neotoma 0.27.0 → 0.28.0

package/README.md

@@ -61,7 +61,7 @@ graph LR
 
 ## What you can do with it
 
-Neotoma v0.27.0 exposes 67 MCP tools and 112 REST paths in its OpenAPI spec. They cover largely the same capabilities, but the MCP server, the REST API, and the CLI are separate implementations, and some checks and attribution differ between them (see Known limitations). The capability surface includes:
+Neotoma v0.28.0 exposes 67 MCP tools and 112 REST paths in its OpenAPI spec. They cover largely the same capabilities, but the MCP server, the REST API, and the CLI are separate implementations, and some checks and attribution differ between them (see Known limitations). The capability surface includes:
 
 **Ingest and store.** Store structured records or raw files in one call. File ingestion extracts text from PDF (with a first-page image fallback), CSV (with adaptive chunking for large files), Parquet, JSON, and plain text; images and audio are stored as raw sources. A committed, keyed structured store started on v0.26.0 that stops partway finishes its missing observations on a same-key retry; a store carrying an interpretation returns `ERR_STORE_WRITE_INCOMPLETE`, and keys left over from earlier versions behave differently over MCP and HTTP (see Known limitations). See Known limitations.
 
@@ -111,12 +111,12 @@ neotoma init
 neotoma setup --tool claude-code
 ```
 
-In v0.27.0, `neotoma setup --tool claude-code` writes the MCP entries and more:
+In the current package source, `neotoma setup --tool claude-code` writes the MCP entries and more. The skill count below includes source changes not yet in published v0.27.0, which contains 12 installable skills; check the package version you actually use:
 
 - Two MCP entries in the project's `.mcp.json`: `neotoma-dev` (development profile, `neotoma.db`) and `neotoma` (production profile, `neotoma.prod.db`). They use separate databases, so an agent on one entry does not see what an agent on the other stored.
 - CLI instruction files for Claude Code, Cursor, and Codex in the project: `.claude/rules/neotoma_cli.mdc`, `.cursor/rules/neotoma_cli.mdc`, and `.codex/neotoma_cli.md`.
 - When `claude` is on your PATH, it runs `claude plugin marketplace add` and `claude plugin install` to install the Neotoma Claude Code plugin (five hooks). Without `claude` on PATH, setup writes everything else and then exits with status 1.
-- When `~/.claude` exists, it links 12 Neotoma skills into `~/.claude/skills`.
+- When `~/.claude` exists, it links 13 Neotoma skills into `~/.claude/skills`.
 
 It also adds two allow rules, `Bash(neotoma:*)` and `Bash(npm install -g neotoma:*)`, to `.claude/settings.local.json` (project scope, the default). The first is a wildcard: Claude Code then runs any `neotoma` command without asking, including destructive ones such as `neotoma reset`, `neotoma storage merge-db`, `neotoma backup restore`, and `neotoma processes kill`. `--scope both` also writes the rules to `~/.claude/settings.json`, and `--skip-permissions` writes none. For Cursor the same two rules go to `.cursor/allowlist.json`; for Codex they go to the user-level `~/.codex/config.toml` whatever the scope.
