memorix 1.6.0 → 1.6.1

package/src/cli/commands/poll.ts

@@ -1,32 +1,32 @@
-import { defineCommand } from 'citty';
-import { computePoll, computeWatermark } from '../../team/poll.js';
-import { getObservationStore } from '../../store/obs-store.js';
+import { defineCommand } from 'citty';
+import { computePoll, computeWatermark } from '../../team/poll.js';
+import { getObservationStore } from '../../store/obs-store.js';
 import { getAllObservations } from '../../memory/observations.js';
 import { withFreshIndex } from '../../memory/freshness.js';
 import { filterReadableObservations } from '../../memory/visibility.js';
 import { emitError, emitResult, getCliProjectContext, resolveCliActorId, shortId } from './operator-shared.js';
-
-export default defineCommand({
-  meta: {
-    name: 'poll',
-    description: 'Get a full project coordination snapshot for an agent',
-  },
-  args: {
-    agentId: { type: 'string', description: 'Agent ID for personalized situational awareness' },
-    markInboxRead: { type: 'boolean', description: 'Mark all inbox messages as read after returning them' },
-    json: { type: 'boolean', description: 'Emit machine-readable JSON output' },
-  },
-  run: async ({ args }) => {
-    const asJson = !!args.json;
-
-    try {
+
+export default defineCommand({
+  meta: {
+    name: 'poll',
+    description: 'Get a full project coordination snapshot for an agent',
+  },
+  args: {
+    agentId: { type: 'string', description: 'Agent ID for personalized situational awareness' },
+    markInboxRead: { type: 'boolean', description: 'Mark all inbox messages as read after returning them' },
+    json: { type: 'boolean', description: 'Emit machine-readable JSON output' },
+  },
+  run: async ({ args }) => {
+    const asJson = !!args.json;
+
+    try {
       const { project, teamStore, identity, reader: activeReader } = await getCliProjectContext();
       const agentId = resolveCliActorId(args.agentId, identity);
       let reader = activeReader;
-
-      let watermark = computeWatermark(0, 0, 0);
-      if (agentId) {
-        const agent = teamStore.getAgent(agentId);
+
+      let watermark = computeWatermark(0, 0, 0);
+      if (agentId) {
+        const agent = teamStore.getAgent(agentId);
         if (!agent || agent.project_id !== project.id) {
           emitError(`Unknown agent "${agentId}"`, asJson);
           return;
@@ -36,45 +36,45 @@ export default defineCommand({
           agentId,
           isTeamMember: agent.status === 'active',
         };
-
-        const lastSeen = agent.last_seen_obs_generation;
-        const currentGen = getObservationStore().getGeneration();
-        const projectObs = await withFreshIndex(() =>
+
+        const lastSeen = agent.last_seen_obs_generation;
+        const currentGen = getObservationStore().getGeneration();
+        const projectObs = await withFreshIndex(() =>
           filterReadableObservations(
             getAllObservations().filter(
               (obs) => obs.projectId === project.id && (obs.writeGeneration ?? 0) > lastSeen,
             ),
             reader,
           ),
-        );
-        watermark = computeWatermark(lastSeen, currentGen, projectObs.length);
-        teamStore.updateWatermark(agentId, currentGen);
-        teamStore.heartbeat(agentId);
-      }
-
-      const poll = computePoll(teamStore, project.id, agentId ?? null, watermark);
-      if (args.markInboxRead && agentId) {
-        teamStore.markAllRead(project.id, agentId);
-      }
-
-      const text = [
-        poll.agent ? `You: ${shortId(poll.agent.agentId)} (${poll.agent.status})` : 'Project-level overview',
-        poll.watermark.newObservationCount > 0
-          ? `${poll.watermark.newObservationCount} new observation(s)`
-          : 'No unseen observations',
-        poll.inbox.unreadCount > 0 ? `${poll.inbox.unreadCount} unread message(s)` : 'Inbox clear',
-        poll.tasks.myInProgress.length > 0
-          ? `${poll.tasks.myInProgress.length} in-progress task(s)`
-          : 'No in-progress tasks',
-        poll.tasks.availableToClaim.length > 0
-          ? `${poll.tasks.availableToClaim.length} task(s) available to claim`
-          : 'No claimable tasks',
-        `Team: ${poll.team.activeAgents.length} active / ${poll.team.totalAgents} total`,
-      ].join('\n');
-
-      emitResult({ project, poll }, text, asJson);
-    } catch (error) {
-      emitError(error instanceof Error ? error.message : String(error), asJson);
-    }
-  },
-});
+        );
+        watermark = computeWatermark(lastSeen, currentGen, projectObs.length);
+        teamStore.updateWatermark(agentId, currentGen);
+        teamStore.heartbeat(agentId);
+      }
+
+      const poll = computePoll(teamStore, project.id, agentId ?? null, watermark);
+      if (args.markInboxRead && agentId) {
+        teamStore.markAllRead(project.id, agentId);
+      }
+
+      const text = [
+        poll.agent ? `You: ${shortId(poll.agent.agentId)} (${poll.agent.status})` : 'Project-level overview',
+        poll.watermark.newObservationCount > 0
+          ? `${poll.watermark.newObservationCount} new observation(s)`
+          : 'No unseen observations',
+        poll.inbox.unreadCount > 0 ? `${poll.inbox.unreadCount} unread message(s)` : 'Inbox clear',
+        poll.tasks.myInProgress.length > 0
+          ? `${poll.tasks.myInProgress.length} in-progress task(s)`
+          : 'No in-progress tasks',
+        poll.tasks.availableToClaim.length > 0
+          ? `${poll.tasks.availableToClaim.length} task(s) available to claim`
+          : 'No claimable tasks',
+        `Team: ${poll.team.activeAgents.length} active / ${poll.team.totalAgents} total`,
+      ].join('\n');
+
+      emitResult({ project, poll }, text, asJson);
+    } catch (error) {
+      emitError(error instanceof Error ? error.message : String(error), asJson);
+    }
+  },
+});

