refactor(store): replace project and skill models with generated models

* Update project creation and retrieval to use generated models
* Modify skill addition and listing to utilize generated models
* Refactor thought handling to incorporate generated models
* Adjust tool annotations to align with new model structure
* Update API calls in the UI to use new ResolveSpec-based endpoints
* Enhance stats retrieval logic to aggregate thought metadata

schema/core.dbml

@@ -19,6 +19,7 @@ Table projects {
 }
 
 Table thought_links {
+  id serial [pk]
   from_id bigint [not null, ref: > thoughts.id]
   to_id bigint [not null, ref: > thoughts.id]
   relation text [not null]