate', 'active', 'very_active'])
+      .describe('Physical activity level during the fast'),
+    lastMealCarbs: z.coerce
+      .number()
+      .min(0)
+      .optional()
+      .describe('Grams of carbs in the last meal before the fast'),
+    sleepHours: z.coerce
+      .number()
+      .min(0)
+      .max(24)
+      .optional()
+      .describe('Hours of sleep the previous night'),
+    completionHistory: z
+      .object({
+        totalFasts: z.coerce.number().min(0),
+        completionRate: z.coerce.number().min(0).max(1),
+      })
+      .optional()
+      .describe('Historical fasting stats (improves scoring accuracy)'),
+    hrvData: z
+      .object({
+        restingHR: z.coerce.number().min(0).optional(),
+        hrv: z.coerce.number().min(0).optional(),
+      })
+      .optional()
+      .describe('Heart rate variability data from wearable'),
+  }),
+  async execute(args, req) {
+    return nomgapAutophagyConfidence(args, { requestId: req.id });
+  },
+});
+
 // ── nomgap.push.pending ───────────────────────────────────────────────────
 
 registerTool({