package/src/cli/commands/reasoning.ts

@@ -1,6 +1,6 @@
-import { defineCommand } from 'citty';
-import { compactSearch } from '../../compact/engine.js';
-import { storeObservation } from '../../memory/observations.js';
+import { defineCommand } from 'citty';
+import { compactSearch } from '../../compact/engine.js';
+import { storeObservation } from '../../memory/observations.js';
 import {
   emitError,
   emitResult,
@@ -9,65 +9,65 @@ import {
   parsePositiveInt,
   resolveCliWriteScope,
 } from './operator-shared.js';
-
-export default defineCommand({
-  meta: {
-    name: 'reasoning',
-    description: 'Store and search decision rationale from the operator CLI',
-  },
-  args: {
-    entity: { type: 'string', description: 'Entity this reasoning applies to' },
-    decision: { type: 'string', description: 'Decision that was made' },
-    rationale: { type: 'string', description: 'Why this approach was chosen' },
-    alternatives: { type: 'string', description: 'Comma-separated alternatives that were considered' },
-    constraints: { type: 'string', description: 'Comma-separated constraints' },
-    expectedOutcome: { type: 'string', description: 'Expected outcome from this decision' },
-    risks: { type: 'string', description: 'Comma-separated risks or downsides' },
-    concepts: { type: 'string', description: 'Comma-separated related concepts' },
-    files: { type: 'string', description: 'Comma-separated file list' },
-    relatedCommits: { type: 'string', description: 'Comma-separated related commit hashes' },
+
+export default defineCommand({
+  meta: {
+    name: 'reasoning',
+    description: 'Store and search decision rationale from the operator CLI',
+  },
+  args: {
+    entity: { type: 'string', description: 'Entity this reasoning applies to' },
+    decision: { type: 'string', description: 'Decision that was made' },
+    rationale: { type: 'string', description: 'Why this approach was chosen' },
+    alternatives: { type: 'string', description: 'Comma-separated alternatives that were considered' },
+    constraints: { type: 'string', description: 'Comma-separated constraints' },
+    expectedOutcome: { type: 'string', description: 'Expected outcome from this decision' },
+    risks: { type: 'string', description: 'Comma-separated risks or downsides' },
+    concepts: { type: 'string', description: 'Comma-separated related concepts' },
+    files: { type: 'string', description: 'Comma-separated file list' },
+    relatedCommits: { type: 'string', description: 'Comma-separated related commit hashes' },
     relatedEntities: { type: 'string', description: 'Comma-separated related entity names' },
     visibility: { type: 'string', description: 'Reasoning visibility: project (default), personal, or team' },
-    query: { type: 'string', description: 'Search query for reasoning traces' },
-    limit: { type: 'string', description: 'Search result limit' },
-    scope: { type: 'string', description: 'project or global scope for search' },
-    json: { type: 'boolean', description: 'Emit machine-readable JSON output' },
-  },
-  run: async ({ args }) => {
-    const action = (args._ as string[])?.[0] || '';
-    const asJson = !!args.json;
-
-    try {
+    query: { type: 'string', description: 'Search query for reasoning traces' },
+    limit: { type: 'string', description: 'Search result limit' },
+    scope: { type: 'string', description: 'project or global scope for search' },
+    json: { type: 'boolean', description: 'Emit machine-readable JSON output' },
