@dxos/assistant-toolkit 0.8.4-main.ae835ea → 0.8.4-main.bc674ce

package/dist/lib/node-esm/index.mjs

@@ -1,23 +1,28 @@
 import { createRequire } from 'node:module';const require = createRequire(import.meta.url);
+import {
+  __export
+} from "./chunk-HSLMI22Q.mjs";
 
 // src/blueprints/design/design-blueprint.ts
 import { ToolId } from "@dxos/ai";
 import { Blueprint } from "@dxos/blueprints";
-import { Obj as Obj9, Ref as Ref6 } from "@dxos/echo";
-import { DataType as DataType7 } from "@dxos/schema";
+import { Ref as Ref6 } from "@dxos/echo";
+import { Text as Text2 } from "@dxos/schema";
 import { trim as trim5 } from "@dxos/util";
 
 // src/functions/agent/prompt.ts
 import * as Array2 from "effect/Array";
 import * as Effect from "effect/Effect";
 import * as Function from "effect/Function";
+import * as Match from "effect/Match";
 import * as Option from "effect/Option";
 import * as Schema from "effect/Schema";
 import { AiService, ConsolePrinter, ModelName } from "@dxos/ai";
 import { AiSession, GenerationObserver, createToolkit } from "@dxos/assistant";
 import { Prompt, Template } from "@dxos/blueprints";
 import { Obj, Ref, Type } from "@dxos/echo";
-import { DatabaseService, TracingService, defineFunction } from "@dxos/functions";
+import { Database } from "@dxos/echo";
+import { TracingService, defineFunction } from "@dxos/functions";
 import { log } from "@dxos/log";
 var __dxlog_file = "/__w/dxos/dxos/packages/core/assistant-toolkit/src/functions/agent/prompt.ts";
 var DEFAULT_MODEL = "@anthropic/claude-opus-4-0";
@@ -36,10 +41,9 @@ var prompt_default = defineFunction({
     * Input object or data.
     * References get auto-resolved.
     */
-    input: Schema.Record({
-      key: Schema.String,
-      value: Schema.Any
-    })
+    input: Schema.Any.pipe(Schema.annotations({
+      title: "Input"
+    }))
   }),
   outputSchema: Schema.Any,
   handler: Effect.fnUntraced(function* ({ data }) {
@@ -47,47 +51,39 @@ var prompt_default = defineFunction({
       input: data.input
     }, {
       F: __dxlog_file,
-      L: 39,
+      L: 41,
       S: this,
       C: (f, a) => f(...a)
     });
-    const input = {
-      ...data.input
-    };
-    for (const key of Object.keys(data.input)) {
-      const value = data.input[key];
-      if (Ref.isRef(value)) {
-        const object = yield* DatabaseService.load(value);
-        input[key] = Obj.toJSON(object);
-      } else {
-        input[key] = JSON.stringify(value);
-      }
-    }
-    yield* DatabaseService.flush({
+    const input = yield* Match.value(data.input).pipe(Match.when((value2) => Ref.isRef(value2), Effect.fnUntraced(function* (ref) {
+      const object = yield* Database.Service.load(ref);
+      return Obj.toJSON(object);
+    })), Match.orElse(() => Effect.succeed(data.input)));
+    yield* Database.Service.flush({
       indexes: true
     });
-    const prompt = yield* DatabaseService.load(data.prompt);
-    const systemPrompt = data.systemPrompt ? yield* DatabaseService.load(data.systemPrompt) : void 0;
+    const prompt = yield* Database.Service.load(data.prompt);
+    const systemPrompt = data.systemPrompt ? yield* Database.Service.load(data.systemPrompt) : void 0;
     yield* TracingService.emitStatus({
       message: `Running ${prompt.id}`
     });
     log.info("starting agent", {
       prompt: prompt.id,
-      input: data.input
+      input
     }, {
       F: __dxlog_file,
-      L: 57,
+      L: 71,
       S: this,
       C: (f, a) => f(...a)
     });
-    const blueprints = yield* Function.pipe(prompt.blueprints, Array2.appendAll(systemPrompt?.blueprints ?? []), Effect.forEach(DatabaseService.loadOption), Effect.map(Array2.filter(Option.isSome)), Effect.map(Array2.map((option) => option.value)));
-    const objects = yield* Function.pipe(prompt.context, Array2.appendAll(systemPrompt?.context ?? []), Effect.forEach(DatabaseService.loadOption), Effect.map(Array2.filter(Option.isSome)), Effect.map(Array2.map((option) => option.value)));
+    const blueprints = yield* Function.pipe(prompt.blueprints, Array2.appendAll(systemPrompt?.blueprints ?? []), Effect.forEach(Database.Service.loadOption), Effect.map(Array2.filter(Option.isSome)), Effect.map(Array2.map((option) => option.value)));
     const toolkit = yield* createToolkit({
       blueprints
     });
-    const promptInstructions = yield* DatabaseService.load(prompt.instructions.source);
+    const objects = yield* Function.pipe(prompt.context, Array2.appendAll(systemPrompt?.context ?? []), Effect.forEach(Database.Service.loadOption), Effect.map(Array2.filter(Option.isSome)), Effect.map(Array2.map((option) => option.value)));
+    const promptInstructions = yield* Database.Service.load(prompt.instructions.source);
     const promptText = Template.process(promptInstructions.content, input);
-    const systemInstructions = systemPrompt ? yield* DatabaseService.load(systemPrompt.instructions.source) : void 0;
+    const systemInstructions = systemPrompt ? yield* Database.Service.load(systemPrompt.instructions.source) : void 0;
     const systemText = systemInstructions ? Template.process(systemInstructions.content, {}) : void 0;
     const session = new AiSession();
     const result = yield* session.run({
@@ -125,7 +121,7 @@ import * as Schema2 from "effect/Schema";
 import { Obj as Obj2 } from "@dxos/echo";
 import { CredentialsService, TracingService as TracingService2, defineFunction as defineFunction2 } from "@dxos/functions";
 import { log as log2 } from "@dxos/log";
-import { DataType } from "@dxos/schema";
+import { Message } from "@dxos/types";
 var __dxlog_file2 = "/__w/dxos/dxos/packages/core/assistant-toolkit/src/functions/discord/fetch-messages.ts";
 var TimeRange = class extends Schema2.String.pipe(Schema2.pattern(/\d+(s|m|h|d)/)).annotations({
   description: "Time range. 1d - 1 day, 2h - 2 hours, 30m - 30 minutes, 15s - 15 seconds.",
@@ -198,11 +194,11 @@ var fetch_messages_default = defineFunction2({
       description: "Exclude messages from these usernames."
     })
   }),
-  handler: Effect2.fnUntraced(function* ({ data: { serverId, channelId, after, last, pageSize = 100, limit = DEFAULT_LIMIT, ignoreUsernames = DEFAULT_IGNORE_USERNAMES } }) {
-    if (!after && !last) {
+  handler: Effect2.fnUntraced(function* ({ data: { serverId, channelId, after, last: last2, pageSize = 100, limit = DEFAULT_LIMIT, ignoreUsernames = DEFAULT_IGNORE_USERNAMES } }) {
+    if (!after && !last2) {
       throw new Error("cannot specify both `after` and `last`");
     }
-    const afterTs = last ? Date.now() / 1e3 - TimeRange.toSeconds(last) : after ?? DEFAULT_AFTER;
+    const afterTs = last2 ? Date.now() / 1e3 - TimeRange.toSeconds(last2) : after ?? DEFAULT_AFTER;
     const rest = yield* DiscordREST;
     let channels = [];
     channels.push(...yield* rest.listGuildChannels(serverId));
@@ -215,7 +211,15 @@ var fetch_messages_default = defineFunction2({
       throw new Error("no channels found");
     }
     for (const channel of channels) {
-      console.log(channel.id, "name" in channel ? channel.name : void 0);
+      log2.info("channel", {
+        id: channel.id,
+        name: "name" in channel ? channel.name : void 0
+      }, {
+        F: __dxlog_file2,
+        L: 136,
+        S: this,
+        C: (f, a) => f(...a)
+      });
     }
     yield* TracingService2.emitStatus({
       message: `Will fetch from channels: ${channels.length}`
@@ -276,7 +280,7 @@ var parseSnowflake = (snowflake) => {
   const discordEpoch = 1420070400000n;
   return new Date(Number((BigInt(snowflake) >> 22n) + discordEpoch));
 };
-var makeMessage = (message) => Obj2.make(DataType.Message, {
+var makeMessage = (message) => Obj2.make(Message.Message, {
   [Obj2.Meta]: {
     keys: [
       {
@@ -316,7 +320,8 @@ var Discord;
 import * as Effect3 from "effect/Effect";
 import * as Schema3 from "effect/Schema";
 import { ArtifactId } from "@dxos/assistant";
-import { DatabaseService as DatabaseService2, defineFunction as defineFunction3 } from "@dxos/functions";
+import { Database as Database2 } from "@dxos/echo";
+import { defineFunction as defineFunction3 } from "@dxos/functions";
 import { Markdown } from "@dxos/plugin-markdown/types";
 var read_default = defineFunction3({
   key: "dxos.org/function/markdown/read",
@@ -331,8 +336,8 @@ var read_default = defineFunction3({
     content: Schema3.String
   }),
   handler: Effect3.fn(function* ({ data: { id } }) {
-    const doc = yield* DatabaseService2.resolve(ArtifactId.toDXN(id), Markdown.Document);
-    const { content } = yield* DatabaseService2.load(doc.content);
+    const doc = yield* Database2.Service.resolve(ArtifactId.toDXN(id), Markdown.Document);
+    const { content } = yield* Database2.Service.load(doc.content);
     return {
       content
     };
@@ -343,7 +348,8 @@ var read_default = defineFunction3({
 import * as Effect4 from "effect/Effect";
 import * as Schema4 from "effect/Schema";
 import { ArtifactId as ArtifactId2 } from "@dxos/assistant";
-import { DatabaseService as DatabaseService3, defineFunction as defineFunction4 } from "@dxos/functions";
+import { Database as Database3, Obj as Obj3 } from "@dxos/echo";
+import { defineFunction as defineFunction4 } from "@dxos/functions";
 import { Markdown as Markdown2 } from "@dxos/plugin-markdown/types";
 var update_default = defineFunction4({
   key: "dxos.org/function/markdown/update",
@@ -359,9 +365,11 @@ var update_default = defineFunction4({
   }),
   outputSchema: Schema4.Void,
   handler: Effect4.fn(function* ({ data: { id, content } }) {
-    const doc = yield* DatabaseService3.resolve(ArtifactId2.toDXN(id), Markdown2.Document);
-    const text = yield* DatabaseService3.load(doc.content);
-    text.content = content;
+    const doc = yield* Database3.Service.resolve(ArtifactId2.toDXN(id), Markdown2.Document);
+    const text = yield* Database3.Service.load(doc.content);
+    Obj3.change(text, (t) => {
+      t.content = content;
+    });
   })
 });
 
@@ -380,97 +388,375 @@ import * as Predicate from "effect/Predicate";
 import * as Schema11 from "effect/Schema";
 import { AiService as AiService3 } from "@dxos/ai";
 import { AiSession as AiSession3, makeToolExecutionServiceFromFunctions as makeToolExecutionServiceFromFunctions2, makeToolResolverFromFunctions as makeToolResolverFromFunctions2 } from "@dxos/assistant";
-import { Filter as Filter2, Obj as Obj6, Ref as Ref3 } from "@dxos/echo";
-import { DatabaseService as DatabaseService8, FunctionInvocationService as FunctionInvocationService2, defineFunction as defineFunction9 } from "@dxos/functions";
+import { Filter as Filter2, Obj as Obj8, Ref as Ref3, Type as Type4 } from "@dxos/echo";
+import { Database as Database8 } from "@dxos/echo";
+import { defineFunction as defineFunction9 } from "@dxos/functions";
+import { FunctionInvocationServiceLayerTest } from "@dxos/functions-runtime/testing";
 import { log as log5 } from "@dxos/log";
-import { DataType as DataType5 } from "@dxos/schema";
+import { LegacyOrganization as LegacyOrganization2, Message as Message2, Organization, Person as Person2 } from "@dxos/types";
 import { trim as trim4 } from "@dxos/util";
 