 
@@ -165,7 +165,7 @@ As agent use expands, reality fragments across chat histories, agent memories, f
 
 | Vision phase | What it means | Status |
 | --- | --- | --- |
-| **P0: Deterministic single-writer state** | Observations the write path does not edit, hash-derived entity IDs, deterministic reduction, field-level provenance, corrections as new observations, per-entity observation history | ✅ **Shipped**: in daily use; a later ordinary write can still replace a correction (see Known limitations) |
+| **P0: Deterministic single-writer state** | Observations the write path does not edit, hash-derived entity IDs, deterministic reduction, field-level provenance, corrections as new observations, per-entity observation history | ✅ **Shipped**: in daily use; a correction stays authoritative on its field until a later correction replaces it |
 | **P1: Multi-user state foundations** | Human and agent identities, attributed writes, tenant isolation, access controls, shared instances | 🟡 **Partially shipped**: hosted multi-user mode with `user_id` tenancy, per-agent identity (AAuth, optional hardware attestation), capability grants, guest tokens, peer federation. Not yet: organizations/workspaces, membership lifecycle, invitations, offboarding |
 | **P2: Authority over state** | Domain ownership, correction rights, supersession, policy ownership, temporary grants, disclosure logs | 🟡 **Mechanisms exist** (corrections, `SUPERSEDES` relationships, per-operation access controls); authority *semantics* (who may correct what, scoped by domain) are future work |
 | **P3: Multi-principal semantics** | Competing interpretations, disputed claims, official positions, consensus vs unresolved disagreement, field-level policies, historical validity | 🔜 Planned: interpretations are first-class today; dispute/official-position semantics are not |

package/dist/actions.d.ts.map

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package/dist/actions.js

@@ -46,6 +46,7 @@ import { IssueTransportError, IssueValidationError } from "./services/issues/err
 import { externalActorFromCallerInput } from "./services/issues/external_actor_builder.js";
 import { getCurrentAAuthAdmission, getCurrentAgentIdentity, getCurrentAttribution, getCurrentExternalActor, runWithAuthenticatedPrincipal, runWithExternalActor, runWithRequestContext, } from "./services/request_context.js";
 import { assertCanWriteProtectedBatch } from "./services/protected_entity_types.js";
+import { createMcpLookupReceiptObserver, observeMcpLookupResponse, } from "./services/mcp_lookup_timing.js";
 import { redactMemberAttribution } from "./services/attribution_redaction.js";
 import { createAgentIdentity as buildAgentIdentity, getAgentIdentityFromRequest, normaliseClientName, } from "./crypto/agent_identity.js";
 import { initServerKeys } from "./services/encryption_service.js";
@@ -81,6 +82,7 @@ import { AnalyzeSchemaCandidatesRequestSchema, AuditUndeclaredFragmentsRequestSc
 import { DEFAULT_OBSERVATION_SOURCE } from "./services/observation_insert.js";
 import { getMimeTypeFromExtension } from "./services/file_text_extraction.js";
 import { queryEntitiesWithCount } from "./shared/action_handlers/entity_handlers.js";
+import { EXACT_IDENTITY_REQUEST_MESSAGE, exactIdentityRequested, readExactIdentity, } from "./shared/action_handlers/exact_identity_read.js";
 import { retrieveEntityByIdentifierWithFallback } from "./shared/action_handlers/entity_identifier_handler.js";
 import { prepareEntitySnapshotWithEmbedding, upsertEntitySnapshotWithEmbedding, } from "./services/entity_snapshot_embedding.js";
 import { isNeotomaEntityId } from "./shared/neotoma_entity_id.js";
@@ -110,6 +112,9 @@ export function getResolvedServerMode() {
     return _resolvedServerMode;
 }
 export const app = express();
+const mcpLookupReceiptObserver = createMcpLookupReceiptObserver();
+if (mcpLookupReceiptObserver)
+    app.use(mcpLookupReceiptObserver);
 // Trust proxy headers (required for express-rate-limit when X-Forwarded-For is present)
 app.set("trust proxy", true);
 // Configure CSP to allow CDN scripts for the uploader and API connects
@@ -232,7 +237,10 @@ app.use(express.json({
         req.rawBody = Buffer.from(buf);
     },
 }));
-app.use(morgan("dev"));
+app.use(morgan("dev", {
+    // Suppress identity-bearing URLs independently of route spelling or method.
+    skip: (req) => exactIdentityRequested(req.query),
+}));
 app.use(cookieParser());
 app.use(unknownFieldsGuard);
 // Sandbox-mode response header. Stamped on every response so clients can
@@ -1764,6 +1772,7 @@ app.all("/mcp", async (req, res) => {
         const authHeader = (req.headers["authorization"] || req.headers["Authorization"]);
         let connectionIdHeader = (req.headers["x-connection-id"] || req.headers["X-Connection-Id"]);
         let bearerValidated = false;
+        let primaryBearerValidated = false;
         // Development connection identities are assigned by this gate, not by the
         // client. A client-sent value is honoured only where the gate would assign
         // the same identity itself: a local caller in development mode. Anywhere
@@ -1812,6 +1821,7 @@ app.all("/mcp", async (req, res) => {
                 // same grants. See src/services/bearer_slots.ts.
                 const slot = matchConfiguredBearer(token);
                 if (slot) {
+                    primaryBearerValidated = slot === "primary";
                     if (slot === "previous") {
                         recordPreviousBearerUse({
                             surface: "mcp",
@@ -1981,6 +1991,8 @@ app.all("/mcp", async (req, res) => {
             return res.status(shaped.status).json(shaped.body);
         }
         // Legacy session path (2025-11-25 and earlier). Unchanged by #2070.
