@semiont/backend 0.4.3 → 0.4.5

package/dist/index.js

@@ -2,7 +2,7 @@
 import winston from 'winston';
 import { z } from 'zod';
 import jwt from 'jsonwebtoken';
-import { email, userId, accessToken, googleCredential, annotationId, resourceId, EventBus, jobId, entityType, assembleAnnotation, userToAgent } from '@semiont/core';
+import { email, userId, accessToken, googleCredential, annotationId, resourceId, userToDid, EventBus, jobId, entityType, assembleAnnotation, userToAgent } from '@semiont/core';
 import { cors } from 'hono/cors';
 import { serve } from '@hono/node-server';
 import { Hono } from 'hono';
@@ -11,6 +11,7 @@ import { SemiontProject, loadEnvironmentConfig } from '@semiont/core/node';
 import { exportBackup, importBackup, readEntityTypesProjection, exportLinkedData, importLinkedData, AnnotationContext, startMakeMeaning, ResourceContext, ResourceOperations } from '@semiont/make-meaning';
 import { PrismaClient } from '@prisma/client';
 import { PrismaPg } from '@prisma/adapter-pg';
+import { setCookie, deleteCookie, getCookie } from 'hono/cookie';
 import { HTTPException } from 'hono/http-exception';
 import Ajv from 'ajv';
 import addFormats from 'ajv-formats';
@@ -613,7 +614,7 @@ var require_timeoutProvider = __commonJS({
     });
     exports$1.timeoutProvider = void 0;
     exports$1.timeoutProvider = {
-      setTimeout: /* @__PURE__ */ __name(function(handler, timeout4) {
+      setTimeout: /* @__PURE__ */ __name(function(handler, timeout2) {
         var args = [];
         for (var _i = 2; _i < arguments.length; _i++) {
           args[_i - 2] = arguments[_i];
@@ -622,12 +623,12 @@ var require_timeoutProvider = __commonJS({
         if (delegate === null || delegate === void 0 ? void 0 : delegate.setTimeout) {
           return delegate.setTimeout.apply(delegate, __spreadArray([
             handler,
-            timeout4
+            timeout2
           ], __read(args)));
         }
         return setTimeout.apply(void 0, __spreadArray([
           handler,
-          timeout4
+          timeout2
         ], __read(args)));
       }, "setTimeout"),
       clearTimeout: /* @__PURE__ */ __name(function(handle) {
@@ -2061,7 +2062,7 @@ var require_intervalProvider = __commonJS({
     });
     exports$1.intervalProvider = void 0;
     exports$1.intervalProvider = {
-      setInterval: /* @__PURE__ */ __name(function(handler, timeout4) {
+      setInterval: /* @__PURE__ */ __name(function(handler, timeout2) {
         var args = [];
         for (var _i = 2; _i < arguments.length; _i++) {
           args[_i - 2] = arguments[_i];
@@ -2070,12 +2071,12 @@ var require_intervalProvider = __commonJS({
         if (delegate === null || delegate === void 0 ? void 0 : delegate.setInterval) {
           return delegate.setInterval.apply(delegate, __spreadArray([
             handler,
-            timeout4
+            timeout2
           ], __read(args)));
         }
         return setInterval.apply(void 0, __spreadArray([
           handler,
-          timeout4
+          timeout2
         ], __read(args)));
       }, "setInterval"),
       clearInterval: /* @__PURE__ */ __name(function(handle) {
@@ -4283,7 +4284,7 @@ var require_firstValueFrom = __commonJS({
     exports$1.firstValueFrom = void 0;
     var EmptyError_1 = require_EmptyError();
     var Subscriber_1 = require_Subscriber();
-    function firstValueFrom4(source, config2) {
+    function firstValueFrom2(source, config2) {
       var hasConfig = typeof config2 === "object";
       return new Promise(function(resolve, reject) {
         var subscriber = new Subscriber_1.SafeSubscriber({
@@ -4303,8 +4304,8 @@ var require_firstValueFrom = __commonJS({
         source.subscribe(subscriber);
       });
     }
-    __name(firstValueFrom4, "firstValueFrom");
-    exports$1.firstValueFrom = firstValueFrom4;
+    __name(firstValueFrom2, "firstValueFrom");
+    exports$1.firstValueFrom = firstValueFrom2;
   }
 });
 
@@ -4402,7 +4403,7 @@ var require_timeout = __commonJS({
         this.info = info;
       }, "TimeoutErrorImpl");
     });
-    function timeout4(config2, schedulerArg) {
+    function timeout2(config2, schedulerArg) {
       var _a = isDate_1.isValidDate(config2) ? {
         first: config2
       } : typeof config2 === "number" ? {
@@ -4444,8 +4445,8 @@ var require_timeout = __commonJS({
         !seen && startTimer(first != null ? typeof first === "number" ? first : +first - scheduler.now() : each);
       });
     }
-    __name(timeout4, "timeout");
-    exports$1.timeout = timeout4;
+    __name(timeout2, "timeout");
+    exports$1.timeout = timeout2;
     function timeoutErrorFactory(info) {
       throw new exports$1.TimeoutError(info);
     }
@@ -4462,7 +4463,7 @@ var require_map = __commonJS({
     exports$1.map = void 0;
     var lift_1 = require_lift();
     var OperatorSubscriber_1 = require_OperatorSubscriber();
-    function map4(project, thisArg) {
+    function map2(project, thisArg) {
       return lift_1.operate(function(source, subscriber) {
         var index = 0;
         source.subscribe(OperatorSubscriber_1.createOperatorSubscriber(subscriber, function(value) {
@@ -4470,8 +4471,8 @@ var require_map = __commonJS({
         }));
       });
     }
-    __name(map4, "map");
-    exports$1.map = map4;
+    __name(map2, "map");
+    exports$1.map = map2;
   }
 });
 
@@ -5501,7 +5502,7 @@ var require_merge = __commonJS({
     var empty_1 = require_empty();
     var args_1 = require_args();
     var from_1 = require_from();
-    function merge4() {
+    function merge2() {
       var args = [];
       for (var _i = 0; _i < arguments.length; _i++) {
         args[_i] = arguments[_i];
@@ -5511,8 +5512,8 @@ var require_merge = __commonJS({
       var sources = args;