+  },
+  run: async ({ args }) => {
+    const action = (args._ as string[])?.[0] || '';
+    const asJson = !!args.json;
+
+    try {
       const { project, reader, identity } = await getCliProjectContext({ searchIndex: action === 'search' });
-
-      switch (action) {
-        case 'store': {
-          const entityName = (args.entity as string | undefined)?.trim();
-          const decision = (args.decision as string | undefined)?.trim();
-          const rationale = (args.rationale as string | undefined)?.trim();
-          if (!entityName || !decision || !rationale) {
-            emitError('entity, decision, and rationale are required for "memorix reasoning store"', asJson);
-            return;
-          }
-
-          const alternatives = parseCsvList(args.alternatives as string | undefined);
-          const constraints = parseCsvList(args.constraints as string | undefined);
-          const risks = parseCsvList(args.risks as string | undefined);
-          const concepts = parseCsvList(args.concepts as string | undefined);
-          const filesModified = parseCsvList(args.files as string | undefined);
-          const relatedCommits = parseCsvList(args.relatedCommits as string | undefined);
-          const relatedEntities = parseCsvList(args.relatedEntities as string | undefined);
-
-          const narrativeParts: string[] = [rationale];
-          if (alternatives.length > 0) {
-            narrativeParts.push(`Alternatives considered: ${alternatives.join('; ')}`);
-          }
-          if (constraints.length > 0) {
-            narrativeParts.push(`Constraints: ${constraints.join('; ')}`);
-          }
-          if (args.expectedOutcome) {
-            narrativeParts.push(`Expected outcome: ${String(args.expectedOutcome).trim()}`);
-          }
+
+      switch (action) {
+        case 'store': {
+          const entityName = (args.entity as string | undefined)?.trim();
+          const decision = (args.decision as string | undefined)?.trim();
+          const rationale = (args.rationale as string | undefined)?.trim();
+          if (!entityName || !decision || !rationale) {
+            emitError('entity, decision, and rationale are required for "memorix reasoning store"', asJson);
+            return;
+          }
+
+          const alternatives = parseCsvList(args.alternatives as string | undefined);
+          const constraints = parseCsvList(args.constraints as string | undefined);
+          const risks = parseCsvList(args.risks as string | undefined);
+          const concepts = parseCsvList(args.concepts as string | undefined);
+          const filesModified = parseCsvList(args.files as string | undefined);
+          const relatedCommits = parseCsvList(args.relatedCommits as string | undefined);
+          const relatedEntities = parseCsvList(args.relatedEntities as string | undefined);
+
+          const narrativeParts: string[] = [rationale];
+          if (alternatives.length > 0) {
+            narrativeParts.push(`Alternatives considered: ${alternatives.join('; ')}`);
+          }
+          if (constraints.length > 0) {
+            narrativeParts.push(`Constraints: ${constraints.join('; ')}`);
+          }
+          if (args.expectedOutcome) {
+            narrativeParts.push(`Expected outcome: ${String(args.expectedOutcome).trim()}`);
+          }
           if (risks.length > 0) {
             narrativeParts.push(`Risks: ${risks.join('; ')}`);
           }
@@ -77,70 +77,70 @@ export default defineCommand({
           );
 