-// src/functions/research/create-document.ts
+// src/crud/graph.ts
+import * as Tool from "@effect/ai/Tool";
+import * as Toolkit from "@effect/ai/Toolkit";
+import * as Context from "effect/Context";
 import * as Effect5 from "effect/Effect";
+import * as Function3 from "effect/Function";
+import * as Option3 from "effect/Option";
 import * as Schema5 from "effect/Schema";
-import { Relation } from "@dxos/echo";
-import { DatabaseService as DatabaseService4, TracingService as TracingService3, defineFunction as defineFunction5 } from "@dxos/functions";
-import { invariant } from "@dxos/invariant";
+import * as SchemaAST from "effect/SchemaAST";
+import { Entity, Filter, Obj as Obj4, Query, Type as Type2 } from "@dxos/echo";
+import { Database as Database4 } from "@dxos/echo";
+import { ReferenceAnnotationId, RelationSourceDXNId, RelationSourceId, RelationTargetDXNId, RelationTargetId, createObject, getTypeAnnotation, getTypeIdentifierAnnotation } from "@dxos/echo/internal";
+import { isEncodedReference } from "@dxos/echo-protocol";
+import { mapAst } from "@dxos/effect";
+import { ContextQueueService } from "@dxos/functions";
 import { DXN, ObjectId } from "@dxos/keys";
 import { log as log3 } from "@dxos/log";
+import { deepMapValues, isNonNullable, trim } from "@dxos/util";
+var __dxlog_file3 = "/__w/dxos/dxos/packages/core/assistant-toolkit/src/crud/graph.ts";
+var Subgraph = Schema5.Struct({
+  /** Objects and relations. */
+  objects: Schema5.Array(Schema5.Any)
+});
+var findRelatedSchema = async (db, anchor) => {
+  const allSchemas = await db.graph.schemaRegistry.query().run();
+  return allSchemas.filter((schema) => {
+    if (getTypeAnnotation(schema)?.kind !== Entity.Kind.Relation) {
+      return false;
+    }
+    return isSchemaAddressableByDxn(anchor, DXN.parse(getTypeAnnotation(schema).sourceSchema)) || isSchemaAddressableByDxn(anchor, DXN.parse(getTypeAnnotation(schema).targetSchema));
+  }).map((schema) => ({
+    kind: "relation",
+    schema
+  }));
+};
+var isSchemaAddressableByDxn = (schema, dxn) => {
+  if (getTypeIdentifierAnnotation(schema) === dxn.toString()) {
+    return true;
+  }
+  const t = dxn.asTypeDXN();
+  if (t) {
+    return t.type === Type2.getTypename(schema);
+  }
+  return false;
+};
+var LocalSearchToolkit = Toolkit.make(Tool.make("search_local_search", {
+  description: "Search the local database for information using a vector index",
+  parameters: {
+    query: Schema5.String.annotations({
+      description: "The query to search for. Could be a question or a topic or a set of keywords."
+    })
+  },
+  success: Schema5.Unknown,
+  failure: Schema5.Never,
+  dependencies: [
+    Database4.Service
+  ]
+}));
+var LocalSearchHandler = LocalSearchToolkit.toLayer({
+  search_local_search: Effect5.fn(function* ({ query }) {
+    const objects = yield* Database4.Service.runQuery(Query.select(Filter.text(query, {
+      type: "vector"
+    })));
+    const results = [
+      ...objects
+    ];
+    const option = yield* Effect5.serviceOption(ContextQueueService);
+    if (Option3.isSome(option)) {
+      const queueObjects = yield* Effect5.promise(() => option.value.queue.queryObjects());
+      results.push(...queueObjects);
+    }
+    return trim`
+      <local_context>
+        ${JSON.stringify(results, null, 2)}
+      </local_context>
+    `;
+  })
+});
+var GraphWriterSchema = class extends Context.Tag("@dxos/assistant/GraphWriterSchema")() {
+};
+var makeGraphWriterToolkit = ({ schema }) => {
+  return Toolkit.make(Tool.make("graph_writer", {
+    description: "Write to the local graph database",
+    parameters: createExtractionSchema(schema).fields,
+    success: Schema5.Unknown,
+    failure: Schema5.Never,
+    dependencies: [
+      Database4.Service,
+      ContextQueueService
+    ]
+  }).annotateContext(Context.make(GraphWriterSchema, {
+    schema
+  })));
+};
+var makeGraphWriterHandler = (toolkit, { onAppend } = {}) => {
+  const { schema } = Context.get(toolkit.tools.graph_writer.annotations, GraphWriterSchema);
+  return toolkit.toLayer({
+    graph_writer: Effect5.fn(function* (input) {
+      const { db } = yield* Database4.Service;
+      const { queue } = yield* ContextQueueService;
+      const data = yield* Effect5.promise(() => sanitizeObjects(schema, input, db, queue));
+      yield* Effect5.promise(() => queue.append(data));
+      const dxns = data.map((obj) => Obj4.getDXN(obj));
+      onAppend?.(dxns);
+      return dxns;
+    })
+  });
+};
+var createExtractionSchema = (types) => {
+  return Schema5.Struct({
+    ...Object.fromEntries(types.map(preprocessSchema).map((schema, index) => [
+      `objects_${getSanitizedSchemaName(types[index])}`,
+      Schema5.optional(Schema5.Array(schema)).annotations({
+        description: `The objects of type: ${Type2.getDXN(types[index])?.asTypeDXN().type}. ${SchemaAST.getDescriptionAnnotation(types[index].ast).pipe(Option3.getOrElse(() => ""))}`
+      })
+    ]))
+  });
+};
+var getSanitizedSchemaName = (schema) => {
+  return Type2.getDXN(schema).asTypeDXN().type.replaceAll(/[^a-zA-Z0-9]+/g, "_");
+};
+var sanitizeObjects = async (types, data, db, queue) => {
+  const entries = types.map((type) => data[`objects_${getSanitizedSchemaName(type)}`]?.map((object) => ({
+    data: object,
+    schema: type
+  })) ?? []).flat();
+  const idMap = /* @__PURE__ */ new Map();
+  const existingIds = /* @__PURE__ */ new Set();
+  const enitties = /* @__PURE__ */ new Map();
+  const resolveId = (id) => {
+    if (ObjectId.isValid(id)) {
+      existingIds.add(id);
+      return DXN.fromLocalObjectId(id);
+    }
+    const mappedId = idMap.get(id);
+    if (mappedId) {
+      return DXN.fromLocalObjectId(mappedId);
+    }
+    return void 0;
+  };
+  const res = entries.map((entry) => {
+    if (ObjectId.isValid(entry.data.id)) {
+      return entry;
+    }
+    idMap.set(entry.data.id, ObjectId.random());
+    entry.data.id = idMap.get(entry.data.id);
+    return entry;
+  }).map((entry) => {
+    const data2 = deepMapValues(entry.data, (value2, recurse) => {
+      if (isEncodedReference(value2)) {
+        const ref = value2["/"];
+        const id = resolveId(ref);
+        if (id) {
+          return {
+            "/": id.toString()
+          };
+        } else {
+          return {
+            "/": `search:?q=${encodeURIComponent(ref)}`
+          };
+        }
+      }
+      return recurse(value2);
+    });
+    if (Entity.getKind(entry.schema) === "relation") {
+      const sourceDxn = resolveId(data2.source);
+      if (!sourceDxn) {
+        log3.warn("source not found", {
+          source: data2.source
+        }, {
+          F: __dxlog_file3,
+          L: 273,
+          S: void 0,
+          C: (f, a) => f(...a)
+        });
+      }
+      const targetDxn = resolveId(data2.target);
+      if (!targetDxn) {
+        log3.warn("target not found", {
+          target: data2.target
+        }, {
+          F: __dxlog_file3,
+          L: 277,
+          S: void 0,
+          C: (f, a) => f(...a)
+        });
+      }
+      delete data2.source;
+      delete data2.target;
+      data2[RelationSourceDXNId] = sourceDxn;
+      data2[RelationTargetDXNId] = targetDxn;
+    }
+    return {
+      data: data2,
+      schema: entry.schema
+    };
+  }).filter((object) => !existingIds.has(object.data.id));
+  const dbObjects = await db.query(Query.select(Filter.id(...existingIds))).run();
+  const queueObjects = await queue?.getObjectsById([
+    ...existingIds
+  ]) ?? [];
+  const objects = [
+    ...dbObjects,
+    ...queueObjects
+  ].filter(isNonNullable);
+  log3.info("objects", {
+    dbObjects,
+    queueObjects,
+    existingIds
+  }, {
+    F: __dxlog_file3,
+    L: 298,
+    S: void 0,
+    C: (f, a) => f(...a)
+  });
+  const missing = Array.from(existingIds).filter((id) => !objects.some((object) => object.id === id));
+  if (missing.length > 0) {
+    throw new Error(`Object IDs do not point to existing objects: ${missing.join(", ")}`);
+  }
+  return res.flatMap(({ data: data2, schema }) => {
+    let skip = false;
+    if (RelationSourceDXNId in data2) {
+      const id = data2[RelationSourceDXNId].asEchoDXN()?.echoId;
+      const obj = objects.find((object) => object.id === id) ?? enitties.get(id);
+      if (obj) {
+        delete data2[RelationSourceDXNId];
+        data2[RelationSourceId] = obj;
+      } else {
+        skip = true;
+      }
+    }
+    if (RelationTargetDXNId in data2) {
+      const id = data2[RelationTargetDXNId].asEchoDXN()?.echoId;
+      const obj = objects.find((object) => object.id === id) ?? enitties.get(id);
+      if (obj) {
+        delete data2[RelationTargetDXNId];
+        data2[RelationTargetId] = obj;
+      } else {
+        skip = true;
+      }
+    }
+    if (!skip) {
+      const obj = createObject(schema, data2);
+      enitties.set(obj.id, obj);
+      return [
+        obj
+      ];
+    }
+    return [];
+  });
+};
+var SoftRef = Schema5.Struct({
+  "/": Schema5.String
+}).annotations({
+  description: "Reference to another object."
+});
+var preprocessSchema = (schema) => {
+  const isRelationSchema = Entity.getKind(schema) === "relation";
+  const go = (ast, visited = /* @__PURE__ */ new Set()) => {
+    if (visited.has(ast)) {
+      return ast;
+    }
+    visited.add(ast);
+    if (SchemaAST.getAnnotation(ast, ReferenceAnnotationId).pipe(Option3.isSome)) {
+      return SoftRef.ast;
+    }
+    return mapAst(ast, (child) => go(child, visited));
+  };
+  return Schema5.make(mapAst(schema.ast, (ast) => go(ast))).pipe(Schema5.omit("id"), Schema5.extend(Schema5.Struct({
+    id: Schema5.String.annotations({
+      description: "The id of this object. Come up with a unique id based on your judgement."
+    })
+  })), isRelationSchema ? Schema5.extend(Schema5.Struct({
+    source: Schema5.String.annotations({
+      description: "The id of the source object for this relation."
+    }),
+    target: Schema5.String.annotations({
+      description: "The id of the target object for this relation."
+    })
+  })) : Function3.identity);
+};
+
+// src/functions/research/document-create.ts
+import * as Effect6 from "effect/Effect";
+import * as Schema6 from "effect/Schema";
+import { ArtifactId as ArtifactId3 } from "@dxos/assistant";
+import { Obj as Obj5, Relation } from "@dxos/echo";
+import { Database as Database5 } from "@dxos/echo";
+import { TracingService as TracingService3, defineFunction as defineFunction5 } from "@dxos/functions";
+import { log as log4 } from "@dxos/log";
 import { Markdown as Markdown3 } from "@dxos/plugin-markdown/types";
-import { DataType as DataType2 } from "@dxos/schema";
-import { trim } from "@dxos/util";
-var __dxlog_file3 = "/__w/dxos/dxos/packages/core/assistant-toolkit/src/functions/research/create-document.ts";
-var create_document_default = defineFunction5({
-  key: "dxos.org/function/research/create-document",
+import { HasSubject } from "@dxos/types";
+import { trim as trim2 } from "@dxos/util";
+var __dxlog_file4 = "/__w/dxos/dxos/packages/core/assistant-toolkit/src/functions/research/document-create.ts";
+var document_create_default = defineFunction5({
+  key: "dxos.org/function/research/document-create",
   name: "Create research document",
   description: "Creates a note summarizing the research.",
-  inputSchema: Schema5.Struct({
-    name: Schema5.String.annotations({
-      description: "Name of the note."
+  inputSchema: Schema6.Struct({
+    subject: ArtifactId3.annotations({
+      description: trim2`
+        ID of the object (organization, contact, etc.) for which the research was performed. 
+      `
+    }),
+    name: Schema6.String.annotations({
+      description: "Name of the document."
     }),
-    content: Schema5.String.annotations({
-      description: trim`
+    content: Schema6.String.annotations({
+      description: trim2`
         Content of the note. 
         Supports (and are prefered) references to research objects using @ syntax and <object> tags (refer to research blueprint instructions).
       `
-    }),
-    // TODO(dmaretskyi): Use a specialized type for this (e.g., ArtifactId renamed as RefFromLLM).
-    target: Schema5.String.annotations({
-      description: trim`
-        Id of the object (organization, contact, etc.) for which the research was performed. 
-        This must be a ulid.
-      `
     })
   }),
-  outputSchema: Schema5.Struct({}),
-  handler: Effect5.fnUntraced(function* ({ data: { target, name, content } }) {
-    log3.info("Creating research document", {
-      target,
+  outputSchema: Schema6.Struct({
+    document: ArtifactId3.annotations({
+      description: "DXN of the created document."
+    })
+  }),
+  handler: Effect6.fnUntraced(function* ({ data: { subject, name, content } }) {
+    log4.info("Creating research document", {
+      subject,
       name,
       content
     }, {
-      F: __dxlog_file3,
+      F: __dxlog_file4,
       L: 43,
       S: this,
       C: (f, a) => f(...a)
     });
-    yield* DatabaseService4.flush({
+    yield* Database5.Service.flush({
       indexes: true
     });
     yield* TracingService3.emitStatus({
       message: "Creating research document..."
     });
-    invariant(ObjectId.isValid(target), void 0, {
-      F: __dxlog_file3,
-      L: 47,
-      S: this,
-      A: [
-        "ObjectId.isValid(target)",
-        ""
-      ]
-    });
-    const targetObj = yield* DatabaseService4.resolve(DXN.fromLocalObjectId(target));
-    const doc = yield* DatabaseService4.add(Markdown3.makeDocument({
+    const target = yield* Database5.Service.resolve(ArtifactId3.toDXN(subject));
+    const object = yield* Database5.Service.add(Markdown3.make({
       name,
       content
     }));
-    yield* DatabaseService4.add(Relation.make(DataType2.HasSubject, {
-      [Relation.Source]: doc,
-      [Relation.Target]: targetObj,
+    yield* Database5.Service.add(Relation.make(HasSubject.HasSubject, {
+      [Relation.Source]: object,
+      [Relation.Target]: target,
       completedAt: (/* @__PURE__ */ new Date()).toISOString()
     }));
-    yield* DatabaseService4.flush({
+    yield* Database5.Service.flush({
       indexes: true
     });
-    log3.info("Created research document", {
-      target,
-      name,
-      content
+    log4.info("Created research document", {
+      subject,
+      object
     }, {
-      F: __dxlog_file3,
-      L: 66,
+      F: __dxlog_file4,
+      L: 70,
       S: this,
       C: (f, a) => f(...a)
     });
-    return {};
+    return {
+      document: Obj5.getDXN(object).toString()
+    };
   })
 });
 
@@ -479,36 +765,42 @@ import * as Toolkit2 from "@effect/ai/Toolkit";
 import * as AnthropicTool from "@effect/ai-anthropic/AnthropicTool";
 import * as Array6 from "effect/Array";
 import * as Effect10 from "effect/Effect";
+import * as Function4 from "effect/Function";
 import * as Layer3 from "effect/Layer";
+import * as Option4 from "effect/Option";
 import * as Schema10 from "effect/Schema";
+import * as String10 from "effect/String";
 import { AiService as AiService2, ConsolePrinter as ConsolePrinter2 } from "@dxos/ai";
 import { AiSession as AiSession2, GenerationObserver as GenerationObserver2, createToolkit as createToolkit2, makeToolExecutionServiceFromFunctions, makeToolResolverFromFunctions } from "@dxos/assistant";
-import { Obj as Obj5 } from "@dxos/echo";
-import { DatabaseService as DatabaseService7, FunctionInvocationService, TracingService as TracingService4, defineFunction as defineFunction8 } from "@dxos/functions";
-import { DataType as DataType4 } from "@dxos/schema";
+import { Template as Template2 } from "@dxos/blueprints";
+import { Entity as Entity2, Obj as Obj7 } from "@dxos/echo";
+import { Database as Database7 } from "@dxos/echo";
+import { TracingService as TracingService4, defineFunction as defineFunction8 } from "@dxos/functions";
+import { FunctionInvocationServiceLayerTestMocked } from "@dxos/functions-runtime/testing";
+import { Person } from "@dxos/types";
 import { trim as trim3 } from "@dxos/util";
 
 // src/functions/exa/exa.ts
-import * as Effect6 from "effect/Effect";
-import * as Schema6 from "effect/Schema";
+import * as Effect7 from "effect/Effect";
+import * as Schema7 from "effect/Schema";
 import Exa from "exa-js";
 import { CredentialsService as CredentialsService2, defineFunction as defineFunction6 } from "@dxos/functions";
 var exa_default = defineFunction6({
   key: "dxos.org/function/exa",
   name: "Exa",
   description: "Search the web for information",
-  inputSchema: Schema6.Struct({
-    query: Schema6.String.annotations({
+  inputSchema: Schema7.Struct({
+    query: Schema7.String.annotations({
       description: "The query to search for."
     })
   }),
-  outputSchema: Schema6.Unknown,
-  handler: Effect6.fnUntraced(function* ({ data: { query } }) {
+  outputSchema: Schema7.Unknown,
+  handler: Effect7.fnUntraced(function* ({ data: { query } }) {
     const credential = yield* CredentialsService2.getCredential({
       service: "exa.ai"
     });
     const exa = new Exa(credential.apiKey);
-    const context = yield* Effect6.promise(async () => exa.searchAndContents(query, {
+    const context = yield* Effect7.promise(async () => exa.searchAndContents(query, {
       type: "auto",
       text: {
         maxCharacters: 3e3
@@ -520,11 +812,11 @@ var exa_default = defineFunction6({
 });
 