       return !sources.length ? empty_1.EMPTY : sources.length === 1 ? innerFrom_1.innerFrom(sources[0]) : mergeAll_1.mergeAll(concurrent)(from_1.from(sources, scheduler));
     }
-    __name(merge4, "merge");
-    exports$1.merge = merge4;
+    __name(merge2, "merge");
+    exports$1.merge = merge2;
   }
 });
 
@@ -5636,7 +5637,7 @@ var require_filter = __commonJS({
     exports$1.filter = void 0;
     var lift_1 = require_lift();
     var OperatorSubscriber_1 = require_OperatorSubscriber();
-    function filter4(predicate, thisArg) {
+    function filter2(predicate, thisArg) {
       return lift_1.operate(function(source, subscriber) {
         var index = 0;
         source.subscribe(OperatorSubscriber_1.createOperatorSubscriber(subscriber, function(value) {
@@ -5644,8 +5645,8 @@ var require_filter = __commonJS({
         }));
       });
     }
-    __name(filter4, "filter");
-    exports$1.filter = filter4;
+    __name(filter2, "filter");
+    exports$1.filter = filter2;
   }
 });
 
@@ -6901,7 +6902,7 @@ var require_take = __commonJS({
     var empty_1 = require_empty();
     var lift_1 = require_lift();
     var OperatorSubscriber_1 = require_OperatorSubscriber();
-    function take4(count) {
+    function take2(count) {
       return count <= 0 ? function() {
         return empty_1.EMPTY;
       } : lift_1.operate(function(source, subscriber) {
@@ -6916,8 +6917,8 @@ var require_take = __commonJS({
         }));
       });
     }
-    __name(take4, "take");
-    exports$1.take = take4;
+    __name(take2, "take");
+    exports$1.take = take2;
   }
 });
 
@@ -7807,7 +7808,7 @@ var require_merge2 = __commonJS({
     var mergeAll_1 = require_mergeAll();
     var args_1 = require_args();
     var from_1 = require_from();
-    function merge4() {
+    function merge2() {
       var args = [];
       for (var _i = 0; _i < arguments.length; _i++) {
         args[_i] = arguments[_i];
@@ -7820,8 +7821,8 @@ var require_merge2 = __commonJS({
         ], __read(args)), scheduler)).subscribe(subscriber);
       });
     }
-    __name(merge4, "merge");
-    exports$1.merge = merge4;
+    __name(merge2, "merge");
+    exports$1.merge = merge2;
   }
 });
 
@@ -12760,6 +12761,127 @@ var openapi_default = {
           "isNewUser"
         ]
       },
+      BrowseFilesResponse: {
+        type: "object",
+        required: [
+          "path",
+          "entries"
+        ],
+        properties: {
+          path: {
+            type: "string",
+            description: "The directory path that was listed, relative to project root"
+          },
+          entries: {
+            type: "array",
+            items: {
+              $ref: "#/components/schemas/DirectoryEntry"
+            }
+          }
+        },
+        additionalProperties: false
+      },
+      DirectoryEntry: {
+        oneOf: [
+          {
+            $ref: "#/components/schemas/FileEntry"
+          },
+          {
+            $ref: "#/components/schemas/DirEntry"
+          }
+        ]
+      },
+      FileEntry: {
+        type: "object",
+        required: [
+          "type",
+          "name",
+          "path",
+          "size",
+          "mtime",
+          "tracked"
+        ],
+        properties: {
+          type: {
+            type: "string",
+            enum: [
+              "file"
+            ]
+          },
+          name: {
+            type: "string",
+            description: "Entry name (basename)"
+          },
+          path: {
+            type: "string",
+            description: "Path relative to project root"
+          },
+          size: {
+            type: "integer",
+            description: "File size in bytes"
+          },
+          mtime: {
+            type: "string",
+            format: "date-time",
+            description: "Last modified time (ISO 8601)"
+          },
+          tracked: {
+            type: "boolean",
+            description: "True if this file is a tracked resource in the Knowledge Base"
+          },
+          resourceId: {
+            type: "string",
+            description: "Resource ID (only when tracked is true)"
+          },
+          entityTypes: {
+            type: "array",
+            items: {
+              type: "string"
+            },
+            description: "Entity types assigned to this resource (only when tracked is true)"
+          },
+          annotationCount: {
+            type: "integer",
+            description: "Number of annotations on this resource (only when tracked is true)"
+          },
+          creator: {
+            type: "string",
+            description: "DID of the user who created the resource (only when tracked is true)"
+          }
+        },
+        additionalProperties: false
+      },
+      DirEntry: {
+        type: "object",
+        required: [
+          "type",
+          "name",
+          "path",
+          "mtime"
+        ],
+        properties: {
+          type: {
+            type: "string",
+            enum: [
+              "dir"
+            ]
+          },
+          name: {
+            type: "string",
+            description: "Entry name (basename)"
+          },
+          path: {
+            type: "string",
+            description: "Path relative to project root"
+          },
+          mtime: {
+            type: "string",
+            format: "date-time",
+            description: "Last modified time (ISO 8601)"
+          }
+        },
+        additionalProperties: false
+      },
       BodyOperationAdd: {
         type: "object",
         properties: {
@@ -13479,6 +13601,10 @@ var openapi_default = {
             minimum: 1,
             maximum: 10,
             description: "Optional density: desired number of assessments per 2000 words of text (1-10)"
+          },
+          language: {
+            type: "string",
+            description: 'BCP 47 language tag for the generated assessment text (e.g. "en", "fr", "de")'