           const result = await storeObservation({
-            entityName,
-            type: 'reasoning',
-            title: decision,
-            narrative: narrativeParts.join('. '),
-            facts: [
-              `Decision: ${decision}`,
-              ...alternatives.map((item) => `Alternative: ${item}`),
-              ...constraints.map((item) => `Constraint: ${item}`),
-              ...(args.expectedOutcome ? [`Expected outcome: ${String(args.expectedOutcome).trim()}`] : []),
-              ...risks.map((item) => `Risk: ${item}`),
-              ...relatedCommits.map((item) => `Commit: ${item}`),
-              ...relatedEntities.map((item) => `Related entity: ${item}`),
-            ],
-            concepts,
-            filesModified,
-            relatedCommits,
-            relatedEntities,
+            entityName,
+            type: 'reasoning',
+            title: decision,
+            narrative: narrativeParts.join('. '),
+            facts: [
+              `Decision: ${decision}`,
+              ...alternatives.map((item) => `Alternative: ${item}`),
+              ...constraints.map((item) => `Constraint: ${item}`),
+              ...(args.expectedOutcome ? [`Expected outcome: ${String(args.expectedOutcome).trim()}`] : []),
+              ...risks.map((item) => `Risk: ${item}`),
+              ...relatedCommits.map((item) => `Commit: ${item}`),
+              ...relatedEntities.map((item) => `Related entity: ${item}`),
+            ],
+            concepts,
+            filesModified,
+            relatedCommits,
+            relatedEntities,
             projectId: project.id,
             source: 'manual',
             ...writeScope,
-          });
-
-          emitResult(
-            { project, observation: result.observation, upserted: result.upserted },
-            `${result.upserted ? 'Updated' : 'Stored'} reasoning trace #${result.observation.id}: ${decision}`,
-            asJson,
-          );
-          return;
-        }
-
-        case 'search': {
-          const query = (args.query as string | undefined)?.trim();
-          if (!query) {
-            emitError('query is required for "memorix reasoning search"', asJson);
-            return;
-          }
-          const scope = (args.scope as string | undefined) === 'global' ? 'global' : 'project';
-          const limit = parsePositiveInt(args.limit as string | undefined, 10);
-          const result = await compactSearch({
-            query,
-            limit,
+          });
+
+          emitResult(
+            { project, observation: result.observation, upserted: result.upserted },
+            `${result.upserted ? 'Updated' : 'Stored'} reasoning trace #${result.observation.id}: ${decision}`,
+            asJson,
+          );
+          return;
+        }
+
+        case 'search': {
+          const query = (args.query as string | undefined)?.trim();
+          if (!query) {
+            emitError('query is required for "memorix reasoning search"', asJson);
+            return;
+          }
+          const scope = (args.scope as string | undefined) === 'global' ? 'global' : 'project';
+          const limit = parsePositiveInt(args.limit as string | undefined, 10);
+          const result = await compactSearch({
+            query,
+            limit,
             type: 'reasoning',
             projectId: scope === 'global' ? undefined : project.id,
             status: 'active',
             reader: scope === 'global' ? {} : reader,
-          });
-          emitResult(
-            { project, scope, entries: result.entries },
-            result.entries.length === 0 ? 'No reasoning traces found.' : `[REASONING] Reasoning traces\n${result.formatted}`,
-            asJson,
-          );
-          return;
-        }
-
-        default:
-          console.log('Memorix Reasoning Commands');
-          console.log('');
-          console.log('Usage:');
+          });
+          emitResult(
+            { project, scope, entries: result.entries },
+            result.entries.length === 0 ? 'No reasoning traces found.' : `[REASONING] Reasoning traces\n${result.formatted}`,
+            asJson,
+          );
+          return;
+        }
+
+        default:
+          console.log('Memorix Reasoning Commands');
+          console.log('');
+          console.log('Usage:');
           console.log('  memorix reasoning store --entity auth --decision "Use SQLite" --rationale "..." [--visibility project|personal|team]');
-          console.log('  memorix reasoning search --query "why sqlite" [--scope project|global --limit 10]');
-      }
-    } catch (error) {
-      emitError(error instanceof Error ? error.message : String(error), asJson);
-    }
-  },
-});
-
+          console.log('  memorix reasoning search --query "why sqlite" [--scope project|global --limit 10]');
+      }
+    } catch (error) {
+      emitError(error instanceof Error ? error.message : String(error), asJson);
+    }
+  },
+});
+