 // src/functions/exa/mock.ts
-import * as Effect7 from "effect/Effect";
-import * as Schema7 from "effect/Schema";
+import * as Effect8 from "effect/Effect";
+import * as Schema8 from "effect/Schema";
 import { defineFunction as defineFunction7 } from "@dxos/functions";
 
-// src/testing/data/exa-search-1748337321991.ts
+// src/functions/exa/data/exa-search-1748337321991.ts
 var exa_search_1748337321991_default = {
   requestId: "324936368a74f4db978982172bc18a6c",
   autopromptString: "AI personal knowledge management tools projects 2024",
@@ -680,7 +972,7 @@ var exa_search_1748337321991_default = {
   }
 };
 
-// src/testing/data/exa-search-1748337331526.ts
+// src/functions/exa/data/exa-search-1748337331526.ts
 var exa_search_1748337331526_default = {
   requestId: "0dc12e344fa649884456960ca1a54954",
   autopromptString: "PKM software artificial intelligence integration open source projects",
@@ -903,7 +1195,7 @@ npm run tauri dev
   }
 };
 
-// src/testing/data/exa-search-1748337344119.ts
+// src/functions/exa/data/exa-search-1748337344119.ts
 var exa_search_1748337344119_default = {
   requestId: "32df0c541f9883180b35e04caece4374",
   autopromptString: "open source AI knowledge management projects features comparison 2024",
@@ -1002,414 +1294,133 @@ var exa_search_1748337344119_default = {
       author: "",
       score: 0.37101393938064575,
       text: "SciPhi simplifies building, deploying, and optimizing Retrieval-Augmented Generation (RAG) systems, empowering developers to focus on AI innovation. Added on: Social &amp; Email: Platform: SciPhi SciPhi simplifies building, deploying, and optimizing Retrieval-Augmented Generation (RAG) systems, empowering developers to focus on AI innovation. Added on: Social &amp; Email: Platform: What is SciPhi? SciPhi is an open-source platform designed to simplify the building, deploying, and scaling of Retrieval-Augmented Generation (RAG) systems. It provides an end-to-end solution for developers, enabling them to focus on AI innovation without worrying about the underlying infrastructure. With tools for automated knowledge graph extraction, document and user management, and robust observability, SciPhi ensures efficient and optimized RAG system deployment. Who will use SciPhi? Developers AI Engineers Data Scientists Tech Startups Research Institutions How to use the SciPhi? Step1: Visit the SciPhi website. Step2: Sign up for an account or log in. Step3: Access the platform's dashboard. Step4: Follow guides to build and deploy your RAG system. Step5: Use tools for knowledge graph extraction and management. Step6: Optimize and monitor your system using provided observability features. SciPhi's Core Features &amp; Benefits The Core Features of SciPhi End-to-End RAG System Deployment Automated Knowledge Graph Extraction Document and User Management Robust Observability Tools The Benefits of SciPhi Simplifies AI Development Speeds Up Deployment Time Enhances System Optimization Reduces Infrastructure Complexity SciPhi's Main Use Cases &amp; Applications Building RAG Systems for AI Applications Deploying Knowledge Graphs Managing Large Document Repositories Optimizing AI System Performance FAQs of SciPhi SciPhi is an open-source platform designed to simplify building, deploying, and optimizing Retrieval-Augmented Generation (RAG) systems. SciPhi is intended for developers, AI engineers, data scientists, tech startups, and research institutions. Core features include end-to-end RAG system deployment, automated knowledge graph extraction, document and user management, and robust observability tools. Visit the SciPhi website, sign up for an account, and follow the guides to build and deploy your RAG system. SciPhi supports web platforms. SciPhi simplifies AI development, speeds up deployment time, enhances system optimization, and reduces infrastructure complexity. Yes, alternatives include LangChain, LlamaIndex, Haystack, and Flower. SciPhi supports building RAG systems for AI applications, deploying knowledge graphs, managing large document repositories, and optimizing AI system performance. You can reach out to their support team via their support email provided on the website. SciPhi offers both free and paid plans. Details on pricing can be found on their website. SciPhi Company Information Website: https://www.sciphi.ai Company Name: SciPhi Support Email: [ema",
-      image: "https://cdn-image.creati.ai/ai-tools/product-image/sciphi.webp",
-      favicon: "https://cdn-image.creati.ai/image/Creatiai.ico"
-    },
-    {
-      id: "https://helpjuice.com/blog/open-source-knowledge-base",
-      title: "The 12 Best Open Source Knowledge Base Software for 2024",
-      url: "https://helpjuice.com/blog/open-source-knowledge-base",
-      author: "Zeeshan Khan",
-      text: "\n \n \n \n \n At Helpjuice / \n \n #Software &amp; Alternatives\n May 15 2025 \n 11m read \n \n \n \n \n On the hunt for the perfect knowledge base software that\u2019s open source? This post will walk you through the best options for your business. \n \n \n \n \n There\u2019s no denying that a knowledge base can make a major impact on your organization.\xA0 Whether it's to help provide better support to your customers or to enable your employees to find the information they need to do their job, a finely-tuned knowledge base can make all the difference when it comes to how knowledge and information flows through your business. And with plenty of options on the market out there, there\u2019s certainly no shortage of open source knowledge base software. But how can you tell you\u2019re not investing time into installing and learning new software that your team won't use anyway? How can you avoid the time and effort put into an open source option that you later determine to not be a good fit for your needs?\xA0 It\u2019s simple\u2014do a little research beforehand. We know, we know\u2014you don\u2019t have endless time to invest in that kind of thing (what with a business to run and all). That\u2019s why we\u2019ve created a helpful list of the must-consider open source knowledge base software that companies of all niches, industries, and sizes should consider.\xA0 We\u2019re even throwing in a little helpful knowledge that should equip you with the information needed to choose the right software for you\u2014like what knowledge base software is in the first place, the benefits of open source software, and how to address your unique needs as a company to choose the right software for you.\xA0 Want to skip ahead on some of the basics of open-source knowledge base software?\xA0 Be our guest.\xA0 The best open source knowledge base software includes: \n BookStack \n OpenKM \n myBase \n eXo \n PHPKB \n Documize \n DocuWiki \n phpMyFAQ \n MediaWiki \n xWiki \n TWiki \n TiddlyWiki \n What is an Open Source Knowledge Base? Before we dive into which open-source knowledge base software you should consider for your business, we should probably ensure we\u2019re on the same page about what exactly open-source knowledge base software is.\xA0 First things first, let\u2019s start with the term knowledge base. A knowledge base is a central place that allows structured storage of information where users can search for and access this information. \xA0Knowledge base software should be the key tool that helps make this process seamless, simplified, and efficient. Knowledge base software is designed to help you create and manage your knowledge base to the best of your ability. this usually includes setting up the knowledge base architecture, creating and editing documentation, searching, and analyzing your knowledge base, and more. Ideally, this is the irreplaceable piece of the puzzle that operates your entire knowledge management system that helps orchestrate, manage, and optimize the flow of knowledge within your organization.\xA0 That part seems pretty clear, right? Next, we\u2019ll move on to",
-      image: "https://static.helpjuice.com/helpjuice_production/uploads/upload/image/4752/direct/1636499945090-Open%20Source%20Knowledge%20Base%20Software.jpg",
-      favicon: "https://static.helpjuice.com/assets/favicon-32x32-161f2153235b710a8ed7b9233ed6b195936bdb57bf1310e720f7fea79547cf9d.png"
-    }
-  ],
-  costDollars: {
-    total: 0.015,
-    search: {
-      neural: 5e-3
-    },
-    contents: {
-      text: 0.01
-    }
-  }
-};
-
-// src/testing/data/index.ts
-var SEARCH_RESULTS = [
-  exa_search_1748337321991_default,
-  exa_search_1748337331526_default,
-  exa_search_1748337344119_default
-];
-
-// src/functions/exa/mock.ts
-var mock_default = defineFunction7({
-  key: "dxos.org/function/exa-mock",
-  name: "Exa mock",
-  description: "Search the web for information",
-  inputSchema: Schema7.Struct({
-    query: Schema7.String.annotations({
-      description: "The query to search for."
-    })
-  }),
-  outputSchema: Schema7.Unknown,
-  handler: Effect7.fnUntraced(function* ({ data: { query } }) {
-    const result = SEARCH_RESULTS.reduce((closest, current) => {
-      if (!current.autopromptString) {
-        return closest;
-      }
-      if (!closest) {
-        return current;
-      }
-      const dist1 = levenshteinDistance(query, current.autopromptString);
-      const dist2 = levenshteinDistance(query, closest.autopromptString || "");
-      const weight1 = dist1 / Math.max(query.length, current.autopromptString.length);
-      const weight2 = dist2 / Math.max(query.length, closest.autopromptString?.length || 0);
-      return weight1 < weight2 ? current : closest;
-    }, null);
-    return result;
-  })
-});
-var levenshteinDistance = (str1, str2) => {
-  const m = str1.length;
-  const n = str2.length;
-  const dp = Array(m + 1).fill(null).map(() => Array(n + 1).fill(0));
-  for (let i = 0; i <= m; i++) {
-    dp[i][0] = i;
-  }
-  for (let j = 0; j <= n; j++) {
-    dp[0][j] = j;
-  }
-  for (let i = 1; i <= m; i++) {
-    for (let j = 1; j <= n; j++) {
-      dp[i][j] = str1[i - 1] === str2[j - 1] ? dp[i - 1][j - 1] : Math.min(dp[i - 1][j - 1], dp[i - 1][j], dp[i][j - 1]) + 1;
-    }
-  }
-  return dp[m][n];
-};
-
-// src/functions/research/graph.ts
-import * as Tool from "@effect/ai/Tool";
-import * as Toolkit from "@effect/ai/Toolkit";
-import * as Context from "effect/Context";
-import * as Effect8 from "effect/Effect";
-import * as Function3 from "effect/Function";
-import * as Option3 from "effect/Option";
-import * as Schema8 from "effect/Schema";
-import * as SchemaAST from "effect/SchemaAST";
-import { Obj as Obj3 } from "@dxos/echo";
-import { Filter, Query } from "@dxos/echo";
-import { EntityKind, ObjectId as ObjectId2, ReferenceAnnotationId, RelationSourceDXNId, RelationSourceId, RelationTargetDXNId, RelationTargetId, create, getEntityKind, getSchemaDXN, getSchemaTypename, getTypeAnnotation, getTypeIdentifierAnnotation } from "@dxos/echo/internal";
-import { isEncodedReference } from "@dxos/echo-protocol";
-import { mapAst } from "@dxos/effect";
-import { ContextQueueService, DatabaseService as DatabaseService5 } from "@dxos/functions";
-import { DXN as DXN2 } from "@dxos/keys";
-import { log as log4 } from "@dxos/log";
-import { deepMapValues, isNonNullable, trim as trim2 } from "@dxos/util";
-var __dxlog_file4 = "/__w/dxos/dxos/packages/core/assistant-toolkit/src/functions/research/graph.ts";
-var Subgraph = Schema8.Struct({
-  /** Objects and relations. */
-  objects: Schema8.Array(Schema8.Any)
-});
-var findRelatedSchema = async (db, anchor) => {
-  const allSchemas = [
-    ...db.graph.schemaRegistry.schemas
-  ];
-  return allSchemas.filter((schema) => {
-    if (getTypeAnnotation(schema)?.kind !== EntityKind.Relation) {
-      return false;
-    }
-    return isSchemaAddressableByDxn(anchor, DXN2.parse(getTypeAnnotation(schema).sourceSchema)) || isSchemaAddressableByDxn(anchor, DXN2.parse(getTypeAnnotation(schema).targetSchema));
-  }).map((schema) => ({
-    schema,
-    kind: "relation"
-  }));
-};
-var isSchemaAddressableByDxn = (schema, dxn) => {
-  if (getTypeIdentifierAnnotation(schema) === dxn.toString()) {
-    return true;
-  }
-  const t = dxn.asTypeDXN();
-  if (t) {
-    return t.type === getSchemaTypename(schema);
-  }
-  return false;
-};
-var LocalSearchToolkit = Toolkit.make(Tool.make("search_local_search", {
-  description: "Search the local database for information using a vector index",
-  parameters: {
-    query: Schema8.String.annotations({
-      description: "The query to search for. Could be a question or a topic or a set of keywords."
-    })
-  },
-  success: Schema8.Unknown,
-  failure: Schema8.Never,
-  dependencies: [
-    DatabaseService5
-  ]
-}));
-var LocalSearchHandler = LocalSearchToolkit.toLayer({
-  search_local_search: Effect8.fn(function* ({ query }) {
-    const { objects } = yield* DatabaseService5.runQuery(Query.select(Filter.text(query, {
-      type: "vector"
-    })));
-    const results = [
-      ...objects
-    ];
-    const option = yield* Effect8.serviceOption(ContextQueueService);
-    if (Option3.isSome(option)) {
-      const queueObjects = yield* Effect8.promise(() => option.value.queue.queryObjects());
-      results.push(...queueObjects);
-    }
-    return trim2`
-      <local_context>
-        ${JSON.stringify(results, null, 2)}
-      </local_context>
-    `;
-  })
-});
-var GraphWriterSchema = class extends Context.Tag("@dxos/assistant/GraphWriterSchema")() {
-};
-var makeGraphWriterToolkit = ({ schema }) => {
-  return Toolkit.make(Tool.make("graph_writer", {
-    description: "Write to the local graph database",
-    parameters: createExtractionSchema(schema).fields,
-    success: Schema8.Unknown,
-    failure: Schema8.Never,
-    dependencies: [
-      DatabaseService5,
-      ContextQueueService
-    ]
-  }).annotateContext(Context.make(GraphWriterSchema, {
-    schema
-  })));
-};
-var makeGraphWriterHandler = (toolkit, { onAppend } = {}) => {
-  const { schema } = Context.get(toolkit.tools.graph_writer.annotations, GraphWriterSchema);
-  return toolkit.toLayer({
-    graph_writer: Effect8.fn(function* (input) {
-      const { db } = yield* DatabaseService5;
-      const { queue } = yield* ContextQueueService;
-      const data = yield* Effect8.promise(() => sanitizeObjects(schema, input, db, queue));
-      yield* Effect8.promise(() => queue.append(data));
-      const dxns = data.map((obj) => Obj3.getDXN(obj));
-      onAppend?.(dxns);
-      return dxns;
-    })
-  });
-};
-var createExtractionSchema = (types) => {
-  return Schema8.Struct({
-    ...Object.fromEntries(types.map(preprocessSchema).map((schema, index) => [
-      `objects_${getSanitizedSchemaName(types[index])}`,
-      Schema8.optional(Schema8.Array(schema)).annotations({
-        description: `The objects of type: ${getSchemaDXN(types[index])?.asTypeDXN().type}. ${SchemaAST.getDescriptionAnnotation(types[index].ast).pipe(Option3.getOrElse(() => ""))}`
-      })
-    ]))
-  });
-};
-var getSanitizedSchemaName = (schema) => {
-  return getSchemaDXN(schema).asTypeDXN().type.replaceAll(/[^a-zA-Z0-9]+/g, "_");
-};
-var sanitizeObjects = async (types, data, db, queue) => {
-  const entries = types.map((type) => data[`objects_${getSanitizedSchemaName(type)}`]?.map((object) => ({
-    data: object,
-    schema: type
-  })) ?? []).flat();
-  const idMap = /* @__PURE__ */ new Map();
-  const existingIds = /* @__PURE__ */ new Set();
-  const enitties = /* @__PURE__ */ new Map();
-  const resolveId = (id) => {
-    if (ObjectId2.isValid(id)) {
-      existingIds.add(id);
-      return DXN2.fromLocalObjectId(id);
-    }
-    const mappedId = idMap.get(id);
-    if (mappedId) {
-      return DXN2.fromLocalObjectId(mappedId);
-    }
-    return void 0;
-  };
-  const res = entries.map((entry) => {
-    if (ObjectId2.isValid(entry.data.id)) {
-      return entry;
-    }
-    idMap.set(entry.data.id, ObjectId2.random());
-    entry.data.id = idMap.get(entry.data.id);
-    return entry;
-  }).map((entry) => {
-    const data2 = deepMapValues(entry.data, (value, recurse) => {
-      if (isEncodedReference(value)) {
-        const ref = value["/"];
-        const id = resolveId(ref);
-        if (id) {
-          return {
-            "/": id.toString()
-          };
-        } else {
-          return {
-            "/": `search:?q=${encodeURIComponent(ref)}`
-          };
-        }
-      }
-      return recurse(value);
-    });
-    if (getEntityKind(entry.schema) === "relation") {
-      const sourceDxn = resolveId(data2.source);
-      if (!sourceDxn) {
-        log4.warn("source not found", {
-          source: data2.source
-        }, {
-          F: __dxlog_file4,
-          L: 281,
-          S: void 0,
-          C: (f, a) => f(...a)
-        });
-      }
-      const targetDxn = resolveId(data2.target);
-      if (!targetDxn) {
-        log4.warn("target not found", {
-          target: data2.target
-        }, {
-          F: __dxlog_file4,
-          L: 285,
-          S: void 0,
-          C: (f, a) => f(...a)
-        });
-      }
-      delete data2.source;
-      delete data2.target;
-      data2[RelationSourceDXNId] = sourceDxn;
-      data2[RelationTargetDXNId] = targetDxn;
-    }
-    return {
-      data: data2,
-      schema: entry.schema
-    };
-  }).filter((object) => !existingIds.has(object.data.id));
-  const { objects: dbObjects } = await db.query(Query.select(Filter.ids(...existingIds))).run();
-  const queueObjects = await queue?.getObjectsById([
-    ...existingIds
-  ]) ?? [];
-  const objects = [
-    ...dbObjects,
-    ...queueObjects
-  ].filter(isNonNullable);
-  log4.info("objects", {
-    dbObjects,
-    queueObjects,
-    existingIds
-  }, {
-    F: __dxlog_file4,
-    L: 306,
-    S: void 0,
-    C: (f, a) => f(...a)
-  });
-  const missing = Array.from(existingIds).filter((id) => !objects.some((object) => object.id === id));
-  if (missing.length > 0) {
-    throw new Error(`Object IDs do not point to existing objects: ${missing.join(", ")}`);
-  }
-  return res.flatMap(({ data: data2, schema }) => {
-    let skip = false;
-    if (RelationSourceDXNId in data2) {
-      const id = data2[RelationSourceDXNId].asEchoDXN()?.echoId;
-      const obj = objects.find((object) => object.id === id) ?? enitties.get(id);
-      if (obj) {
-        delete data2[RelationSourceDXNId];
-        data2[RelationSourceId] = obj;
-      } else {
-        skip = true;
-      }
-    }
-    if (RelationTargetDXNId in data2) {
-      const id = data2[RelationTargetDXNId].asEchoDXN()?.echoId;
-      const obj = objects.find((object) => object.id === id) ?? enitties.get(id);
-      if (obj) {
-        delete data2[RelationTargetDXNId];
-        data2[RelationTargetId] = obj;
-      } else {
-        skip = true;
-      }
+      image: "https://cdn-image.creati.ai/ai-tools/product-image/sciphi.webp",
+      favicon: "https://cdn-image.creati.ai/image/Creatiai.ico"
+    },
+    {
+      id: "https://helpjuice.com/blog/open-source-knowledge-base",
+      title: "The 12 Best Open Source Knowledge Base Software for 2024",
+      url: "https://helpjuice.com/blog/open-source-knowledge-base",
+      author: "Zeeshan Khan",
+      text: "\n \n \n \n \n At Helpjuice / \n \n #Software &amp; Alternatives\n May 15 2025 \n 11m read \n \n \n \n \n On the hunt for the perfect knowledge base software that\u2019s open source? This post will walk you through the best options for your business. \n \n \n \n \n There\u2019s no denying that a knowledge base can make a major impact on your organization.\xA0 Whether it's to help provide better support to your customers or to enable your employees to find the information they need to do their job, a finely-tuned knowledge base can make all the difference when it comes to how knowledge and information flows through your business. And with plenty of options on the market out there, there\u2019s certainly no shortage of open source knowledge base software. But how can you tell you\u2019re not investing time into installing and learning new software that your team won't use anyway? How can you avoid the time and effort put into an open source option that you later determine to not be a good fit for your needs?\xA0 It\u2019s simple\u2014do a little research beforehand. We know, we know\u2014you don\u2019t have endless time to invest in that kind of thing (what with a business to run and all). That\u2019s why we\u2019ve created a helpful list of the must-consider open source knowledge base software that companies of all niches, industries, and sizes should consider.\xA0 We\u2019re even throwing in a little helpful knowledge that should equip you with the information needed to choose the right software for you\u2014like what knowledge base software is in the first place, the benefits of open source software, and how to address your unique needs as a company to choose the right software for you.\xA0 Want to skip ahead on some of the basics of open-source knowledge base software?\xA0 Be our guest.\xA0 The best open source knowledge base software includes: \n BookStack \n OpenKM \n myBase \n eXo \n PHPKB \n Documize \n DocuWiki \n phpMyFAQ \n MediaWiki \n xWiki \n TWiki \n TiddlyWiki \n What is an Open Source Knowledge Base? Before we dive into which open-source knowledge base software you should consider for your business, we should probably ensure we\u2019re on the same page about what exactly open-source knowledge base software is.\xA0 First things first, let\u2019s start with the term knowledge base. A knowledge base is a central place that allows structured storage of information where users can search for and access this information. \xA0Knowledge base software should be the key tool that helps make this process seamless, simplified, and efficient. Knowledge base software is designed to help you create and manage your knowledge base to the best of your ability. this usually includes setting up the knowledge base architecture, creating and editing documentation, searching, and analyzing your knowledge base, and more. Ideally, this is the irreplaceable piece of the puzzle that operates your entire knowledge management system that helps orchestrate, manage, and optimize the flow of knowledge within your organization.\xA0 That part seems pretty clear, right? Next, we\u2019ll move on to",
+      image: "https://static.helpjuice.com/helpjuice_production/uploads/upload/image/4752/direct/1636499945090-Open%20Source%20Knowledge%20Base%20Software.jpg",
+      favicon: "https://static.helpjuice.com/assets/favicon-32x32-161f2153235b710a8ed7b9233ed6b195936bdb57bf1310e720f7fea79547cf9d.png"
     }
-    if (!skip) {
-      const obj = create(schema, data2);
-      enitties.set(obj.id, obj);
-      return [
-        obj
-      ];
+  ],
+  costDollars: {
+    total: 0.015,
+    search: {
+      neural: 5e-3
+    },
+    contents: {
+      text: 0.01
     }
-    return [];
-  });
+  }
 };
-var SoftRef = Schema8.Struct({
-  "/": Schema8.String
-}).annotations({
-  description: "Reference to another object."
+
+// src/functions/exa/data/index.ts
+var SEARCH_RESULTS = [
+  exa_search_1748337321991_default,
+  exa_search_1748337331526_default,
+  exa_search_1748337344119_default
+];
+
+// src/functions/exa/mock.ts
+var mock_default = defineFunction7({
+  key: "dxos.org/function/exa-mock",
+  name: "Exa mock",
+  description: "Search the web for information",
+  inputSchema: Schema8.Struct({
+    query: Schema8.String.annotations({
+      description: "The query to search for."
+    })
+  }),
+  outputSchema: Schema8.Unknown,
+  handler: Effect8.fnUntraced(function* ({ data: { query } }) {
+    const result = SEARCH_RESULTS.reduce((closest, current) => {
+      if (!current.autopromptString) {
+        return closest;
+      }
+      if (!closest) {
+        return current;
+      }
+      const dist1 = levenshteinDistance(query, current.autopromptString);
+      const dist2 = levenshteinDistance(query, closest.autopromptString || "");
+      const weight1 = dist1 / Math.max(query.length, current.autopromptString.length);
+      const weight2 = dist2 / Math.max(query.length, closest.autopromptString?.length || 0);
+      return weight1 < weight2 ? current : closest;
+    }, null);
+    return result;
+  })
 });
-var preprocessSchema = (schema) => {
-  const isRelationSchema = getEntityKind(schema) === "relation";
-  const go = (ast, visited = /* @__PURE__ */ new Set()) => {
-    if (visited.has(ast)) {
-      return ast;
-    }
-    visited.add(ast);
-    if (SchemaAST.getAnnotation(ast, ReferenceAnnotationId).pipe(Option3.isSome)) {
-      return SoftRef.ast;
+var levenshteinDistance = (str1, str2) => {
+  const m = str1.length;
+  const n = str2.length;
+  const dp = Array(m + 1).fill(null).map(() => Array(n + 1).fill(0));
+  for (let i = 0; i <= m; i++) {
+    dp[i][0] = i;
+  }
+  for (let j = 0; j <= n; j++) {
+    dp[0][j] = j;
+  }
+  for (let i = 1; i <= m; i++) {
+    for (let j = 1; j <= n; j++) {
+      dp[i][j] = str1[i - 1] === str2[j - 1] ? dp[i - 1][j - 1] : Math.min(dp[i - 1][j - 1], dp[i - 1][j], dp[i][j - 1]) + 1;
     }
-    return mapAst(ast, (child) => go(child, visited));
-  };
-  return Schema8.make(mapAst(schema.ast, (ast) => go(ast))).pipe(Schema8.omit("id"), Schema8.extend(Schema8.Struct({
-    id: Schema8.String.annotations({
-      description: "The id of this object. Come up with a unique id based on your judgement."
-    })
-  })), isRelationSchema ? Schema8.extend(Schema8.Struct({
-    source: Schema8.String.annotations({
-      description: "The id of the source object for this relation."
-    }),
-    target: Schema8.String.annotations({
-      description: "The id of the target object for this relation."
-    })
-  })) : Function3.identity);
+  }
+  return dp[m][n];
 };
 
