fix(sdk-core): configure Agent to use correct service URL for SDS queries

The Agent was using the default PDS service URL from the OAuth session
even when querying SDS repositories, causing 'Could not find repo' errors.
This configures the Agent's XRPC URI to use the specified server URL
(PDS or SDS) so queries are routed to the correct service endpoint.

- Set agent.api.xrpc.uri to the serverUrl in Repository constructor
- Ensures SDS repository queries reach the SDS server
- Resolves 400 errors when listing hypercerts/collections from organizations
- All 317 tests passing

Fixes 'Could not find repo' errors when querying shared repositories.

Author: bitbeckers

.changeset/fix-agent-service-url.md

@@ -0,0 +1,5 @@
+---
+"@hypercerts-org/sdk-core": patch
+---
+
+Fix Agent service URL configuration to ensure queries are routed to the correct server (PDS or SDS). The Agent now explicitly uses the serverUrl provided to the Repository constructor, resolving "Could not find repo" errors when querying SDS repositories.

.changeset/pagination-and-react-hooks-fix.md

@@ -17,6 +17,8 @@ Add pagination support and fix React hooks for SDS operations
 **Bug Fixes (sdk-core):**
 - Fix permissions parsing in `CollaboratorOperationsImpl.list()` to match actual SDS API format (object with boolean flags)
 - Prevent `TypeError: permissionArray.includes is not a function` by correctly handling permissions as objects
+- Fix Agent service URL configuration to route queries to the correct server (PDS or SDS)
+- Resolve "Could not find repo" errors when querying SDS repositories by ensuring Agent uses SDS service endpoint
 - Update test mocks to use the actual SDS API response format
 
 **Bug Fixes (sdk-react):**

packages/sdk-core/src/repository/Repository.ts

@@ -181,6 +181,11 @@ export class Repository {
 
     // Create Agent with OAuth session
     this.agent = new Agent(session);
+
+    // Configure Agent to use the specified server URL (PDS or SDS)
+    // This ensures queries are routed to the correct server
+    this.agent.api.xrpc.uri = new URL(serverUrl);
+
     this.lexiconRegistry.addToAgent(this.agent);
 
     // Register hypercert lexicons