+        // A qualified lookup can disconnect while stale-session recovery is still pending.
+        const mcpLookupTiming = primaryBearerValidated ? observeMcpLookupResponse(req, res) : undefined;
         // Get or create transport
         let transport = sessionId ? mcpTransports.get(sessionId) : undefined;
         let serverInstance = sessionId
@@ -2118,6 +2130,7 @@ app.all("/mcp", async (req, res) => {
             // The gate's resolved connection id: the MCP server reads this, never
             // the request's X-Connection-Id header.
             mcpConnectionId: connectionIdHeader ?? null,
+            mcpLookupTiming,
         }, () => transport.handleRequest(req, res, req.body));
     }
     catch (error) {
@@ -2188,13 +2201,18 @@ function redactSensitiveFields(obj) {
     }
     return redacted;
 }
+function redactEntityReadInput(value) {
+    return exactIdentityRequested(value)
+        ? { read_mode: "exact_identity" }
+        : redactSensitiveFields(value);
+}
 function logDebug(event, req, extra) {
     const safe = {
         method: req.method,
         path: req.path,
-        query: redactSensitiveFields(req.query),
+        query: redactEntityReadInput(req.query),
         headers: redactHeaders(req.headers),
-        body: redactSensitiveFields(req.body),
+        body: redactEntityReadInput(req.body),
         ...(extra ? redactSensitiveFields(extra) : {}),
     };
     // eslint-disable-next-line no-console
@@ -2204,9 +2222,9 @@ function logWarn(event, req, extra) {
     const safe = {
         method: req.method,
         path: req.path,
-        query: redactSensitiveFields(req.query),
+        query: redactEntityReadInput(req.query),
         headers: redactHeaders(req.headers),
-        body: redactSensitiveFields(req.body),
+        body: redactEntityReadInput(req.body),
         ...(extra ? redactSensitiveFields(extra) : {}),
     };
     // eslint-disable-next-line no-console
@@ -2234,9 +2252,9 @@ function logError(event, req, error, extra) {
     const payload = {
         method: req.method,
         path: req.path,
-        query: redactSensitiveFields(req.query),
+        query: redactEntityReadInput(req.query),
         headers: redactHeaders(req.headers),
-        body: redactSensitiveFields(req.body),
+        body: redactEntityReadInput(req.body),
         error: error instanceof Error
             ? {
                 name: error.name,
@@ -4294,6 +4312,18 @@ function handleApiError(req, res, error, defaultMessage, errorCode = "DB_QUERY_F
 // (POST body, or query-string params coerced by coerceEntitiesQueryParams).
 // REQUIRES AUTHENTICATION - all queries filtered by authenticated user_id.
 async function runEntitiesQuery(req, res, rawInput) {
+    if (exactIdentityRequested(rawInput)) {
+        try {
+            const userId = await getAuthenticatedUserId(req);
+            const exact_identity = await readExactIdentity(rawInput, userId);
+            if (!exact_identity)
+                return sendError(res, 400, "VALIDATION_ERROR", EXACT_IDENTITY_REQUEST_MESSAGE);
+            return res.set("Cache-Control", "no-store").json({ exact_identity });
+        }
+        catch (error) {
+            return handleApiError(req, res, error, "Could not verify exact identity");
+        }
+    }
     const parsed = EntitiesQueryRequestSchema.safeParse(rawInput);
     if (!parsed.success) {
         logWarn("ValidationError:entities_query", req, {
@@ -4416,6 +4446,8 @@ function coerceEntitiesQueryParams(query) {
 // `GET /entities?entity_type=...&search=...` no longer hit a 404 and silently
 // degrade. REQUIRES AUTHENTICATION - identical user scoping to the POST path.
 app.get("/entities", async (req, res) => {
+    if (exactIdentityRequested(req.query))
+        return sendError(res, 400, "VALIDATION_ERROR", "Exact identity requires POST /entities/query.");
     return runEntitiesQuery(req, res, coerceEntitiesQueryParams(req.query));
 });
 // POST /api/entities/query - Query entities with filters
@@ -4926,7 +4958,42 @@ app.get("/schemas", async (req, res) => {
         // restricted WHICH entity types appear; it never corrected the version, so
         // it could not compensate. `userId` is already required above, so scoping
         // here changes no caller's authorization, only the accuracy of the version.