-// raw-loader:/__w/dxos/dxos/packages/core/assistant-toolkit/src/functions/research/instructions-research.tpl?raw
-var instructions_research_default = "You are the Research Agent.\n\nThe Research Agent is an expert assistant that conducts in-depth research using real-time web search.\nThe Research Agent outputs results in a structured format matching the schema provided.\n\nThe Research Agent is equipped with the ability to:\n\n- Generate precise and effective search queries \n- Request web pages by query (through a `web_search` tool)\n- Read the full content of retrieved pages\n- Synthesize accurate, clear, and structured answers using reliable information from the retrieved content\n- Search the local database for information using a vector index (through a `local_search` tool)\n\nThe Research Agent always follows these principles:\n\n- Relevance First: The Research Agent only returns facts supported by content in retrieved web pages. The Research Agent never fabricates or guesses information.\n- Summarize, Don't Copy: The Research Agent synthesizes and rephrases content in its own words. The Research Agent quotes only when necessary.\n- Multiple Sources: The Research Agent cross-references at least 2 sources before drawing conclusions, unless the information is directly stated and non-controversial.\n- Transparency: The Research Agent mentions which sources were used and explains how it arrived at conclusions.\n- Accuracy Over Brevity: The Research Agent prefers detailed, technically accurate explanations over shallow summaries.\n- The Research Agent admits uncertainty rather than misleading.\n- The Research Agent picks the most concrete schema types for extracted information.\n- The Research Agent fills schema fields completely with information it is confident about, and omits fields it is not confident about.\n- When outputting results, the Research Agent adds extra data that fits the schema even if not directly related to the user's question.\n- The Research Agent creates relations and references between new objects found and what's already in the database.\n- The Research Agent does not create objects that are already in the database.\n- The Research Agent re-uses existing object IDs as references when enriching existing objects.\n- The Research Agent ALWAYS calls the `graph_writer` at the end to save the data. This conversation will be deleted, so only the data written to the graph will be preserved.\n\nThe Research Agent may be asked for:\n\n- Technical explanations\n- Literature reviews  \n- Comparisons\n- Emerging trends\n- Implementation strategies\n\nThe Research Agent begins by interpreting the user's request, then:\n\nThe Research Agent breaks it into sub-questions (if applicable).\n\nFor each sub-question, the Research Agent generates a clear, concise web search query.\n\nThe Research Agent uses `web_search`(query) to retrieve information.\n\nThe Research Agent extracts and synthesizes relevant answers.\n\nThe Research Agent's output includes:\n\n- A clear, structured answer to the user's question\n- A citation list or link list of sources used\n\nOptionally, the Research Agent provides follow-up suggestions or questions for deeper inquiry.\n\nHere's how the Research Agent operates:\n\n1. The Research Agent analyzes the user's request and identifies key topics to search for (3 or more), printing them out.\n2. The Research Agent performs a web search for each topic.\n3. The Research Agent reads and analyzes results, cross references information from multiple sources, and represents conflicting information as ranges of possible values.\n\n4. The Research Agent searches the local database for information using a vector index that might link to the user's question.\n6. The Research Agent creates relations and references between new objects and existing database objects when related, using existing object IDs as references.\n7. The Research Agent selects the most concrete schema types for extracted information, using multiple types as needed, and prints its decision and reasoning.\n5. The Research Agent creates a clear, structured answer to the user's question.\n8. The Research Agent submits results using the specific schema.\n\nIMPORTANT:\n\n- The Research Agent always runs the `local_search` tool to search the local database at least once before submitting results.\n- The Research Agent does not create objects that already exist in the database.\n- Ids that are not in the database are human-readable strings like `ivan_zhao_1`.\n\nStatus reporting:\n\nThe Research Agent reports its status frequently using the `<status>` tags: <status>Searching for Google Founders</status>\nThe Research Agent reports its status in-between each tool call and before submitting results.\n\n<example>\n\nBased on my research, I can now provide information about Google and it's founders.\n\nThe following objects are already in the database, I will not submit them again, but I'll re-use their IDs as references:\n\n- 01JWRDEHPB5TT2JQQQC15038BT Google\n- 01JWRDEHPA14CYW2NW9FAH6DJJ Larry Page\n- 01JWRDEHPBN0BBJP57B9S108W6 Sergey Brin\n\nI will use the following schema to construct new objects:\n\n- type:dxos.org/type/Organization for Alphabet Inc.\n- type:dxos.org/type/Person for Ivan Zhao\n- type:dxos.org/type/Person for Simon Last\n- dxn:type:dxos.org/relation/Employer for Ivan's employer\n- dxn:type:dxos.org/relation/Employer for Simon's employer\n\n<status>Formatting results</status>\n\n</example>";
-
 // src/functions/research/research-graph.ts
 import * as Effect9 from "effect/Effect";
 import * as Layer2 from "effect/Layer";
 import * as Schema9 from "effect/Schema";
-import { Obj as Obj4, Query as Query2, Ref as Ref2, Type as Type2 } from "@dxos/echo";
+import { Obj as Obj6, Query as Query2, Ref as Ref2, Type as Type3 } from "@dxos/echo";
+import { Database as Database6 } from "@dxos/echo";
+import { SystemTypeAnnotation } from "@dxos/echo/internal";
 import { Queue } from "@dxos/echo-db";
-import { ContextQueueService as ContextQueueService2, DatabaseService as DatabaseService6, QueueService } from "@dxos/functions";
+import { ContextQueueService as ContextQueueService2, QueueService } from "@dxos/functions";
 var ResearchGraph = Schema9.Struct({
-  queue: Type2.Ref(Queue)
-}).pipe(Type2.Obj({
+  queue: Type3.Ref(Queue)
+}).pipe(Type3.object({
   typename: "dxos.org/type/ResearchGraph",
   version: "0.1.0"
-}));
+}), SystemTypeAnnotation.set(true));
 var queryResearchGraph = Effect9.fn("queryResearchGraph")(function* () {
-  const { objects } = yield* DatabaseService6.runQuery(Query2.type(ResearchGraph));
+  const objects = yield* Database6.Service.runQuery(Query2.type(ResearchGraph));
   return objects.at(0);
 });
 var createResearchGraph = Effect9.fn("createResearchGraph")(function* () {
   const queue = yield* QueueService.createQueue();
-  return yield* DatabaseService6.add(Obj4.make(ResearchGraph, {
+  return yield* Database6.Service.add(Obj6.make(ResearchGraph, {
     queue: Ref2.fromDXN(queue.dxn)
   }));
 });
 var contextQueueLayerFromResearchGraph = Layer2.unwrapEffect(Effect9.gen(function* () {
   const researchGraph = (yield* queryResearchGraph()) ?? (yield* createResearchGraph());
-  const researchQueue = yield* DatabaseService6.load(researchGraph.queue);
+  const researchQueue = yield* Database6.Service.load(researchGraph.queue);
   return ContextQueueService2.layer(researchQueue);
 }));
 
