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/skills.dbml

@@ -20,6 +20,7 @@ Table agent_guardrails {
 }
 
 Table project_skills {
+  id serial [pk]
   project_id uuid [not null, ref: > projects.guid]
   skill_id uuid [not null, ref: > agent_skills.id]
   created_at timestamptz [not null, default: `now()`]
@@ -31,6 +32,7 @@ Table project_skills {
 }
 
 Table project_guardrails {
+  id serial [pk]
   project_id uuid [not null, ref: > projects.guid]
   guardrail_id uuid [not null, ref: > agent_guardrails.id]
   created_at timestamptz [not null, default: `now()`]