-        const allSchemas = await schemaRegistry.listEntityTypes(keyword, userId);
+        const catalog = await schemaRegistry.listEntityTypesResult(keyword, userId);
+        const allSchemas = catalog.entity_types;
+        const summary = req.query.summary === "true";
+        if (summary) {
+            const selected = filterEntityType
+                ? allSchemas.filter((schema) => schema.entity_type === filterEntityType)
+                : allSchemas;
+            const sorted = [...selected].sort((a, b) => a.entity_type.localeCompare(b.entity_type));
+            const page = sorted.slice(offset, offset + limit);
+            const reasons = [...catalog.registry_coverage.reasons];
+            if (filterEntityType)
+                reasons.push("filtered");
+            if (offset !== 0 || page.length !== sorted.length)
+                reasons.push("paginated");
+            const complete = catalog.registry_coverage.state === "complete" && reasons.length === 0;
+            return res.json({
+                schemas: page.map(({ entity_type, schema_version, field_names, planning, planning_error }) => ({
+                    entity_type,
+                    schema_version,
+                    field_count: field_names.length,
+                    ...(planning ? { planning } : {}),
+                    ...(planning_error ? { planning_error } : {}),
+                })),
+                total: sorted.length,
+                limit,
+                offset,
+                registry_coverage: {
+                    ...catalog.registry_coverage,
+                    state: complete ? "complete" : "unknown",
+                    reasons: [...new Set(reasons)].sort(),
+                    returned_count: page.length,
+                    exhausted: complete,
+                    scope: { ...catalog.registry_coverage.scope, entity_type: filterEntityType || null },
+                },
+            });
+        }
         // Filter to only show global schemas (user_id is null) or user-specific schemas for this user
         // Also fetch metadata (including icons) for each schema
         const { data: dbSchemas, error: dbError } = await db
@@ -4957,6 +5024,16 @@ app.get("/schemas", async (req, res) => {
         const paginatedSchemas = sortedSchemas.slice(offset, offset + limit);
         return res.json({
             schemas: paginatedSchemas,
+            registry_coverage: {
+                ...catalog.registry_coverage,
+                state: "unknown",
+                exhausted: false,
+                returned_count: paginatedSchemas.length,
+                reasons: [
+                    ...new Set([...catalog.registry_coverage.reasons, "legacy_filtered_view"]),
+                ].sort(),
+                scope: { ...catalog.registry_coverage.scope, entity_type: filterEntityType || null },
+            },
             total: productionSchemas.length,
             limit,
             offset,
@@ -8574,12 +8651,14 @@ app.post("/get_entity_snapshot", async (req, res) => {
     }
     // Materialization is derived state. Validate owned current authority before
     // serving its row, including restrictive corruption acquisition failures.
+    // The check reads the entity's lifecycle authority rows, not its whole
+    // observation history (#2792).
     try {
-        const { isEntityDeleted } = await import("./services/deletion.js");
+        const { isOwnedEntityHiddenAfterCutover } = await import("./services/current_state_reads.js");
         const { hasRecordedEntityLifecycleCutover } = await import("./services/entity_lifecycle_storage.js");
         const { getDb } = await import("./repositories/db/connection.js");
         if ((await hasRecordedEntityLifecycleCutover(await getDb())) &&
-            (await isEntityDeleted(entity_id, userId)))
+            (await isOwnedEntityHiddenAfterCutover(entity_id, userId)))
             return sendError(res, 404, "RESOURCE_NOT_FOUND", "Entity not found");
     }
     catch (err) {
@@ -9872,7 +9951,7 @@ app.post("/update_schema_incremental", async (req, res) => {
     }
     try {
         const userId = await getAuthenticatedUserId(req, parsed.data.user_id);
-        const { entity_type, fields_to_add, fields_to_remove, canonical_name_fields, schema_version, 
+        const { entity_type, fields_to_add, fields_to_remove, canonical_name_fields, planning, schema_version, 
         // #2374: no local `= false` default. `user_specific` stays
         // `undefined` when the caller omitted it, so `updateSchemaIncremental`
         // can defer to whichever scope its own read resolved instead of being
@@ -9948,6 +10027,7 @@ app.post("/update_schema_incremental", async (req, res) => {
                 // re-key (the MCP server handler had it, but this Express route — which
                 // the CLI offline transport uses — did not).
                 canonical_name_fields,
+                planning,
                 schema_version,
                 user_specific,
                 // #2374: pass userId unconditionally — same reasoning as the MCP