+// raw-loader:/__w/dxos/dxos/packages/core/assistant-toolkit/src/functions/research/research-instructions.tpl?raw
+var research_instructions_default = "You are the Research Agent.\n\nThe Research Agent is an expert assistant that conducts in-depth research using real-time web search.\nThe Research Agent outputs results in a structured format matching the schema provided.\n\nThe Research Agent is equipped with the ability to:\n\n- Generate precise and effective search queries \n- Request web pages by query.\n- Synthesize accurate, clear, and structured answers using reliable information from the retrieved content\n{{#if entityExtraction}}\n- Search the local database for information using a vector index (through a `local_search` tool)\n{{/if}}\n\nThe Research Agent always follows these principles:\n\n- Relevance First: The Research Agent only returns facts supported by content in retrieved web pages. The Research Agent never fabricates or guesses information.\n- Summarize, Don't Copy: The Research Agent synthesizes and rephrases content in its own words. The Research Agent quotes only when necessary.\n- Multiple Sources: The Research Agent cross-references at least 2 sources before drawing conclusions, unless the information is directly stated and non-controversial.\n- Transparency: The Research Agent mentions which sources were used and explains how it arrived at conclusions.\n- Accuracy Over Brevity: The Research Agent prefers detailed, technically accurate explanations over shallow summaries.\n- The Research Agent admits uncertainty rather than misleading.\n{{#if entityExtraction}}\n- The Research Agent picks the most concrete schema types for extracted information.\n- The Research Agent fills schema fields completely with information it is confident about, and omits fields it is not confident about.\n- When outputting results, the Research Agent adds extra data that fits the schema even if not directly related to the user's question.\n- The Research Agent creates relations and references between new objects found and what's already in the database.\n- The Research Agent does not create objects that are already in the database.\n- The Research Agent re-uses existing object IDs as references when enriching existing objects.\n- The Research Agent ALWAYS calls the `graph_writer` at the end to save the data. This conversation will be deleted, so only the data written to the graph will be preserved.\n{{/if}}\n\nThe Research Agent may be asked for:\n\n- Technical explanations\n- Literature reviews  \n- Comparisons\n- Emerging trends\n- Implementation strategies\n\nThe Research Agent begins by interpreting the user's request, then:\n\nThe Research Agent breaks it into sub-questions (if applicable).\n\nFor each sub-question, the Research Agent generates a clear, concise web search query.\n\nThe Research Agent extracts and synthesizes relevant answers.\n\nThe Research Agent's output includes:\n\n- A clear, structured answer to the user's question\n- A citation list or link list of sources used\n\nOptionally, the Research Agent provides follow-up suggestions or questions for deeper inquiry.\n\nHere's how the Research Agent operates:\n\n1. The Research Agent analyzes the user's request and identifies key topics to search for (3 or more), printing them out.\n2. The Research Agent performs a web search for each topic.\n3. The Research Agent reads and analyzes results, cross references information from multiple sources, and represents conflicting information as ranges of possible values.\n\n{{#if entityExtraction}}\n4. The Research Agent searches the local database for information using a vector index that might link to the user's question.\n6. The Research Agent creates relations and references between new objects and existing database objects when related, using existing object IDs as references.\n7. The Research Agent selects the most concrete schema types for extracted information, using multiple types as needed, and prints its decision and reasoning.\n5. The Research Agent creates a clear, structured answer to the user's question.\n8. The Research Agent submits results using the specific schema.\n{{/if}}\n\n{{#if entityExtraction}}\nIMPORTANT:\n- The Research Agent always runs the `local_search` tool to search the local database at least once before submitting results.\n- The Research Agent does not create objects that already exist in the database.\n- Ids that are not in the database are human-readable strings like `ivan_zhao_1`.\n{{/if}}\n\nStatus reporting:\n\nThe Research Agent reports its status frequently using the `<status>` tags: <status>Searching for Google Founders</status>\nThe Research Agent reports its status in-between each tool call and before submitting results.\n\n{{#if entityExtraction}}\n<example>\n\nBased on my research, I can now provide information about Google and it's founders.\n\nThe following objects are already in the database, I will not submit them again, but I'll re-use their IDs as references:\n\n- 01JWRDEHPB5TT2JQQQC15038BT Google\n- 01JWRDEHPA14CYW2NW9FAH6DJJ Larry Page\n- 01JWRDEHPBN0BBJP57B9S108W6 Sergey Brin\n\nI will use the following schema to construct new objects:\n\n- type:dxos.org/type/Organization for Alphabet Inc.\n- type:dxos.org/type/Person for Ivan Zhao\n- type:dxos.org/type/Person for Simon Last\n- dxn:type:dxos.org/relation/Employer for Ivan's employer\n- dxn:type:dxos.org/relation/Employer for Simon's employer\n\n<status>Formatting results</status>\n\n</example>\n{{/if}}\n\nLast content block is the full research note -- the result of the research.\n";
+
 // src/functions/research/types.ts
-import { DataType as DataType3 } from "@dxos/schema";
+import { Text } from "@dxos/schema";
+import { Event, HasConnection, HasRelationship, LegacyOrganization, LegacyPerson, Project, Task } from "@dxos/types";
 var ResearchDataTypes = [
   // Objects
-  DataType3.Event,
-  DataType3.LegacyOrganization,
-  DataType3.LegacyPerson,
-  DataType3.Project,
-  DataType3.Task,
-  DataType3.Text,
+  Event.Event,
+  LegacyOrganization,
+  Task.Task,
+  Text.Text,
   // Relations
-  // TODO(wittjosiah): Until views (e.g. table) support relations this needs to be expressed via organization ref.
-  // DataType.Employer,
-  DataType3.HasRelationship,
-  DataType3.HasConnection
+  // TODO(wittjosiah): Until views (e.g., Table) support relations this needs to be expressed via organization ref.
+  // Employer.Employer,
+  LegacyPerson,
+  Project.Project,
+  HasRelationship.HasRelationship,
+  HasConnection.HasConnection
 ];
 
 // src/functions/research/research.ts
@@ -1417,40 +1428,46 @@ var research_default = defineFunction8({
   key: "dxos.org/function/research",
   name: "Research",
   description: trim3`
-    Research the web for information. 
+    Search the web to research information about the given subject.
     Inserts structured data into the research graph. 
-    Will return research summary and the objects created.
+    Creates a research summary and returns the objects created.
   `,
   inputSchema: Schema10.Struct({
     query: Schema10.String.annotations({
       description: trim3`
-        The query to search for.
-        If doing research on an object, load it first and pass it as a JSON string.
+        The search query.
+        If doing research on an object then load it first and pass it as JSON.
       `
     }),
-    researchInstructions: Schema10.optional(Schema10.String).annotations({
+    instructions: Schema10.optional(Schema10.String).annotations({
       description: trim3`
         The instructions for the research agent. 
-        E.g., preference on fast responses or in-depth analysis, number of web searcher or the objects created.
       `
     }),
     // TOOD(burdon): Move to context.
     mockSearch: Schema10.optional(Schema10.Boolean).annotations({
       description: "Whether to use the mock search tool.",
       default: false
+    }),
+    entityExtraction: Schema10.optional(Schema10.Boolean).annotations({
+      description: trim3`
+        Whether to extract structured entities from the research. 
+        Experimental feature only enable if user explicitly requests it.
+      `,
+      default: false
     })
   }),
   outputSchema: Schema10.Struct({
-    note: Schema10.optional(Schema10.String).annotations({
-      description: "A note from the research agent."
+    document: Schema10.optional(Schema10.String).annotations({
+      description: "The generated research document."
     }),
     objects: Schema10.Array(Schema10.Unknown).annotations({
-      description: "The structured objects created as a result of the research."
+      description: "Structured objects created during the research process."
     })
   }),
-  handler: Effect10.fnUntraced(function* ({ data: { query, mockSearch, researchInstructions } }) {
+  handler: Effect10.fnUntraced(function* ({ data: { query, instructions: instructions6, mockSearch = false, entityExtraction = false } }) {
     if (mockSearch) {
-      const mockPerson = yield* DatabaseService7.add(Obj5.make(DataType4.Person, {
+      const mockPerson = yield* Database7.Service.add(Obj7.make(Person.Person, {
         preferredName: "John Doe",
         emails: [
           {
@@ -1464,52 +1481,52 @@ var research_default = defineFunction8({
         ]
       }));
       return {
-        note: trim3`
-            The research run in test-mode and was mocked. 
-            Proceed as usual.
-            We reference John Doe to test reference: ${Obj5.getDXN(mockPerson)}
+        document: trim3`
+            The research ran in test-mode and was mocked. Proceed as usual.
+            We reference John Doe to test reference: ${Obj7.getDXN(mockPerson)}
           `,
         objects: [
-          Obj5.toJSON(mockPerson)
+          Obj7.toJSON(mockPerson)
         ]
       };
     }
-    yield* DatabaseService7.flush({
+    yield* Database7.Service.flush({
       indexes: true
     });
     yield* TracingService4.emitStatus({
-      message: "Researching..."
-    });
-    const objectDXNs = [];
-    const GraphWriterToolkit = makeGraphWriterToolkit({
-      schema: ResearchDataTypes
-    });
-    const GraphWriterHandler = makeGraphWriterHandler(GraphWriterToolkit, {
-      onAppend: (dxns) => objectDXNs.push(...dxns)
+      message: "Starting research..."
     });
     const NativeWebSearch = Toolkit2.make(AnthropicTool.WebSearch_20250305({}));
-    const toolkit = yield* createToolkit2({
-      toolkit: Toolkit2.merge(LocalSearchToolkit, GraphWriterToolkit, NativeWebSearch)
-    }).pipe(Effect10.provide(Layer3.mergeAll(
-      //
-      GraphWriterHandler,
-      LocalSearchHandler
-    ).pipe(Layer3.provide(contextQueueLayerFromResearchGraph))));
+    let toolkit = NativeWebSearch;
+    let handlers = Layer3.empty;
+    const objectDXNs = [];
+    if (entityExtraction) {
+      const GraphWriterToolkit = makeGraphWriterToolkit({
+        schema: ResearchDataTypes
+      });
+      const GraphWriterHandler = makeGraphWriterHandler(GraphWriterToolkit, {
+        onAppend: (dxns) => objectDXNs.push(...dxns)
+      });
+      toolkit = Toolkit2.merge(toolkit, LocalSearchToolkit, GraphWriterToolkit);
+      handlers = Layer3.mergeAll(handlers, LocalSearchHandler, GraphWriterHandler).pipe(Layer3.provide(contextQueueLayerFromResearchGraph));
+    }
+    const finishedToolkit = yield* createToolkit2({
+      toolkit
+    }).pipe(Effect10.provide(handlers));
     const session = new AiSession2();
     const result = yield* session.run({
       prompt: query,
-      system: instructions_research_default + (researchInstructions ? `
-
-<research_instructions>${researchInstructions}</research_instructions>` : ""),
-      toolkit,
+      system: join(Template2.process(research_instructions_default, {
+        entityExtraction
+      }), instructions6 && `<instructions>${instructions6}</instructions>`),
+      toolkit: finishedToolkit,
       observer: GenerationObserver2.fromPrinter(new ConsolePrinter2({
         tag: "research"
       }))
     });
-    const note = result.at(-1)?.blocks.filter((block) => block._tag === "text").at(-1)?.text;
-    const objects = yield* Effect10.forEach(objectDXNs, (dxn) => DatabaseService7.resolve(dxn)).pipe(Effect10.map(Array6.map((obj) => Obj5.toJSON(obj))));
+    const objects = yield* Effect10.forEach(objectDXNs, (dxn) => Database7.Service.resolve(dxn)).pipe(Effect10.map(Array6.map((obj) => Entity2.toJSON(obj))));
     return {
-      note,
+      document: extractLastTextBlock(result),
       objects
     };
   }, Effect10.provide(Layer3.mergeAll(
@@ -1522,7 +1539,7 @@ var research_default = defineFunction8({
     makeToolExecutionServiceFromFunctions(Toolkit2.make(), Layer3.empty)
   ).pipe(Layer3.provide(
     // TODO(dmaretskyi): This should be provided by environment.
-    Layer3.mergeAll(FunctionInvocationService.layerTestMocked({
+    Layer3.mergeAll(FunctionInvocationServiceLayerTestMocked({
       functions: [
         exa_default,
         mock_default
@@ -1530,10 +1547,14 @@ var research_default = defineFunction8({
     }))
   ))))
 });
+var join = (...strings) => strings.filter(Boolean).join("\n\n");
+var extractLastTextBlock = (result) => {
+  return Function4.pipe(result, Array6.last, Option4.map(Function4.flow((_) => _.blocks, Array6.reverse, Array6.dropWhile((_) => _._tag === "summary"), Array6.takeWhile((_) => _._tag === "text"), Array6.reverse, Array6.map((_) => _.text), Array6.reduce("", String10.concat))), Option4.getOrElse(() => ""));
+};
 