           }
         }
       },
@@ -13504,6 +13630,10 @@ var openapi_default = {
             minimum: 2,
             maximum: 12,
             description: "Optional density: desired number of comments per 2000 words of text (2-12)"
+          },
+          language: {
+            type: "string",
+            description: "BCP 47 language tag for the generated comment text (e.g. 'en', 'fr', 'de')"
           }
         }
       },
@@ -14694,6 +14824,20 @@ var openapi_default = {
               }
             ]
           },
+          generator: {
+            description: "Software agent that produced or processed this resource (W3C Web Annotation model)",
+            oneOf: [
+              {
+                $ref: "#/components/schemas/Agent"
+              },
+              {
+                type: "array",
+                items: {
+                  $ref: "#/components/schemas/Agent"
+                }
+              }
+            ]
+          },
           conformsTo: {
             description: "Profile/shape URI this resource description conforms to.",
             oneOf: [
@@ -15219,6 +15363,10 @@ var openapi_default = {
           },
           created: {
             type: "string"
+          },
+          token: {
+            type: "string",
+            description: "The validated JWT token string for the current session"
           }
         },
         required: [
@@ -15232,7 +15380,8 @@ var openapi_default = {
           "isActive",
           "termsAcceptedAt",
           "lastLogin",
-          "created"
+          "created",
+          "token"
         ]
       },
       SvgSelector: {
@@ -15703,22 +15852,16 @@ var OAuthService = class {
 var authMiddleware = /* @__PURE__ */ __name(async (c, next) => {
   const logger2 = c.get("logger");
   const authHeader = c.req.header("Authorization");
-  if (!authHeader || !authHeader.startsWith("Bearer ")) {
-    logger2.warn("Authentication failed: Missing Authorization header", {
-      type: "auth_failed",
-      reason: "missing_header",
-      path: c.req.path,
-      method: c.req.method
-    });
-    return c.json({
-      error: "Unauthorized"
-    }, 401);
+  let tokenStr;
+  if (authHeader?.startsWith("Bearer ")) {
+    tokenStr = authHeader.substring(7).trim();
+  } else {
+    tokenStr = getCookie(c, "semiont-token");
   }
-  const tokenStr = authHeader.substring(7).trim();
   if (!tokenStr) {
-    logger2.warn("Authentication failed: Empty token", {
+    logger2.warn("Authentication failed: No token", {
       type: "auth_failed",
-      reason: "empty_token",
+      reason: "missing_token",
       path: c.req.path,
       method: c.req.method
     });
@@ -15729,6 +15872,7 @@ var authMiddleware = /* @__PURE__ */ __name(async (c, next) => {
   try {
     const user = await OAuthService.getUserFromToken(accessToken(tokenStr));
     c.set("user", user);
+    c.set("token", tokenStr);
     logger2.debug("Authentication successful", {
       type: "auth_success",
       userId: user.id,
@@ -15920,6 +16064,13 @@ authRouter.post("/api/tokens/password", validateRequestBody("PasswordAuthRequest
         lastLogin: /* @__PURE__ */ new Date()
       }
     });
+    setCookie(c, "semiont-token", token, {
+      httpOnly: true,
+      secure: process.env.NODE_ENV === "production",
+      sameSite: "Lax",
+      path: "/",
+      maxAge: 7 * 24 * 60 * 60
+    });
     const response = {
       success: true,
       user: {
@@ -15955,6 +16106,13 @@ authRouter.post("/api/tokens/google", validateRequestBody("GoogleAuthRequest"),
     }
     const googleUser = await OAuthService.verifyGoogleToken(googleCredential(access_token));
     const { user, token, isNewUser } = await OAuthService.createOrUpdateUser(googleUser);
+    setCookie(c, "semiont-token", token, {
+      httpOnly: true,
+      secure: process.env.NODE_ENV === "production",
+      sameSite: "Lax",
+      path: "/",
+      maxAge: 7 * 24 * 60 * 60
+    });
     const response = {
       success: true,
       user: {
@@ -16051,6 +16209,7 @@ authRouter.post("/api/tokens/refresh", validateRequestBody("TokenRefreshRequest"
 });
 authRouter.get("/api/users/me", authMiddleware, async (c) => {
   const user = c.get("user");
+  const token = c.get("token");
   const response = {
     id: user.id,
     email: user.email,
@@ -16062,7 +16221,8 @@ authRouter.get("/api/users/me", authMiddleware, async (c) => {
     isActive: user.isActive,
     termsAcceptedAt: user.termsAcceptedAt?.toISOString() || null,
     lastLogin: user.lastLogin?.toISOString() || null,
-    created: user.createdAt.toISOString()
+    created: user.createdAt.toISOString(),
+    token
   };
   return c.json(response, 200);
 });
@@ -16104,6 +16264,9 @@ authRouter.post("/api/users/accept-terms", authMiddleware, async (c) => {
   return c.json(response, 200);
 });
 authRouter.post("/api/users/logout", authMiddleware, async (c) => {
+  deleteCookie(c, "semiont-token", {
+    path: "/"
+  });
   return c.json({
     success: true,
     message: "Logged out successfully"
@@ -16375,8 +16538,8 @@ exchangeRouter.post("/api/admin/exchange/backup", async (c) => {
   (async () => {
     try {
       await exportBackup({
-        eventStore: mm.kb.eventStore,
-        content: mm.kb.content,
+        eventStore: mm.knowledgeSystem.kb.eventStore,
+        content: mm.knowledgeSystem.kb.content,
         sourceUrl
       }, nodeWritable);
     } catch (err) {
@@ -16475,8 +16638,8 @@ exchangeRouter.post("/api/moderate/exchange/export", async (c) => {
   (async () => {
     try {
       await exportLinkedData({
-        views: mm.kb.views,
-        content: mm.kb.content,
+        views: mm.knowledgeSystem.kb.views,
+        content: mm.knowledgeSystem.kb.content,
         sourceUrl,
         entityTypes,
         includeArchived