package/src/cli/commands/serve-http.ts

@@ -29,13 +29,19 @@ import { canManageObservation, filterReadableObservations } from '../../memory/v
 import { parseTcpPortOrReport } from '../port.js';
 import { mcpFileUriToPath } from '../mcp-root-path.js';
 
-export const DEFAULT_SESSION_TIMEOUT_MS = 30 * 60 * 1000;
+/**
+ * HTTP MCP is a shared control plane. A normal thinking break should not
+ * silently invalidate a client session. Operators can choose a shorter GC
+ * window, or set 0 to disable idle GC entirely.
+ */
+export const DEFAULT_SESSION_TIMEOUT_MS = 12 * 60 * 60 * 1000;
+export const EXPIRED_SESSION_TTL_MS = 10 * 60 * 1000;
 
 export function parseSessionTimeoutMs(raw: string | undefined): number {
   const value = raw?.trim();
   if (!value) return DEFAULT_SESSION_TIMEOUT_MS;
   const parsed = Number(value);
-  if (!Number.isFinite(parsed) || parsed <= 0) return DEFAULT_SESSION_TIMEOUT_MS;
+  if (!Number.isFinite(parsed) || parsed < 0) return DEFAULT_SESSION_TIMEOUT_MS;
   return Math.floor(parsed);
 }
 
@@ -132,7 +138,11 @@ export default defineCommand({
     console.error(`[memorix] HTTP transport starting on ${host}:${port}`);
     console.error(`[memorix] Project root: ${projectRoot}`);
     const sessionTimeoutMs = parseSessionTimeoutMs(process.env.MEMORIX_SESSION_TIMEOUT_MS);
-    console.error(`[memorix] HTTP session idle timeout: ${Math.round(sessionTimeoutMs / 60000)}min (${sessionTimeoutMs}ms)`);
+    console.error(
+      sessionTimeoutMs === 0
+        ? '[memorix] HTTP session idle timeout: disabled'
+        : `[memorix] HTTP session idle timeout: ${Math.round(sessionTimeoutMs / 60000)}min (${sessionTimeoutMs}ms)`,
+    );
 
     // Per-project TeamStore cache (Option B) — each dataDir gets its own TeamStore instance.
     // This ensures true isolation between projects in HTTP control-plane mode.
@@ -166,6 +176,9 @@ export default defineCommand({
 
     // Session activity tracking (for GC timeout)
     const sessionLastActivity = new Map<string, number>();
+    // Keep a short-lived tombstone so an expired client gets an actionable
+    // reinitialize response instead of a generic bad request.
+    const expiredSessions = new Map<string, number>();
 
     // Probe session noise reduction: defer init logs, suppress short-lived sessions
     let suppressedProbeCount = 0;
@@ -182,6 +195,30 @@ export default defineCommand({
       }
     }
 