 // src/functions/research/index.ts
 (function(Research2) {
-  Research2.create = create_document_default;
+  Research2.create = document_create_default;
   Research2.research = research_default;
 })(Research || (Research = {}));
 var Research;
@@ -1545,7 +1566,7 @@ var entity_extraction_default = defineFunction9({
   name: "Entity Extraction",
   description: "Extracts entities from emails and transcripts.",
   inputSchema: Schema11.Struct({
-    source: DataType5.Message.annotations({
+    source: Message2.Message.annotations({
       description: "Email or transcript to extract entities from."
     }),
     // TODO(dmaretskyi): Consider making this an array of blueprints instead.
@@ -1554,18 +1575,19 @@ var entity_extraction_default = defineFunction9({
     })
   }),
   outputSchema: Schema11.Struct({
-    entities: Schema11.optional(Schema11.Array(Obj6.Any).annotations({
+    entities: Schema11.optional(Schema11.Array(Type4.Obj).annotations({
       description: "Extracted entities."
     }))
   }),
-  handler: Effect11.fnUntraced(function* ({ data: { source, instructions: instructions6 } }) {
-    const contact = yield* extractContact(source);
+  handler: Effect11.fnUntraced(function* ({ data: { source: message, instructions: instructions6 } }) {
+    const tags = Obj8.getMeta(message)?.tags;
+    const contact = yield* extractContact(message.sender, tags);
     let organization = null;
     if (contact && !contact.organization) {
       const created = [];
       const GraphWriterToolkit = makeGraphWriterToolkit({
         schema: [
-          DataType5.LegacyOrganization
+          LegacyOrganization2
         ]
       }).pipe();
       const GraphWriterHandler = makeGraphWriterHandler(GraphWriterToolkit, {
@@ -1579,7 +1601,7 @@ var entity_extraction_default = defineFunction9({
             ${instructions6 ? "<user_intructions>" + instructions6 + "</user_intructions>" : ""},
           `,
         prompt: JSON.stringify({
-          source,
+          source: message,
           contact
         }),
         toolkit
@@ -1587,10 +1609,15 @@ var entity_extraction_default = defineFunction9({
       if (created.length > 1) {
         throw new Error("Multiple organizations created");
       } else if (created.length === 1) {
-        organization = yield* DatabaseService8.resolve(created[0], DataType5.Organization);
-        Obj6.getMeta(organization).tags ??= [];
-        Obj6.getMeta(organization).tags.push(...Obj6.getMeta(source)?.tags ?? []);
-        contact.organization = Ref3.make(organization);
+        organization = yield* Database8.Service.resolve(created[0], Organization.Organization);
+        Obj8.change(organization, (org) => {
+          const meta = Obj8.getMeta(org);
+          meta.tags ??= [];
+          meta.tags.push(...tags ?? []);
+        });
+        Obj8.change(contact, (c) => {
+          c.organization = Ref3.make(organization);
+        });
       }
     }
     return {
@@ -1601,24 +1628,24 @@ var entity_extraction_default = defineFunction9({
     };
   }, Effect11.provide(Layer4.mergeAll(AiService3.model("@anthropic/claude-sonnet-4-0"), makeToolResolverFromFunctions2([], Toolkit3.make()), makeToolExecutionServiceFromFunctions2(Toolkit3.make(), Layer4.empty)).pipe(Layer4.provide(
     // TODO(dmaretskyi): This should be provided by environment.
-    Layer4.mergeAll(FunctionInvocationService2.layerTest())
+    Layer4.mergeAll(FunctionInvocationServiceLayerTest())
   ))))
 });
-var extractContact = Effect11.fn("extractContact")(function* (message) {
-  const name = message.sender.name;
-  const email = message.sender.email;
+var extractContact = Effect11.fn("extractContact")(function* (actor, tags) {
+  const name = actor.name;
+  const email = actor.email;
   if (!email) {
     log5.warn("email is required for contact extraction", {
-      sender: message.sender
+      actor
     }, {
       F: __dxlog_file5,
-      L: 97,
+      L: 112,
       S: this,
       C: (f, a) => f(...a)
     });
     return void 0;
   }
-  const { objects: existingContacts } = yield* DatabaseService8.runQuery(Filter2.type(DataType5.Person));
+  const existingContacts = yield* Database8.Service.runQuery(Filter2.type(Person2.Person));
   const existingContact = existingContacts.find((contact) => contact.emails?.some((contactEmail) => contactEmail.value === email));
   if (existingContact) {
     log5.info("Contact already exists", {
@@ -1626,25 +1653,31 @@ var extractContact = Effect11.fn("extractContact")(function* (message) {
       existingContact
     }, {
       F: __dxlog_file5,
-      L: 110,
+      L: 125,
       S: this,
       C: (f, a) => f(...a)
     });
     return existingContact;
   }
-  const newContact = Obj6.make(DataType5.Person, {
-    [Obj6.Meta]: {
-      tags: Obj6.getMeta(message)?.tags
-    },
+  const newContact = Obj8.make(Person2.Person, {
+    ...tags ? {
+      [Obj8.Meta]: {
+        tags: [
+          ...tags
+        ]
+      }
+    } : {},
     emails: [
       {
         value: email
       }
     ]
   });
-  yield* DatabaseService8.add(newContact);
+  yield* Database8.Service.add(newContact);
   if (name) {
-    newContact.fullName = name;
+    Obj8.change(newContact, (c) => {
+      c.fullName = name;
+    });
   }
   const emailDomain = email.split("@")[1]?.toLowerCase();
   if (!emailDomain) {
@@ -1652,7 +1685,7 @@ var extractContact = Effect11.fn("extractContact")(function* (message) {
       email
     }, {
       F: __dxlog_file5,
-      L: 128,
+      L: 143,
       S: this,
       C: (f, a) => f(...a)
     });
@@ -1662,11 +1695,11 @@ var extractContact = Effect11.fn("extractContact")(function* (message) {
     emailDomain
   }, {
     F: __dxlog_file5,
-    L: 132,
+    L: 147,
     S: this,
     C: (f, a) => f(...a)
   });
-  const { objects: existingOrganisations } = yield* DatabaseService8.runQuery(Filter2.type(DataType5.Organization));
+  const existingOrganisations = yield* Database8.Service.runQuery(Filter2.type(Organization.Organization));
   const matchingOrg = existingOrganisations.find((org) => {
     if (org.website) {
       try {
@@ -1679,7 +1712,7 @@ var extractContact = Effect11.fn("extractContact")(function* (message) {
           error: e
         }, {
           F: __dxlog_file5,
-          L: 150,
+          L: 165,
           S: this,
           C: (f, a) => f(...a)
         });
@@ -1693,11 +1726,13 @@ var extractContact = Effect11.fn("extractContact")(function* (message) {
       organization: matchingOrg
     }, {
       F: __dxlog_file5,
-      L: 158,
+      L: 176,
       S: this,
       C: (f, a) => f(...a)
     });
-    newContact.organization = Ref3.make(matchingOrg);
+    Obj8.change(newContact, (c) => {
+      c.organization = Ref3.make(matchingOrg);
+    });
   }
   return newContact;
 });
@@ -1713,17 +1748,18 @@ import * as FetchHttpClient2 from "@effect/platform/FetchHttpClient";
 import * as HttpClient from "@effect/platform/HttpClient";
 import * as Array9 from "effect/Array";
 import * as Effect13 from "effect/Effect";
-import * as Function4 from "effect/Function";
+import * as Function5 from "effect/Function";
 import * as Schema12 from "effect/Schema";
-import { Filter as Filter4, Obj as Obj8, Query as Query4, Ref as Ref5 } from "@dxos/echo";
-import { DatabaseService as DatabaseService10, defineFunction as defineFunction10, withAuthorization } from "@dxos/functions";
+import { Filter as Filter4, Obj as Obj10, Query as Query4, Ref as Ref5 } from "@dxos/echo";
+import { Database as Database10 } from "@dxos/echo";
+import { CredentialsService as CredentialsService3, defineFunction as defineFunction10, withAuthorization } from "@dxos/functions";
 import { log as log7 } from "@dxos/log";
-import { DataType as DataType6 } from "@dxos/schema";
+import { Person as Person3, Project as Project2, Task as Task2 } from "@dxos/types";
 
 // src/sync/sync.ts
 import * as Effect12 from "effect/Effect";
-import { Filter as Filter3, Obj as Obj7, Query as Query3, Ref as Ref4 } from "@dxos/echo";
-import { DatabaseService as DatabaseService9 } from "@dxos/functions";
+import { Filter as Filter3, Obj as Obj9, Query as Query3, Ref as Ref4 } from "@dxos/echo";
+import { Database as Database9 } from "@dxos/echo";
 import { failedInvariant } from "@dxos/invariant";
 import { log as log6 } from "@dxos/log";
 var __dxlog_file6 = "/__w/dxos/dxos/packages/core/assistant-toolkit/src/sync/sync.ts";
@@ -1734,7 +1770,7 @@ var syncObjects = Effect12.fn("syncObjects")(function* (objs, { foreignKeyId })
       if (!Ref4.isRef(obj[key])) continue;
       const ref = obj[key];
       if (!ref.target) continue;
-      if (Obj7.getDXN(ref.target).isLocalObjectId()) {
+      if (Obj9.getDXN(ref.target).isLocalObjectId()) {
         const [target] = yield* syncObjects([
           ref.target
         ], {
@@ -1743,26 +1779,26 @@ var syncObjects = Effect12.fn("syncObjects")(function* (objs, { foreignKeyId })
         obj[key] = Ref4.make(target);
       }
     }
-    const schema = Obj7.getSchema(obj) ?? failedInvariant("No schema.");
-    const foreignId = Obj7.getKeys(obj, foreignKeyId)[0]?.id ?? failedInvariant("No foreign key.");
-    const { objects: [existing] } = yield* DatabaseService9.runQuery(Query3.select(Filter3.foreignKeys(schema, [
+    const schema = Obj9.getSchema(obj) ?? failedInvariant("No schema.");
+    const foreignId = Obj9.getKeys(obj, foreignKeyId)[0]?.id ?? failedInvariant("No foreign key.");
+    const [existing] = yield* Database9.Service.runQuery(Query3.select(Filter3.foreignKeys(schema, [
       {
         source: foreignKeyId,
         id: foreignId
       }
     ])));
     log6("sync object", {
-      type: Obj7.getTypename(obj),
+      type: Obj9.getTypename(obj),
       foreignId,
-      existing: existing ? Obj7.getDXN(existing) : void 0
+      existing: existing ? Obj9.getDXN(existing) : void 0
     }, {
       F: __dxlog_file6,
-      L: 47,
+      L: 48,
       S: this,
       C: (f, a) => f(...a)
     });
     if (!existing) {
-      yield* DatabaseService9.add(obj);
+      yield* Database9.Service.add(obj);
       return obj;
     } else {
       copyObjectData(existing, obj);
@@ -1773,23 +1809,25 @@ var syncObjects = Effect12.fn("syncObjects")(function* (objs, { foreignKeyId })
   });
 });
 var copyObjectData = (existing, newObj) => {
-  for (const key of Object.keys(newObj)) {
-    if (typeof key !== "string" || key === "id") continue;
-    if (typeof newObj[key] !== "string" && typeof newObj[key] !== "number" && typeof newObj[key] !== "boolean" && !Ref4.isRef(newObj[key])) continue;
-    existing[key] = newObj[key];
-  }
-  for (const key of Object.keys(existing)) {
-    if (typeof key !== "string" || key === "id") continue;
-    if (!(key in newObj)) {
-      delete existing[key];
+  Obj9.change(existing, (obj) => {
+    for (const key of Object.keys(newObj)) {
+      if (typeof key !== "string" || key === "id") continue;
+      if (typeof newObj[key] !== "string" && typeof newObj[key] !== "number" && typeof newObj[key] !== "boolean" && !Ref4.isRef(newObj[key])) continue;
+      obj[key] = newObj[key];
     }
-  }
-  for (const foreignKey of Obj7.getMeta(newObj).keys) {
-    Obj7.deleteKeys(existing, foreignKey.source);
-    Obj7.getMeta(existing).keys.push({
-      ...foreignKey
-    });
-  }
+    for (const key of Object.keys(obj)) {
+      if (typeof key !== "string" || key === "id") continue;
+      if (!(key in newObj)) {
+        delete obj[key];
+      }
+    }
+    for (const foreignKey of Obj9.getMeta(newObj).keys) {
+      Obj9.deleteKeys(obj, foreignKey.source);
+      Obj9.getMeta(obj).keys.push({
+        ...foreignKey
+      });
+    }
+  });
 };
 