@@ -16587,7 +16750,7 @@ function registerCreateResource(router) {
     const arrayBuffer = await file.arrayBuffer();
     const contentBuffer = Buffer.from(arrayBuffer);
     const eventBus2 = c.get("eventBus");
-    const resourceId21 = await ResourceOperations.createResource({
+    const resourceId20 = await ResourceOperations.createResource({
       name,
       content: contentBuffer,
       format,
@@ -16595,9 +16758,9 @@ function registerCreateResource(router) {
       entityTypes,
       creationMethod: creationMethod || void 0,
       storageUri: storageUri || void 0
-    }, userId(user.id), eventBus2);
+    }, userId(userToDid(user)), eventBus2);
     return c.json({
-      resourceId: resourceId21
+      resourceId: resourceId20
     }, 202);
   });
 }
@@ -16912,7 +17075,7 @@ function registerGetResourceUri(router) {
     }
     const acceptHeader = c.req.header("Accept") || "application/ld+json";
     if (acceptHeader.includes("text/") || acceptHeader.includes("image/") || acceptHeader.includes("application/pdf")) {
-      const { kb } = c.get("makeMeaning");
+      const { knowledgeSystem: { kb } } = c.get("makeMeaning");
       let resource;
       try {
         resource = await ResourceContext.getResourceMetadata(resourceId(id), kb);
@@ -17026,7 +17189,7 @@ function registerUpdateResource(router) {
     const body = c.get("validatedBody");
     const user = c.get("user");
     const eventBus2 = c.get("eventBus");
-    const { kb } = c.get("makeMeaning");
+    const { knowledgeSystem: { kb } } = c.get("makeMeaning");
     const doc = await ResourceContext.getResourceMetadata(resourceId(id), kb);
     if (!doc) {
       throw new HTTPException(404, {
@@ -17035,7 +17198,7 @@ function registerUpdateResource(router) {
     }
     await ResourceOperations.updateResource({
       resourceId: resourceId(id),
-      userId: userId(user.id),
+      userId: userId(userToDid(user)),
       currentArchived: doc.archived,
       updatedArchived: body.archived,
       currentEntityTypes: doc.entityTypes,
@@ -17105,7 +17268,7 @@ function registerAnnotateReferencesStream(router, jobQueue) {
       });
     }
     const eventBus2 = c.get("eventBus");
-    const { kb } = c.get("makeMeaning");
+    const { knowledgeSystem: { kb } } = c.get("makeMeaning");
     const resource = await ResourceContext.getResourceMetadata(resourceId(id), kb);
     if (!resource) {
       throw new HTTPException(404, {
@@ -17117,7 +17280,7 @@ function registerAnnotateReferencesStream(router, jobQueue) {
       metadata: {
         id: jobId(`job-${nanoid()}`),
         type: "reference-annotation",
-        userId: userId(user.id),
+        userId: userId(userToDid(user)),
         userName: user.name || user.email,
         userEmail: user.email,
         userDomain: user.domain,
@@ -17307,7 +17470,7 @@ function registerAnnotateHighlightsStream(router, jobQueue) {
       });
     }
     const eventBus2 = c.get("eventBus");
-    const { kb } = c.get("makeMeaning");
+    const { knowledgeSystem: { kb } } = c.get("makeMeaning");
     const resource = await ResourceContext.getResourceMetadata(resourceId(id), kb);
     if (!resource) {
       throw new HTTPException(404, {
@@ -17319,7 +17482,7 @@ function registerAnnotateHighlightsStream(router, jobQueue) {
       metadata: {
         id: jobId(`job-${nanoid()}`),
         type: "highlight-annotation",
-        userId: userId(user.id),
+        userId: userId(userToDid(user)),
         userName: user.name || user.email,
         userEmail: user.email,
         userDomain: user.domain,
@@ -17495,7 +17658,7 @@ function registerAnnotateAssessmentsStream(router, jobQueue) {
   router.post("/resources/:id/annotate-assessments-stream", validateRequestBody("AnnotateAssessmentsStreamRequest"), async (c) => {
     const { id } = c.req.param();
     const body = c.get("validatedBody");
-    const { instructions, tone, density } = body;
+    const { instructions, tone, density, language } = body;
     if (density !== void 0 && (typeof density !== "number" || density < 1 || density > 10)) {
       throw new HTTPException(400, {
         message: "Invalid density. Must be a number between 1 and 10."
@@ -17517,7 +17680,7 @@ function registerAnnotateAssessmentsStream(router, jobQueue) {
       });
     }
     const eventBus2 = c.get("eventBus");
-    const { kb } = c.get("makeMeaning");
+    const { knowledgeSystem: { kb } } = c.get("makeMeaning");
     const resource = await ResourceContext.getResourceMetadata(resourceId(id), kb);
     if (!resource) {
       throw new HTTPException(404, {
@@ -17529,7 +17692,7 @@ function registerAnnotateAssessmentsStream(router, jobQueue) {
       metadata: {
         id: jobId(`job-${nanoid()}`),
         type: "assessment-annotation",
-        userId: userId(user.id),
+        userId: userId(userToDid(user)),
         userName: user.name || user.email,
         userEmail: user.email,
         userDomain: user.domain,
@@ -17541,7 +17704,8 @@ function registerAnnotateAssessmentsStream(router, jobQueue) {
         resourceId: resourceId(id),
         instructions,
         tone,
-        density
+        density,
+        language
       }
     };
     await jobQueue.createJob(job);
@@ -17716,7 +17880,7 @@ function registerAnnotateCommentsStream(router, jobQueue) {
   router.post("/resources/:id/annotate-comments-stream", validateRequestBody("AnnotateCommentsStreamRequest"), async (c) => {
     const { id } = c.req.param();
     const body = c.get("validatedBody");
-    const { instructions, tone, density } = body;
+    const { instructions, tone, density, language } = body;
     if (density !== void 0 && (typeof density !== "number" || density < 2 || density > 12)) {
       throw new HTTPException(400, {
         message: "Invalid density. Must be a number between 2 and 12."