+    function forgetExpiredSessions(now = Date.now()): void {
+      for (const [sessionId, expiresAt] of expiredSessions) {
+        if (expiresAt <= now) expiredSessions.delete(sessionId);
+      }
+    }
+
+    function sendUnknownSession(res: ServerResponse, sessionId: string | undefined, jsonRpc = false): void {
+      const expired = Boolean(sessionId && expiredSessions.has(sessionId));
+      const message = expired
+        ? 'MCP session expired after inactivity. Initialize a new session and retry the request.'
+        : 'MCP session not found. Initialize a new session and retry the request.';
+      if (jsonRpc) {
+        res.writeHead(404, { 'Content-Type': 'application/json' });
+        res.end(JSON.stringify({
+          jsonrpc: '2.0',
+          error: { code: -32001, message },
+          id: null,
+        }));
+        return;
+      }
+      res.writeHead(404, { 'Content-Type': 'text/plain' });
+      res.end(message);
+    }
+
     /**
      * Parse JSON body from IncomingMessage
      */
@@ -360,6 +397,11 @@ export default defineCommand({
         return;
       }
 
+      if (sessionId) {
+        sendUnknownSession(res, sessionId, true);
+        return;
+      }
+
       if (!sessionId && isInitializeRequest(body)) {
         // New session — create transport + server
         let createdState: SessionState | null = null;
@@ -488,8 +530,12 @@ export default defineCommand({
     async function handleGet(req: IncomingMessage, res: ServerResponse) {
       const sessionId = req.headers['mcp-session-id'] as string | undefined;
       if (!sessionId || !sessions.has(sessionId)) {
-        res.writeHead(400, { 'Content-Type': 'text/plain' });
-        res.end('Invalid or missing session ID');
+        if (!sessionId) {
+          res.writeHead(400, { 'Content-Type': 'text/plain' });
+          res.end('Missing MCP session ID');
+          return;
+        }
+        sendUnknownSession(res, sessionId);
         return;
       }
 
@@ -502,8 +548,12 @@ export default defineCommand({
     async function handleDelete(req: IncomingMessage, res: ServerResponse) {
       const sessionId = req.headers['mcp-session-id'] as string | undefined;
       if (!sessionId || !sessions.has(sessionId)) {
-        res.writeHead(400, { 'Content-Type': 'text/plain' });
-        res.end('Invalid or missing session ID');
+        if (!sessionId) {
+          res.writeHead(400, { 'Content-Type': 'text/plain' });
+          res.end('Missing MCP session ID');
+          return;
+        }
+        sendUnknownSession(res, sessionId);
         return;
       }
 
@@ -1414,6 +1464,7 @@ export default defineCommand({
       // Lightweight health check — responds immediately, no heavy init required.
       // This is the readiness signal for background start / status.
       if (url.pathname === '/health') {
+        const { getEmbeddingRuntimeHealth } = await import('../../embedding/provider.js');
         res.writeHead(200, { 'Content-Type': 'application/json' });
         res.end(JSON.stringify({
           status: 'ok',
@@ -1421,6 +1472,7 @@ export default defineCommand({
           port,
           uptime: Math.round(process.uptime()),
           pid: process.pid,
+          embedding: getEmbeddingRuntimeHealth(),
         }));
         return;
       }
@@ -1491,6 +1543,12 @@ export default defineCommand({
       await serveDashStatic(req, res);
     });
 
+    // MCP session continuity is independent from one TCP socket. Keep Node's
+    // socket timeout above its 5s default while the session map remains the
+    // actual continuity boundary.
+    httpServer.keepAliveTimeout = 60_000;
+    httpServer.headersTimeout = 65_000;
+
     httpServer.listen(port, host, () => {
       // Write readiness file — background start polls this for out-of-band readiness detection
       try {
@@ -1521,10 +1579,13 @@ export default defineCommand({
     const gcInterval = setInterval(() => {
       maybeProbeSummary(); // Flush suppressed probe count periodically
       const now = Date.now();
+      forgetExpiredSessions(now);
+      if (SESSION_TIMEOUT_MS === 0) return;
       for (const [sid, state] of sessions) {
         const lastActive = sessionLastActivity.get(sid) ?? 0;
         if (now - lastActive > SESSION_TIMEOUT_MS) {
           console.error(`[memorix] Session ${sid.slice(0, 8)}… timed out (idle ${Math.round((now - lastActive) / 60000)}min), closing`);
+          expiredSessions.set(sid, now + EXPIRED_SESSION_TTL_MS);
           state.transport.close().catch(() => {});
           sessions.delete(sid);
           sessionLastActivity.delete(sid);