 // src/util/graphql.ts
@@ -1819,7 +1857,7 @@ query Issues($teamId: String!, $after: DateTimeOrDuration!) {
             updatedAt
             description
             assignee { id, name }
-            state { 
+            state {
                 name
             }
             project {
@@ -1850,15 +1888,16 @@ var sync_issues_default = defineFunction10({
     })
   }),
   handler: Effect13.fnUntraced(function* ({ data }) {
-    const client = yield* HttpClient.HttpClient.pipe(Effect13.map(withAuthorization({
+    const credential = yield* CredentialsService3.getCredential({
       service: "linear.app"
-    })));
-    const after = yield* getLatestUpdateTimestamp(data.team, DataType6.Task);
+    });
+    const client = yield* HttpClient.HttpClient.pipe(Effect13.map(withAuthorization(credential.apiKey)));
+    const after = yield* getLatestUpdateTimestamp(data.team, Task2.Task);
     log7.info("will fetch", {
       after
     }, {
       F: __dxlog_file7,
-      L: 91,
+      L: 93,
       S: this,
       C: (f, a) => f(...a)
     });
@@ -1876,7 +1915,7 @@ var sync_issues_default = defineFunction10({
       count: tasks.length
     }, {
       F: __dxlog_file7,
-      L: 104,
+      L: 106,
       S: this,
       C: (f, a) => f(...a)
     });
@@ -1889,16 +1928,16 @@ var sync_issues_default = defineFunction10({
   }, Effect13.provide(FetchHttpClient2.layer))
 });
 var getLatestUpdateTimestamp = Effect13.fnUntraced(function* (teamId, dataType) {
-  const { objects: existingTasks } = yield* DatabaseService10.runQuery(Query4.type(dataType).select(Filter4.foreignKeys(dataType, [
+  const existingTasks = yield* Database10.Service.runQuery(Query4.type(dataType).select(Filter4.foreignKeys(dataType, [
     {
       source: LINEAR_TEAM_ID_KEY,
       id: teamId
     }
   ])));
-  return Function4.pipe(existingTasks, Array9.map((task) => Obj8.getKeys(task, LINEAR_UPDATED_AT_KEY).at(0)?.id), Array9.filter((x) => x !== void 0), Array9.reduce("2025-01-01T00:00:00.000Z", (acc, x) => x > acc ? x : acc));
+  return Function5.pipe(existingTasks, Array9.map((task) => Obj10.getKeys(task, LINEAR_UPDATED_AT_KEY).at(0)?.id), Array9.filter((x) => x !== void 0), Array9.reduce("2025-01-01T00:00:00.000Z", (acc, x) => x > acc ? x : acc));
 });
-var mapLinearPerson = (person, { teamId }) => Obj8.make(DataType6.Person, {
-  [Obj8.Meta]: {
+var mapLinearPerson = (person, { teamId }) => Obj10.make(Person3.Person, {
+  [Obj10.Meta]: {
     keys: [
       {
         id: person.id,
@@ -1912,8 +1951,8 @@ var mapLinearPerson = (person, { teamId }) => Obj8.make(DataType6.Person, {
   },
   nickname: person.name
 });
-var mapLinearIssue = (issue, { teamId }) => Obj8.make(DataType6.Task, {
-  [Obj8.Meta]: {
+var mapLinearIssue = (issue, { teamId }) => Obj10.make(Task2.Task, {
+  [Obj10.Meta]: {
     keys: [
       {
         id: issue.id,
@@ -1936,8 +1975,8 @@ var mapLinearIssue = (issue, { teamId }) => Obj8.make(DataType6.Task, {
   })),
   // TODO(dmaretskyi): Sync those (+ linear team as org?).
   // state: issue.state.name,
-  project: !issue.project ? void 0 : Ref5.make(DataType6.makeProject({
-    [Obj8.Meta]: {
+  project: !issue.project ? void 0 : Ref5.make(Project2.make({
+    [Obj10.Meta]: {
       keys: [
         {
           id: issue.project.id,
@@ -1962,15 +2001,16 @@ var Linear;
 // src/functions/tasks/read.ts
 import * as Effect14 from "effect/Effect";
 import * as Schema13 from "effect/Schema";
-import { ArtifactId as ArtifactId3 } from "@dxos/assistant";
-import { DatabaseService as DatabaseService11, defineFunction as defineFunction11 } from "@dxos/functions";
+import { ArtifactId as ArtifactId4 } from "@dxos/assistant";
+import { Database as Database11 } from "@dxos/echo";
+import { defineFunction as defineFunction11 } from "@dxos/functions";
 import { Markdown as Markdown4 } from "@dxos/plugin-markdown/types";
 var read_default2 = defineFunction11({
   key: "dxos.org/function/markdown/read-tasks",
   name: "Read",
   description: "Read markdown tasks.",
   inputSchema: Schema13.Struct({
-    id: ArtifactId3.annotations({
+    id: ArtifactId4.annotations({
       description: "The ID of the document to read."
     })
   }),
@@ -1978,8 +2018,8 @@ var read_default2 = defineFunction11({
     content: Schema13.String
   }),
   handler: Effect14.fn(function* ({ data: { id } }) {
-    const doc = yield* DatabaseService11.resolve(ArtifactId3.toDXN(id), Markdown4.Document);
-    const { content } = yield* DatabaseService11.load(doc.content);
+    const doc = yield* Database11.Service.resolve(ArtifactId4.toDXN(id), Markdown4.Document);
+    const { content } = yield* Database11.Service.load(doc.content);
     const lines = content.split("\n");
     const len = String(lines.length).length;
     const numbered = lines.map((line, i) => `${String(i + 1).padStart(len, " ")}. ${line}`).join("\n");
@@ -1992,8 +2032,9 @@ var read_default2 = defineFunction11({
 // src/functions/tasks/update.ts
 import * as Effect15 from "effect/Effect";
 import * as Schema14 from "effect/Schema";
-import { ArtifactId as ArtifactId4 } from "@dxos/assistant";
-import { DatabaseService as DatabaseService12, defineFunction as defineFunction12 } from "@dxos/functions";
+import { ArtifactId as ArtifactId5 } from "@dxos/assistant";
+import { Database as Database12 } from "@dxos/echo";
+import { defineFunction as defineFunction12 } from "@dxos/functions";
 import { Markdown as Markdown5 } from "@dxos/plugin-markdown/types";
 
 // src/functions/tasks/task-list.ts
@@ -2130,7 +2171,7 @@ var update_default2 = defineFunction12({
   name: "Update markdown",
   description: "Creates and updates tasks in markdown documents.",
   inputSchema: Schema14.Struct({
-    id: ArtifactId4.annotations({
+    id: ArtifactId5.annotations({
       description: "The ID of the document to update."
     }),
     operations: Schema14.optional(Schema14.Array(Schema14.Any.annotations({
@@ -2144,8 +2185,8 @@ var update_default2 = defineFunction12({
     })
   }),
   handler: Effect15.fn(function* ({ data: { id, operations = [] } }) {
-    const doc = yield* DatabaseService12.resolve(ArtifactId4.toDXN(id), Markdown5.Document);
-    const { content } = yield* DatabaseService12.load(doc.content);
+    const doc = yield* Database12.Service.resolve(ArtifactId5.toDXN(id), Markdown5.Document);
+    const { content } = yield* Database12.Service.load(doc.content);
     const taskManager = new MarkdownTasks(content);
     if (operations.length > 0) {
       taskManager.applyOperations(operations);
@@ -2174,28 +2215,27 @@ var instructions = trim5`
   When replying to the user, be terse with your comments about design doc handling.
   Do not announce when you read or write the design spec document.
 `;
-var blueprint = Obj9.make(Blueprint.Blueprint, {
+var blueprint = Blueprint.make({
   key: "dxos.org/blueprint/design",
   name: "Design Spec",
   description: "Preserve the conversation in the design spec.",
   instructions: {
-    source: Ref6.make(DataType7.makeText(instructions))
+    source: Ref6.make(Text2.make(instructions))
   },
   tools: [
     Document.read,
     Document.update
   ].map((fn9) => ToolId.make(fn9.key))
 });
-var design_blueprint_default = blueprint;
 
 // src/blueprints/design/index.ts
-var design_default = design_blueprint_default;
+var design_default = blueprint;
 
 // src/blueprints/discord/discord-blueprint.ts
 import { ToolId as ToolId2 } from "@dxos/ai";
 import { Blueprint as Blueprint2 } from "@dxos/blueprints";
-import { Obj as Obj10, Ref as Ref7 } from "@dxos/echo";
-import { DataType as DataType8 } from "@dxos/schema";
+import { Ref as Ref7 } from "@dxos/echo";
+import { Text as Text3 } from "@dxos/schema";
 import { trim as trim6 } from "@dxos/util";
 var instructions2 = trim6`
   You are able to fetch messages from Discord servers.
@@ -2204,27 +2244,26 @@ var instructions2 = trim6`
 
   DXOS serverId: 837138313172353095
 `;
-var blueprint2 = Obj10.make(Blueprint2.Blueprint, {
+var blueprint2 = Blueprint2.make({
   key: "dxos.org/blueprint/discord",
   name: "Discord",
   description: "Discord integration.",
   instructions: {
-    source: Ref7.make(DataType8.makeText(instructions2))
+    source: Ref7.make(Text3.make(instructions2))
   },
   tools: [
     ToolId2.make(Discord.fetch.key)
   ]
 });
-var discord_blueprint_default = blueprint2;
 
 // src/blueprints/discord/index.ts
-var discord_default = discord_blueprint_default;
+var discord_default = blueprint2;
 
 // src/blueprints/linear/linear-blueprint.ts
 import { ToolId as ToolId3 } from "@dxos/ai";
 import { Blueprint as Blueprint3 } from "@dxos/blueprints";
-import { Obj as Obj11, Ref as Ref8 } from "@dxos/echo";
-import { DataType as DataType9 } from "@dxos/schema";
+import { Ref as Ref8 } from "@dxos/echo";
+import { Text as Text4 } from "@dxos/schema";
 import { trim as trim7 } from "@dxos/util";
 var instructions3 = trim7`
   You are able to sync Linear workspaces.
@@ -2234,27 +2273,26 @@ var instructions3 = trim7`
 
   DXOS teamId: 1127c63a-6f77-4725-9229-50f6cd47321c
 `;
-var blueprint3 = Obj11.make(Blueprint3.Blueprint, {
+var blueprint3 = Blueprint3.make({
   key: "dxos.org/blueprint/linear",
   name: "Linear",
   description: "Syncs Linear workspaces.",
   instructions: {
-    source: Ref8.make(DataType9.makeText(instructions3))
+    source: Ref8.make(Text4.make(instructions3))
   },
   tools: [
     Linear.sync
   ].map((tool) => ToolId3.make(tool.key))
 });
-var linear_blueprint_default = blueprint3;
 
 // src/blueprints/linear/index.ts
-var linear_default = linear_blueprint_default;
+var linear_default = blueprint3;
 
 // src/blueprints/planning/planning-blueprint.ts
 import { ToolId as ToolId4 } from "@dxos/ai";
 import { Blueprint as Blueprint4 } from "@dxos/blueprints";
-import { Obj as Obj12, Ref as Ref9 } from "@dxos/echo";
-import { DataType as DataType10 } from "@dxos/schema";
+import { Ref as Ref9 } from "@dxos/echo";
+import { Text as Text5 } from "@dxos/schema";
 import { trim as trim8 } from "@dxos/util";
 var instructions4 = trim8`
   You are a task management agent that maintains hierarchical task lists where each line is a task.
@@ -2327,81 +2365,86 @@ var instructions4 = trim8`
   - When creating subtasks, consider the parent task's completion status
   - Be precise with task descriptions and hierarchy levels
 `;
-var blueprint4 = Obj12.make(Blueprint4.Blueprint, {
+var blueprint4 = Blueprint4.make({
   key: "dxos.org/blueprint/planning",
   name: "Planning",
   description: "Plans and tracks complex tasks with artifact management.",
   instructions: {
-    source: Ref9.make(DataType10.makeText(instructions4))
+    source: Ref9.make(Text5.make(instructions4))
   },
   tools: [
     Tasks.read,
     Tasks.update
   ].map((fn9) => ToolId4.make(fn9.key))
 });
-var planning_blueprint_default = blueprint4;
 
 // src/blueprints/planning/index.ts
-var planning_default = planning_blueprint_default;
+var planning_default = blueprint4;
 
 // src/blueprints/research/research-blueprint.ts
 import { ToolId as ToolId5 } from "@dxos/ai";
 import { Blueprint as Blueprint5 } from "@dxos/blueprints";
-import { Obj as Obj13, Ref as Ref10 } from "@dxos/echo";
-import { DataType as DataType11 } from "@dxos/schema";
+import { Ref as Ref10 } from "@dxos/echo";
+import { Text as Text6 } from "@dxos/schema";
 import { trim as trim9 } from "@dxos/util";
 var instructions5 = trim9`
   {{! Research }}
 
   You are an analyst that does research tasks using tools that scrape the web and create structured data.
-  The result of the research is a set of structured entities forming an interconnected graph.
-  When you are done, reply with the created objects.
-  Do not print the data, instead reply with inline references to the created objects.
-  Those will be later substituted with the pills representing the created objects.
-  Print the rest of the created objects as block references after the main note.
-
-  <example>
-    Based on my research, Google was founded by @dxn:queue:data:B6INSIBY3CBEF4M5VZRYBCMAHQMPYK5AJ:01K24XMVHSZHS97SG1VTVQDM5Z:01K24XPK464FSCKVQJAB2H662M and @dxn:queue:data:B6INSIBY3CBEF4M5VZRYBCMAHQMPYK5AJ:01K24XMVHSZHS97SG1VTVQDM5Z:01K24XPK46K31DDW62PBW9H2ZQ
-
-    <object><dxn>dxn:queue:data:B6INSIBY3CBEF4M5VZRYBCMAHQMPYK5AJ:01K24XMVHSZHS97SG1VTVQDM5Z:01K24XPK464FSCKVQJAB2H662M</dxn></object>
-    <object><dxn>dxn:queue:data:B6INSIBY3CBEF4M5VZRYBCMAHQMPYK5AJ:01K24XMVHSZHS97SG1VTVQDM5Z:01K24XPK46K31DDW62PBW9H2ZQ</dxn></object>
-    <object><dxn>dxn:queue:data:B6INSIBY3CBEF4M5VZRYBCMAHQMPYK5AJ:01K24XMVHSZHS97SG1VTVQDM5Z:01K24XPK46K31DDW62PBW92333</dxn></object>
-  </example>
+  Structured data extraction is an experimental feature -- only enable it if the user explicitly requests it in the prompt.
+  Prefer updating existing notes instead of creating new ones.
+
+  <strcutured_mode>
+    When you are done, reply with the created objects.
+    Do not print the data, instead reply with inline references to the created objects.
+    Those will be later substituted with the pills representing the created objects.
+    Print the rest of the created objects as block references after the main note.
+
+    <example>
+      Based on my research, Google was founded by @dxn:queue:data:B6INSIBY3CBEF4M5VZRYBCMAHQMPYK5AJ:01K24XMVHSZHS97SG1VTVQDM5Z:01K24XPK464FSCKVQJAB2H662M and @dxn:queue:data:B6INSIBY3CBEF4M5VZRYBCMAHQMPYK5AJ:01K24XMVHSZHS97SG1VTVQDM5Z:01K24XPK46K31DDW62PBW9H2ZQ
+
+      <object><dxn>dxn:queue:data:B6INSIBY3CBEF4M5VZRYBCMAHQMPYK5AJ:01K24XMVHSZHS97SG1VTVQDM5Z:01K24XPK464FSCKVQJAB2H662M</dxn></object>
+      <object><dxn>dxn:queue:data:B6INSIBY3CBEF4M5VZRYBCMAHQMPYK5AJ:01K24XMVHSZHS97SG1VTVQDM5Z:01K24XPK46K31DDW62PBW9H2ZQ</dxn></object>
+      <object><dxn>dxn:queue:data:B6INSIBY3CBEF4M5VZRYBCMAHQMPYK5AJ:01K24XMVHSZHS97SG1VTVQDM5Z:01K24XPK46K31DDW62PBW92333</dxn></object>
+    </example>
+  </structured_mode>
+
+  <unstructured_mode>
+    Reply normally with the text mode of the result of your research.
+  </unstructured_mode>
 `;
-var blueprint5 = Obj13.make(Blueprint5.Blueprint, {
+var blueprint5 = Blueprint5.make({
   key: "dxos.org/blueprint/research",
   name: "Research",
   description: "Researches the web and creates structured data.",
   instructions: {
-    source: Ref10.make(DataType11.makeText(instructions5))
+    source: Ref10.make(Text6.make(instructions5))
   },
   tools: [
     Research.create,
     Research.research
   ].map((fn9) => ToolId5.make(fn9.key))
 });
-var research_blueprint_default = blueprint5;
 
 // src/blueprints/research/index.ts
-var research_default2 = research_blueprint_default;
+var research_default2 = blueprint5;
 
 // src/blueprints/websearch/websearch-blueprint.ts
 import { ToolId as ToolId6 } from "@dxos/ai";
 import { Blueprint as Blueprint6 } from "@dxos/blueprints";
-import { Obj as Obj14, Ref as Ref11 } from "@dxos/echo";
-import { DataType as DataType12 } from "@dxos/schema";
-var blueprint6 = Obj14.make(Blueprint6.Blueprint, {
+import { Ref as Ref11 } from "@dxos/echo";
+import { Text as Text7 } from "@dxos/schema";
+var blueprint6 = Blueprint6.make({
   key: "dxos.org/blueprint/web-search",
   name: "Web Search",
   description: "Search the web.",
   instructions: {
-    source: Ref11.make(DataType12.makeText(""))
+    source: Ref11.make(Text7.make())
   },
   tools: [
     ToolId6.make("AnthropicWebSearch")
   ]
 });
-var websearch_blueprint_default = blueprint6;
 