@@ -17738,7 +17902,7 @@ function registerAnnotateCommentsStream(router, jobQueue) {
       });
     }
     const eventBus2 = c.get("eventBus");
-    const { kb } = c.get("makeMeaning");
+    const { knowledgeSystem: { kb } } = c.get("makeMeaning");
     const resource = await ResourceContext.getResourceMetadata(resourceId(id), kb);
     if (!resource) {
       throw new HTTPException(404, {
@@ -17750,7 +17914,7 @@ function registerAnnotateCommentsStream(router, jobQueue) {
       metadata: {
         id: jobId(`job-${nanoid()}`),
         type: "comment-annotation",
-        userId: userId(user.id),
+        userId: userId(userToDid(user)),
         userName: user.name || user.email,
         userEmail: user.email,
         userDomain: user.domain,
@@ -17762,7 +17926,8 @@ function registerAnnotateCommentsStream(router, jobQueue) {
         resourceId: resourceId(id),
         instructions,
         tone,
-        density
+        density,
+        language
       }
     };
     await jobQueue.createJob(job);
@@ -18130,7 +18295,7 @@ function registerAnnotateTagsStream(router, jobQueue) {
       });
     }
     const eventBus2 = c.get("eventBus");
-    const { kb } = c.get("makeMeaning");
+    const { knowledgeSystem: { kb } } = c.get("makeMeaning");
     const resource = await ResourceContext.getResourceMetadata(resourceId(id), kb);
     if (!resource) {
       throw new HTTPException(404, {
@@ -18142,7 +18307,7 @@ function registerAnnotateTagsStream(router, jobQueue) {
       metadata: {
         id: jobId(`job-${nanoid()}`),
         type: "tag-annotation",
-        userId: userId(user.id),
+        userId: userId(userToDid(user)),
         userName: user.name || user.email,
         userEmail: user.email,
         userDomain: user.domain,
@@ -18318,134 +18483,6 @@ function registerAnnotateTagsStream(router, jobQueue) {
   });
 }
 __name(registerAnnotateTagsStream, "registerAnnotateTagsStream");
-
-// src/routes/resources/routes/llm-context.ts
-var import_rxjs2 = __toESM(require_cjs());
-var import_operators2 = __toESM(require_operators());
-function registerGetResourceLLMContext(router) {
-  router.get("/resources/:id/llm-context", async (c) => {
-    const { id } = c.req.param();
-    const query = c.req.query();
-    const eventBus2 = c.get("eventBus");
-    const depth = query.depth ? Number(query.depth) : 2;
-    const maxResources = query.maxResources ? Number(query.maxResources) : 10;
-    const includeContent = query.includeContent === "false" ? false : true;
-    const includeSummary = query.includeSummary === "true" ? true : false;
-    if (depth < 1 || depth > 3) {
-      throw new HTTPException(400, {
-        message: 'Query parameter "depth" must be between 1 and 3'
-      });
-    }
-    if (maxResources < 1 || maxResources > 20) {
-      throw new HTTPException(400, {
-        message: 'Query parameter "maxResources" must be between 1 and 20'
-      });
-    }
-    eventBus2.get("gather:resource-requested").next({
-      resourceId: resourceId(id),
-      options: {
-        depth,
-        maxResources,
-        includeContent,
-        includeSummary
-      }
-    });
-    try {
-      const result = await (0, import_rxjs2.firstValueFrom)((0, import_rxjs2.merge)(eventBus2.get("gather:resource-complete").pipe((0, import_operators2.filter)((e) => e.resourceId === id), (0, import_operators2.map)((e) => ({
-        ok: true,
-        context: e.context
-      }))), eventBus2.get("gather:resource-failed").pipe((0, import_operators2.filter)((e) => e.resourceId === id), (0, import_operators2.map)((e) => ({
-        ok: false,
-        error: e.error
-      })))).pipe((0, import_operators2.take)(1), (0, import_operators2.timeout)(3e4)));
-      if (!result.ok) {
-        throw result.error;
-      }
-      return c.json(result.context);
-    } catch (error) {
-      if (error instanceof Error) {
-        if (error.message === "Resource not found") {
-          throw new HTTPException(404, {
-            message: "Resource not found"
-          });
-        }
-        if (error.name === "TimeoutError") {
-          throw new HTTPException(504, {
-            message: "Context gathering timed out"
-          });
-        }
-      }
-      throw error;
-    }
-  });
-}
-__name(registerGetResourceLLMContext, "registerGetResourceLLMContext");
-
-// src/routes/resources/routes/annotation-llm-context.ts
-var import_rxjs3 = __toESM(require_cjs());
-var import_operators3 = __toESM(require_operators());
-function registerGetAnnotationLLMContext(router) {
-  router.get("/resources/:resourceId/annotations/:annotationId/llm-context", async (c) => {
-    const { resourceId: resourceIdParam, annotationId: annotationIdParam } = c.req.param();
-    const query = c.req.query();
-    const eventBus2 = c.get("eventBus");
-    const includeSourceContext = query.includeSourceContext === "false" ? false : true;
-    const includeTargetContext = query.includeTargetContext === "false" ? false : true;
-    const contextWindow = query.contextWindow ? Number(query.contextWindow) : 1e3;
-    if (contextWindow < 100 || contextWindow > 5e3) {
-      throw new HTTPException(400, {
-        message: 'Query parameter "contextWindow" must be between 100 and 5000'
-      });
-    }
-    eventBus2.get("gather:requested").next({
-      annotationId: annotationId(annotationIdParam),
-      resourceId: resourceId(resourceIdParam),
-      options: {
-        includeSourceContext,
-        includeTargetContext,
-        contextWindow
-      }
-    });
-    try {
-      const result = await (0, import_rxjs3.firstValueFrom)((0, import_rxjs3.merge)(eventBus2.get("gather:complete").pipe((0, import_operators3.filter)((e) => e.annotationId === annotationIdParam), (0, import_operators3.map)((e) => ({
-        ok: true,
-        response: e.response
-      }))), eventBus2.get("gather:failed").pipe((0, import_operators3.filter)((e) => e.annotationId === annotationIdParam), (0, import_operators3.map)((e) => ({
-        ok: false,
-        error: e.error
-      })))).pipe((0, import_operators3.take)(1), (0, import_operators3.timeout)(3e4)));
-      if (!result.ok) {
-        throw result.error;
-      }
-      return c.json(result.response);
-    } catch (error) {
-      if (error instanceof Error) {
-        if (error.message === "Annotation not found") {
-          throw new HTTPException(404, {
-            message: "Annotation not found"
-          });
-        }
-        if (error.message === "Source resource not found") {
-          throw new HTTPException(404, {
-            message: "Source resource not found"
-          });
-        }
-        if (error.message === "Source content not found") {
-          throw new HTTPException(404, {
-            message: "Source content not found"
-          });
-        }
-        if (error.name === "TimeoutError") {
-          throw new HTTPException(504, {
-            message: "Context gathering timed out"
-          });
-        }
-      }
-      throw error;
-    }
-  });
-}
-__name(registerGetAnnotationLLMContext, "registerGetAnnotationLLMContext");
 function registerGetReferencedBy(router) {
   router.get("/resources/:id/referenced-by", async (c) => {
     const { id } = c.req.param();
@@ -18453,11 +18490,11 @@ function registerGetReferencedBy(router) {
     const eventBus2 = c.get("eventBus");
     const correlationId = crypto.randomUUID();
     try {
-      const response = await eventBusRequest(eventBus2, "bind:referenced-by-requested", {
+      const response = await eventBusRequest(eventBus2, "browse:referenced-by-requested", {
         correlationId,
         resourceId: resourceId(id),
         motivation
-      }, "bind:referenced-by-result", "bind:referenced-by-failed");
+      }, "browse:referenced-by-result", "browse:referenced-by-failed");
       return c.json(response);
     } catch (error) {
       if (error instanceof Error && error.name === "TimeoutError") {
@@ -18492,7 +18529,7 @@ function registerBindSearchStream(router) {
       });
     }
     const eventBus2 = c.get("eventBus");
-    const { kb } = c.get("makeMeaning");
+    const { knowledgeSystem: { kb } } = c.get("makeMeaning");
     const resource = await ResourceContext.getResourceMetadata(resourceId(id), kb);
     if (!resource) {
       throw new HTTPException(404, {
@@ -18520,7 +18557,7 @@ function registerBindSearchStream(router) {
         if (closeStreamCallback) closeStreamCallback();
       }, "cleanup");
       try {
-        subscriptions.push(eventBus2.get("bind:search-results").subscribe(async (event) => {
+        subscriptions.push(eventBus2.get("match:search-results").subscribe(async (event) => {
           if (event.correlationId !== correlationId) return;
           if (isStreamClosed) return;
           logger2.info("Bind search completed", {
@@ -18533,7 +18570,7 @@ function registerBindSearchStream(router) {
                 referenceId: event.referenceId,
                 results: event.results
               }),
-              event: "bind:search-results",
+              event: "match:search-results",
               id: String(Date.now())
             });
           } catch (error) {
@@ -18541,7 +18578,7 @@ function registerBindSearchStream(router) {
           }
           cleanup();
         }));
-        subscriptions.push(eventBus2.get("bind:search-failed").subscribe(async (event) => {
+        subscriptions.push(eventBus2.get("match:search-failed").subscribe(async (event) => {
           if (event.correlationId !== correlationId) return;
           if (isStreamClosed) return;
           logger2.error("Bind search failed", {
@@ -18554,7 +18591,7 @@ function registerBindSearchStream(router) {
                 referenceId: event.referenceId,
                 error: event.error.message
               }),
-              event: "bind:search-failed",
+              event: "match:search-failed",
               id: String(Date.now())
             });
           } catch (error) {
@@ -18562,7 +18599,7 @@ function registerBindSearchStream(router) {
           }
           cleanup();
         }));
-        eventBus2.get("bind:search-requested").next({
+        eventBus2.get("match:search-requested").next({
           correlationId,
           referenceId,
           context,
@@ -18580,7 +18617,7 @@ function registerBindSearchStream(router) {
               referenceId,
               error: error instanceof Error ? error.message : "Search failed"
             }),
-            event: "bind:search-failed",
+            event: "match:search-failed",
             id: String(Date.now())
           });
         } catch (sseError) {
@@ -18636,7 +18673,7 @@ function registerTokenRoutes(router) {
         token: body.token,
         name: body.name,
         content: body.content,
-        userId: userId(user.id),
+        userId: userId(userToDid(user)),
         archiveOriginal: body.archiveOriginal
       }, "yield:clone-created", "yield:clone-create-failed");
       return c.json({
@@ -18779,7 +18816,7 @@ function registerGetEventStream(router) {
     logger2.info("Client connecting to resource events stream", {
       resourceId: rId
     });
-    const { eventStore } = c.get("makeMeaning");
+    const { knowledgeSystem: { kb: { eventStore } } } = c.get("makeMeaning");
     const query = new EventQuery(eventStore.log.storage);
     const events = await query.getResourceEvents(rId);
     if (events.length === 0) {
@@ -18928,7 +18965,7 @@ function registerCreateAnnotation(router) {
     const eventBus2 = c.get("eventBus");
     eventBus2.get("mark:create").next({
       annotation,
-      userId: userId(user.id),
+      userId: userId(userToDid(user)),
       resourceId: resourceId(id)
     });
     return c.json({
@@ -18974,7 +19011,7 @@ function registerDeleteAnnotation(router) {
     const eventBus2 = c.get("eventBus");
     eventBus2.get("mark:delete").next({
       annotationId: annotationId(annotationIdParam),
-      userId: userId(user.id),
+      userId: userId(userToDid(user)),
       resourceId: resourceId(resourceIdParam)
     });
     return c.body(null, 202);
@@ -18990,7 +19027,7 @@ function registerUpdateAnnotationBody(router) {
     eventBus2.get("mark:update-body").next({
       annotationId: annotationId(annotationIdParam),
       resourceId: resourceId(resourceIdParam),
-      userId: userId(user.id),
+      userId: userId(userToDid(user)),
       operations: request.operations
     });
     return c.body(null, 202);
@@ -19017,7 +19054,7 @@ function registerYieldResourceStream(router, jobQueue) {
       });
     }
     const eventBus2 = c.get("eventBus");
-    const { kb } = c.get("makeMeaning");
+    const { knowledgeSystem: { kb } } = c.get("makeMeaning");
     logger2.info("Starting resource generation", {
       language: body.language
     });
@@ -19053,7 +19090,7 @@ function registerYieldResourceStream(router, jobQueue) {
       metadata: {
         id: jobId(`job-${nanoid()}`),
         type: "generation",
-        userId: userId(user.id),
+        userId: userId(userToDid(user)),
         userName: user.name || user.email,
         userEmail: user.email,
         userDomain: user.domain,
@@ -19214,15 +19251,130 @@ function registerYieldResourceStream(router, jobQueue) {
   });
 }
 __name(registerYieldResourceStream, "registerYieldResourceStream");
+init_logger();
+function registerGatherAnnotationStream(router) {