 // src/blueprints/websearch/websearch-toolkit.ts
 import * as Toolkit4 from "@effect/ai/Toolkit";
@@ -2409,46 +2452,402 @@ import * as AnthropicTool2 from "@effect/ai-anthropic/AnthropicTool";
 var WebSearchToolkit = Toolkit4.make(AnthropicTool2.WebSearch_20250305({}));
 
 // src/blueprints/websearch/index.ts
-var websearch_default = websearch_blueprint_default;
-
-// src/plugins.tsx
+var websearch_default = blueprint6;
+
+// src/toolkits/AssistantToolkit.ts
+var AssistantToolkit_exports = {};
+__export(AssistantToolkit_exports, {
+  AssistantToolkit: () => AssistantToolkit,
+  layer: () => layer3,
+  tools: () => tools
+});
+import * as Tool2 from "@effect/ai/Tool";
+import * as Toolkit5 from "@effect/ai/Toolkit";
+import * as Effect16 from "effect/Effect";
+import * as Record from "effect/Record";
 import * as Schema15 from "effect/Schema";
-import React from "react";
-import { Capabilities, contributes, createSurface } from "@dxos/app-framework";
-import { Type as Type3 } from "@dxos/echo";
-import { JsonFilter } from "@dxos/react-ui-syntax-highlighter";
-var MapSchema = Schema15.Struct({
-  coordinates: Type3.Format.GeoPoint
-}).pipe(Type3.Obj({
-  typename: "example.com/type/Map",
-  version: "0.1.0"
-}));
-var isImage = (data) => false;
-var capabilities = [
-  contributes(Capabilities.ReactSurface, createSurface({
-    id: "plugin-image",
-    role: "card--extrinsic",
-    filter: (data) => isImage(data.value),
-    component: ({ data }) => /* @__PURE__ */ React.createElement("img", {
-      className: "grow object-cover",
-      src: `data:image/jpeg;base64,${data.value.source.data}`,
-      alt: data.value.prompt ?? `Generated image [id=${data.value.id}]`
+import { AiContextService, ArtifactId as ArtifactId6 } from "@dxos/assistant";
+import { Database as Database13 } from "@dxos/echo";
+import { trim as trim10 } from "@dxos/util";
+var AssistantToolkit = Toolkit5.make(Tool2.make("context-add", {
+  description: trim10`
+      Adds the object to the chat context.
+    `,
+  parameters: {
+    id: ArtifactId6.annotations({
+      description: "The ID of the document to add."
     })
-  })),
+  },
+  success: Schema15.Void,
+  failure: Schema15.Never,
+  dependencies: [
+    AiContextService,
+    Database13.Service
+  ]
+}), Tool2.make("context-remove", {
+  description: trim10`
+      Removes the object from the chat context.
+    `,
+  parameters: {
+    id: ArtifactId6.annotations({
+      description: "The ID of the document to remove."
+    })
+  },
+  success: Schema15.Void,
+  failure: Schema15.Never,
+  dependencies: [
+    AiContextService,
+    Database13.Service
+  ]
+}));
+var tools = Record.keys(AssistantToolkit.tools);
+var layer3 = () => AssistantToolkit.toLayer({
+  ["context-add"]: Effect16.fnUntraced(function* ({ id }) {
+    const { binder } = yield* AiContextService;
+    const { db } = yield* Database13.Service;
+    const ref = db.makeRef(ArtifactId6.toDXN(id, db.spaceId));
+    yield* Effect16.promise(() => binder.bind({
+      blueprints: [],
+      objects: [
+        ref
+      ]
+    }));
+  }),
+  ["context-remove"]: Effect16.fnUntraced(function* ({ id }) {
+    const { binder } = yield* AiContextService;
+    const { db } = yield* Database13.Service;
+    const ref = db.makeRef(ArtifactId6.toDXN(id, db.spaceId));
+    yield* Effect16.promise(() => binder.unbind({
+      blueprints: [],
+      objects: [
+        ref
+      ]
+    }));
+  })
+});
+
+// src/toolkits/SystemToolkit.ts
+var SystemToolkit_exports = {};
+__export(SystemToolkit_exports, {
+  SystemToolkit: () => SystemToolkit,
+  layer: () => layer4,
+  tools: () => tools2
+});
+import * as Tool3 from "@effect/ai/Tool";
+import * as Toolkit6 from "@effect/ai/Toolkit";
+import * as Effect17 from "effect/Effect";
+import * as Record2 from "effect/Record";
+import * as Schema16 from "effect/Schema";
+import { ArtifactId as ArtifactId7 } from "@dxos/assistant";
+import { DXN as DXN2, Database as Database14, Entity as Entity3, Filter as Filter5, Obj as Obj11, Relation as Relation2, Tag as Tag2, Type as Type5 } from "@dxos/echo";
+import { invariant } from "@dxos/invariant";
+import { trim as trim11 } from "@dxos/util";
+var __dxlog_file8 = "/__w/dxos/dxos/packages/core/assistant-toolkit/src/toolkits/SystemToolkit.ts";
+var SystemToolkit = Toolkit6.make(
   //
-  // Default
+  // Schema
   //
-  contributes(Capabilities.ReactSurface, createSurface({
-    id: "plugin-default",
-    role: "card--extrinsic",
-    position: "fallback",
-    component: ({ role, data }) => /* @__PURE__ */ React.createElement(JsonFilter, {
-      data
-    })
-  }))
-];
+  Tool3.make("schema-list", {
+    description: trim11`
+      Lists schemas definitions.
+    `,
+    parameters: {
+      // TODO(wittjosiah): Remove this once parameter-less tools are fixed.
+      limit: Schema16.Number
+    },
+    // TODO(dmaretskyi): Effect returns ({ result, encodedResult })
+    success: Schema16.Any,
+    failure: Schema16.Never,
+    dependencies: [
+      Database14.Service
+    ]
+  }),
+  Tool3.make("schema-add", {
+    description: trim11`
+      Adds a schema to the space.
+      The name will be used when displayed to the user.
+      The typename must be in the format of "example.com/type/Type".
+    `,
+    parameters: {
+      name: Schema16.String,
+      typename: Schema16.String,
+      jsonSchema: Schema16.Any
+    },
+    success: Schema16.Any,
+    failure: Schema16.Never,
+    dependencies: [
+      Database14.Service
+    ]
+  }),
+  //
+  // Query
+  //
+  Tool3.make("query", {
+    description: trim11`
+      Queries objects in the space.
+      Get the typename from the schema-list tool.
+    `,
+    parameters: {
+      typename: Schema16.String
+    },
+    success: Schema16.Any,
+    failure: Schema16.Never,
+    dependencies: [
+      Database14.Service
+    ]
+  }),
+  //
+  // Objects
+  //
+  Tool3.make("object-create", {
+    description: trim11`
+      Creates a new object and adds it to the current space.
+      Get the schema from the schema-list tool and ensure that the data matches the corresponding schema.
+    `,
+    parameters: {
+      typename: Schema16.String,
+      data: Schema16.Any
+    },
+    success: Schema16.Any,
+    failure: Schema16.Never,
+    dependencies: [
+      Database14.Service
+    ]
+  }),
+  Tool3.make("object-delete", {
+    description: trim11`
+      Deletes the object.
+    `,
+    parameters: {
+      id: ArtifactId7.annotations({
+        description: "The ID of the object."
+      })
+    },
+    success: Schema16.Any,
+    failure: Schema16.Never,
+    dependencies: [
+      Database14.Service
+    ]
+  }),
+  Tool3.make("object-update", {
+    description: trim11`
+      Updates the object properties.
+    `,
+    parameters: {
+      id: ArtifactId7.annotations({
+        description: "The ID of the object."
+      }),
+      properties: Schema16.Record({
+        key: Schema16.String,
+        value: Schema16.Any
+      })
+    },
+    success: Schema16.Any,
+    failure: Schema16.Never,
+    dependencies: [
+      Database14.Service
+    ]
+  }),
+  //
+  // Relations
+  //
+  Tool3.make("relation-create", {
+    description: trim11`
+      Creates a new relation and adds it to the current space.
+      Get the schema from the schema-list tool and ensure that the data matches the corresponding schema.
+    `,
+    parameters: {
+      typename: Schema16.String,
+      source: ArtifactId7.annotations({
+        description: "The ID of the source object."
+      }),
+      target: ArtifactId7.annotations({
+        description: "The ID of the target object."
+      }),
+      data: Schema16.Any.annotations({
+        description: "The data to be stored in the relation."
+      })
+    },
+    success: Schema16.Any,
+    failure: Schema16.Never,
+    dependencies: [
+      Database14.Service
+    ]
+  }),
+  Tool3.make("relation-delete", {
+    description: trim11`
+      Deletes the relation.
+    `,
+    parameters: {
+      id: ArtifactId7.annotations({
+        description: "The ID of the relation."
+      })
+    },
+    success: Schema16.Any,
+    failure: Schema16.Never,
+    dependencies: [
+      Database14.Service
+    ]
+  }),
+  //
+  // Tags
+  //
+  Tool3.make("tag-add", {
+    description: trim11`
+      Adds a tag to an object.
+      Tags are objects of type ${Tag2.Tag.typename}.
+    `,
+    parameters: {
+      tagId: ArtifactId7.annotations({
+        description: "The ID of the tag."
+      }),
+      objectId: ArtifactId7.annotations({
+        description: "The ID of the object."
+      })
+    },
+    success: Schema16.Any,
+    failure: Schema16.Never,
+    dependencies: [
+      Database14.Service
+    ]
+  }),
+  Tool3.make("tag-remove", {
+    description: trim11`
+      Removes a tag from an object.
+      Tags are objects of type ${Tag2.Tag.typename}.
+    `,
+    parameters: {
+      tagId: ArtifactId7.annotations({
+        description: "The ID of the tag."
+      }),
+      objectId: ArtifactId7.annotations({
+        description: "The ID of the object."
+      })
+    },
+    success: Schema16.Any,
+    failure: Schema16.Never,
+    dependencies: [
+      Database14.Service
+    ]
+  })
+);
+var tools2 = Record2.keys(SystemToolkit.tools);
+var layer4 = () => SystemToolkit.toLayer({
+  ["schema-list"]: Effect17.fnUntraced(function* () {
+    const { db } = yield* Database14.Service;
+    const schema = yield* Effect17.promise(() => db.schemaRegistry.query({
+      location: [
+        "database",
+        "runtime"
+      ]
+    }).run());
+    return schema.map((schema2) => {
+      const meta = Type5.getMeta(schema2);
+      return {
+        typename: Type5.getTypename(schema2),
+        jsonSchema: Type5.toJsonSchema(schema2),
+        kind: meta?.sourceSchema ? "relation" : "record"
+      };
+    });
+  }),
+  ["schema-add"]: Effect17.fnUntraced(function* ({ name, typename, jsonSchema }) {
+    const { db } = yield* Database14.Service;
+    yield* Effect17.promise(() => db.schemaRegistry.register([
+      {
+        typename,
+        version: "0.1.0",
+        jsonSchema,
+        name
+      }
+    ]));
+  }),
+  ["query"]: Effect17.fnUntraced(function* ({ typename }) {
+    const objects = yield* Database14.Service.runQuery(Filter5.typename(typename));
+    return objects;
+  }),
+  ["object-create"]: Effect17.fnUntraced(function* ({ typename, data }) {
+    const { db } = yield* Database14.Service;
+    const schema = yield* Effect17.promise(() => db.schemaRegistry.query({
+      typename,
+      location: [
+        "database",
+        "runtime"
+      ]
+    }).first());
+    invariant(Type5.isObjectSchema(schema), "Schema is not an object schema", {
+      F: __dxlog_file8,
+      L: 238,
+      S: this,
+      A: [
+        "Type.isObjectSchema(schema)",
+        "'Schema is not an object schema'"
+      ]
+    });
+    const object = db.add(Obj11.make(schema, data));
+    return object;
+  }),
+  ["object-delete"]: Effect17.fnUntraced(function* ({ id }) {
+    const { db } = yield* Database14.Service;
+    const object = yield* Database14.Service.resolve(DXN2.parse(id));
+    db.remove(object);
+    return object;
+  }),
+  ["object-update"]: Effect17.fnUntraced(function* ({ id, properties }) {
+    const object = yield* Database14.Service.resolve(DXN2.parse(id));
+    Entity3.change(object, (obj) => {
+      for (const [key, value2] of Object.entries(properties)) {
+        obj[key] = value2;
+      }
+    });
+    return object;
+  }),
+  ["relation-create"]: Effect17.fnUntraced(function* ({ typename, source, target, data }) {
+    const { db } = yield* Database14.Service;
+    const schema = yield* Effect17.promise(() => db.schemaRegistry.query({
+      typename,
+      location: [
+        "database",
+        "runtime"
+      ]
+    }).first());
+    invariant(Type5.isRelationSchema(schema), "Schema is not a relation schema", {
+      F: __dxlog_file8,
+      L: 267,
+      S: this,
+      A: [
+        "Type.isRelationSchema(schema)",
+        "'Schema is not a relation schema'"
+      ]
+    });
+    const sourceObj = yield* Database14.Service.resolve(DXN2.parse(source));
+    const targetObj = yield* Database14.Service.resolve(DXN2.parse(target));
+    const relation = db.add(Relation2.make(schema, {
+      [Relation2.Source]: sourceObj,
+      [Relation2.Target]: targetObj,
+      ...data
+    }));
+    return relation;
+  }),
+  ["relation-delete"]: Effect17.fnUntraced(function* ({ id }) {
+    const { db } = yield* Database14.Service;
+    const relation = yield* Database14.Service.resolve(DXN2.parse(id));
+    db.remove(relation);
+    return relation;
+  }),
+  ["tag-add"]: Effect17.fnUntraced(function* ({ tagId, objectId }) {
+    const object = yield* Database14.Service.resolve(DXN2.parse(objectId));
+    Entity3.change(object, (obj) => Entity3.addTag(obj, DXN2.parse(tagId).toString()));
+    return object;
+  }),
+  ["tag-remove"]: Effect17.fnUntraced(function* ({ tagId, objectId }) {
+    const object = yield* Database14.Service.resolve(DXN2.parse(objectId));
+    Entity3.change(object, (obj) => Entity3.removeTag(obj, DXN2.parse(tagId).toString()));
+    return object;
+  })
+});
 export {
   Agent,
+  AssistantToolkit_exports as AssistantToolkit,
   design_default as DesignBlueprint,
   Discord,
   discord_default as DiscordBlueprint,
@@ -2458,17 +2857,16 @@ export {
   linear_default as LinearBlueprint,
   LocalSearchHandler,
   LocalSearchToolkit,
-  MapSchema,
   planning_default as PlanningBlueprint,
   Research,
   research_default2 as ResearchBlueprint,
   ResearchDataTypes,
   ResearchGraph,
   Subgraph,
+  SystemToolkit_exports as SystemToolkit,
   Tasks,
   websearch_default as WebSearchBlueprint,
   WebSearchToolkit,
-  capabilities,
   contextQueueLayerFromResearchGraph,
   createExtractionSchema,
   createResearchGraph,