+  router.post("/resources/:resourceId/annotations/:annotationId/gather-annotation-stream", validateRequestBody("GatherAnnotationStreamRequest"), async (c) => {
+    const { resourceId: resourceIdParam, annotationId: annotationIdParam } = c.req.param();
+    const body = c.get("validatedBody");
+    const contextWindow = body.contextWindow ?? 1e3;
+    const eventBus2 = c.get("eventBus");
+    const logger2 = getLogger().child({
+      component: "gather-annotation-stream",
+      resourceId: resourceIdParam,
+      annotationId: annotationIdParam
+    });
+    const user = c.get("user");
+    if (!user) {
+      throw new HTTPException(401, {
+        message: "Authentication required"
+      });
+    }
+    eventBus2.get("gather:requested").next({
+      annotationId: annotationId(annotationIdParam),
+      resourceId: resourceId(resourceIdParam),
+      options: {
+        includeSourceContext: true,
+        includeTargetContext: true,
+        contextWindow
+      }
+    });
+    logger2.info("Emitted gather:requested", {
+      annotationId: annotationIdParam,
+      contextWindow
+    });
+    c.header("X-Accel-Buffering", "no");
+    c.header("Cache-Control", "no-cache, no-transform");
+    return streamSSE(c, async (stream) => {
+      let isStreamClosed = false;
+      const subscriptions = [];
+      let keepAliveInterval = null;
+      const streamPromise = new Promise((resolve) => {
+        const cleanup = /* @__PURE__ */ __name(() => {
+          if (isStreamClosed) return;
+          isStreamClosed = true;
+          if (keepAliveInterval) clearInterval(keepAliveInterval);
+          subscriptions.forEach((sub) => sub.unsubscribe());
+          resolve();
+        }, "cleanup");
+        subscriptions.push(eventBus2.get("gather:annotation-progress").subscribe(async (event) => {
+          if (isStreamClosed) return;
+          try {
+            await writeTypedSSE(stream, {
+              data: JSON.stringify({
+                message: event.message,
+                percentage: event.percentage
+              }),
+              event: "gather:annotation-progress",
+              id: String(Date.now())
+            });
+          } catch {
+            cleanup();
+          }
+        }));
+        subscriptions.push(eventBus2.get("gather:complete").subscribe(async (event) => {
+          if (event.annotationId !== annotationIdParam) return;
+          if (isStreamClosed) return;
+          try {
+            await writeTypedSSE(stream, {
+              data: JSON.stringify({
+                annotationId: event.annotationId,
+                response: event.response
+              }),
+              event: "gather:annotation-finished",
+              id: String(Date.now())
+            });
+          } catch {
+          }
+          cleanup();
+        }));
+        subscriptions.push(eventBus2.get("gather:failed").subscribe(async (event) => {
+          if (event.annotationId !== annotationIdParam) return;
+          if (isStreamClosed) return;
+          try {
+            await writeTypedSSE(stream, {
+              data: JSON.stringify({
+                annotationId: event.annotationId,
+                error: event.error
+              }),
+              event: "gather:failed",
+              id: String(Date.now())
+            });
+          } catch {
+          }
+          cleanup();
+        }));
+        keepAliveInterval = setInterval(async () => {
+          if (isStreamClosed) {
+            clearInterval(keepAliveInterval);
+            return;
+          }
+          try {
+            await stream.writeSSE({
+              data: ":keep-alive"
+            });
+          } catch {
+            cleanup();
+          }
+        }, 3e4);
+        c.req.raw.signal.addEventListener("abort", () => {
+          logger2.info("Client disconnected from gather stream");
+          cleanup();
+        });
+      });
+      return streamPromise;
+    });
+  });
+}
+__name(registerGatherAnnotationStream, "registerGatherAnnotationStream");
 function registerGetAnnotationHistory(router) {
   router.get("/resources/:resourceId/annotations/:annotationId/history", async (c) => {
-    const { resourceId: resourceId21, annotationId: annotationId6 } = c.req.param();
+    const { resourceId: resourceId20, annotationId: annotationId6 } = c.req.param();
     const eventBus2 = c.get("eventBus");
     const correlationId = crypto.randomUUID();
     try {
       const response = await eventBusRequest(eventBus2, "browse:annotation-history-requested", {
         correlationId,
-        resourceId: resourceId(resourceId21),
+        resourceId: resourceId(resourceId20),
         annotationId: annotationId(annotationId6)
       }, "browse:annotation-history-result", "browse:annotation-history-failed");
       return c.json(response);
@@ -19261,8 +19413,6 @@ function createResourcesRouter(jobQueue) {
   registerAnnotateAssessmentsStream(resourcesRouter2, jobQueue);
   registerAnnotateCommentsStream(resourcesRouter2, jobQueue);
   registerAnnotateTagsStream(resourcesRouter2, jobQueue);
-  registerGetResourceLLMContext(resourcesRouter2);
-  registerGetAnnotationLLMContext(resourcesRouter2);
   registerGetReferencedBy(resourcesRouter2);
   registerBindSearchStream(resourcesRouter2);
   registerGetResourceAnnotations(resourcesRouter2);
@@ -19270,6 +19420,7 @@ function createResourcesRouter(jobQueue) {
   registerGetAnnotation(resourcesRouter2);
   registerUpdateAnnotationBody(resourcesRouter2);
   registerYieldResourceStream(resourcesRouter2, jobQueue);
+  registerGatherAnnotationStream(resourcesRouter2);
   registerGetAnnotationHistory(resourcesRouter2);
   registerDeleteAnnotation(resourcesRouter2);
   registerGetEvents(resourcesRouter2);
@@ -19290,7 +19441,7 @@ function registerGetAnnotationUri(router) {
   router.get("/annotations/:id", async (c) => {
     const { id } = c.req.param();
     const query = c.req.query();
-    const { kb } = c.get("makeMeaning");
+    const { knowledgeSystem: { kb } } = c.get("makeMeaning");
     const resourceIdParam = query.resourceId;
     if (!resourceIdParam) {
       throw new HTTPException(400, {
@@ -19330,9 +19481,9 @@ var operationsRouter = createAnnotationRouter();
 operationsRouter.get("/api/annotations/:id/context", async (c) => {
   const { id } = c.req.param();
   const query = c.req.query();
-  const { kb } = c.get("makeMeaning");
-  const resourceId21 = query.resourceId;
-  if (!resourceId21) {
+  const { knowledgeSystem: { kb } } = c.get("makeMeaning");
+  const resourceId20 = query.resourceId;
+  if (!resourceId20) {
     throw new HTTPException(400, {
       message: "resourceId query parameter is required"
     });
@@ -19350,7 +19501,7 @@ operationsRouter.get("/api/annotations/:id/context", async (c) => {
     });
   }
   try {
-    const response = await AnnotationContext.getAnnotationContext(annotationId(id), resourceId(resourceId21), contextBefore, contextAfter, kb);
+    const response = await AnnotationContext.getAnnotationContext(annotationId(id), resourceId(resourceId20), contextBefore, contextAfter, kb);
     return c.json(response);
   } catch (error) {
     if (error instanceof Error && error.message === "Annotation not found") {
@@ -19379,15 +19530,15 @@ operationsRouter.get("/api/annotations/:id/context", async (c) => {
 operationsRouter.get("/api/annotations/:id/summary", async (c) => {
   const { id } = c.req.param();
   const query = c.req.query();
-  const { kb, gathererInferenceClient: inferenceClient } = c.get("makeMeaning");
-  const resourceId21 = query.resourceId;
-  if (!resourceId21) {
+  const { knowledgeSystem: { gatherer } } = c.get("makeMeaning");
+  const resourceId20 = query.resourceId;
+  if (!resourceId20) {
     throw new HTTPException(400, {
       message: "resourceId query parameter is required"
     });
   }
   try {
-    const response = await AnnotationContext.generateAnnotationSummary(annotationId(id), resourceId(resourceId21), kb, inferenceClient);
+    const response = await gatherer.generateAnnotationSummary(annotationId(id), resourceId(resourceId20));
     return c.json(response);
   } catch (error) {
     if (error instanceof Error && error.message === "Annotation not found") {
@@ -19420,9 +19571,9 @@ entityTypesRouter.use("/api/entity-types/*", authMiddleware);
 entityTypesRouter.get("/api/entity-types", async (c) => {
   const eventBus2 = c.get("eventBus");
   const correlationId = crypto.randomUUID();
-  const response = await eventBusRequest(eventBus2, "mark:entity-types-requested", {
+  const response = await eventBusRequest(eventBus2, "browse:entity-types-requested", {
     correlationId
-  }, "mark:entity-types-result", "mark:entity-types-failed");
+  }, "browse:entity-types-result", "browse:entity-types-failed");
   return c.json(response, 200);
 });
 entityTypesRouter.post("/api/entity-types", validateRequestBody("AddEntityTypeRequest"), async (c) => {
@@ -19436,7 +19587,7 @@ entityTypesRouter.post("/api/entity-types", validateRequestBody("AddEntityTypeRe
   const eventBus2 = c.get("eventBus");
   eventBus2.get("mark:add-entity-type").next({
     tag: body.tag,
-    userId: userId(user.id)
+    userId: userId(userToDid(user))
   });
   return c.body(null, 202);
 });
@@ -19452,7 +19603,7 @@ entityTypesRouter.post("/api/entity-types/bulk", validateRequestBody("BulkAddEnt
   for (const tag of body.tags) {
     eventBus2.get("mark:add-entity-type").next({
       tag,
-      userId: userId(user.id)
+      userId: userId(userToDid(user))
     });
   }
   return c.body(null, 202);
@@ -19466,7 +19617,7 @@ globalEventsRouter.use("/api/events/stream", authMiddleware);
 globalEventsRouter.get("/api/events/stream", async (c) => {
   const logger2 = getRouteLogger4();
   logger2.info("Client connecting to global events stream");
-  const { eventStore } = c.get("makeMeaning");
+  const { knowledgeSystem: { kb: { eventStore } } } = c.get("makeMeaning");
   return streamSSE(c, async (stream) => {
     await stream.writeSSE({
       data: JSON.stringify({
@@ -19593,11 +19744,11 @@ function createJobsRouter(_jobQueue, authMiddleware2) {
 __name(createJobsRouter, "createJobsRouter");
 
 // src/routes/participants/attention-channels.ts
-var import_rxjs4 = __toESM(require_cjs());
+var import_rxjs2 = __toESM(require_cjs());
 var channels = /* @__PURE__ */ new Map();
 function getOrCreateChannel(participantId) {
   if (!channels.has(participantId)) {
-    channels.set(participantId, new import_rxjs4.Subject());
+    channels.set(participantId, new import_rxjs2.Subject());
   }
   return channels.get(participantId);
 }
@@ -19707,6 +19858,46 @@ var participantsRouter = new Hono();
 participantsRouter.use("/api/participants/*", authMiddleware);
 registerBeckon(participantsRouter);
 registerAttentionStream(participantsRouter);
+var browseRouter = new Hono();
+browseRouter.use("/api/browse/*", authMiddleware);
+browseRouter.get("/api/browse/files", async (c) => {
+  const reqPath = c.req.query("path") ?? "";
+  const sort = c.req.query("sort");
+  if (sort !== void 0 && sort !== "name" && sort !== "mtime" && sort !== "annotationCount") {
+    throw new HTTPException(400, {
+      message: 'Invalid sort value. Must be "name", "mtime", or "annotationCount".'
+    });
+  }
+  const eventBus2 = c.get("eventBus");
+  const correlationId = crypto.randomUUID();
+  try {
+    const response = await eventBusRequest(eventBus2, "browse:directory-requested", {
+      correlationId,
+      path: reqPath,
+      sort
+    }, "browse:directory-result", "browse:directory-failed");
+    return c.json(response);
+  } catch (error) {
+    if (error instanceof Error) {
+      if (error.name === "TimeoutError") {
+        throw new HTTPException(504, {
+          message: "Request timed out"
+        });
+      }
+      if (error.message === "path not found") {
+        throw new HTTPException(404, {
+          message: error.message
+        });
+      }
+      if (error.message === "path escapes project root") {
+        throw new HTTPException(400, {
+          message: error.message
+        });
+      }
+    }
+    throw error;
+  }
+});
 
 // src/middleware/security-headers.ts
 var securityHeaders = /* @__PURE__ */ __name(() => {
@@ -19873,6 +20064,7 @@ app.route("/", globalEventsRouter);
 var jobsRouter = createJobsRouter(makeMeaning.jobQueue, authMiddleware);
 app.route("/", jobsRouter);
 app.route("/", participantsRouter);
+app.route("/", browseRouter);
 app.get("/api", (c) => {
   const acceptHeader = c.req.header("Accept") || "";
   const userAgent = c.req.header("User-Agent") || "";
@@ -19885,7 +20077,8 @@ app.get("/api", (c) => {
   return c.redirect(redirectUrl);
 });
 app.get("/api/openapi.json", (c) => {
-  const openApiPath = path.join(__dirname$1, "../../../specs/openapi.json");
+  const distPath = path.join(__dirname$1, "openapi.json");
+  const openApiPath = fs.existsSync(distPath) ? distPath : path.join(__dirname$1, "../../../specs/openapi.json");
   const openApiContent = fs.readFileSync(openApiPath, "utf-8");
   const openApiSpec = JSON.parse(openApiContent);
   const port2 = backendService.port || 4e3;
@@ -19952,7 +20145,7 @@ if (config.env?.NODE_ENV !== "test") {
       });
     }
     try {
-      const entityTypes = await makeMeaning.graphDb.getEntityTypes();
+      const entityTypes = await makeMeaning.knowledgeSystem.kb.graph.getEntityTypes();
       logger.info("Loaded entity types from graph database", {
         count: entityTypes.length
       });