refactor(store,tools): migrate IDs from UUID to bigserial int64

All internal entity lookups now use bigserial primary keys (int64) while
GUIDs are retained for external/public identification. Updated store
functions (TouchProject, UpdateThoughtMetadata, AddThoughtAttachment) to
query by id instead of guid, added GetThoughtByID, changed semanticSearch
and all tool helpers to use *int64 project IDs, and updated retry/backfill
workers to use int64 thought IDs throughout.

schema/core.dbml

@@ -5,7 +5,7 @@ Table thoughts {
   metadata jsonb [default: `'{}'::jsonb`]
   created_at timestamptz [default: `now()`]
   updated_at timestamptz [default: `now()`]
-  project_id uuid [ref: > projects.guid]
+  project_id bigint [ref: > projects.id]
   archived_at timestamptz
 }
 
@@ -19,7 +19,7 @@ Table projects {
 }
 
 Table thought_links {
-  id serial [pk]
+  id bigserial [pk]
   from_id bigint [not null, ref: > thoughts.id]
   to_id bigint [not null, ref: > thoughts.id]
   relation text [not null]
@@ -35,7 +35,7 @@ Table thought_links {
 Table embeddings {
   id bigserial [pk]
   guid uuid [unique, not null, default: `gen_random_uuid()`]
-  thought_id uuid [not null, ref: > thoughts.guid]
+  thought_id bigint [not null, ref: > thoughts.id]
   model text [not null]
   dim int [not null]
   embedding vector [not null]

schema/files.dbml

@@ -1,8 +1,8 @@
 Table stored_files {
   id bigserial [pk]
   guid uuid [unique, not null, default: `gen_random_uuid()`]
-  thought_id uuid [ref: > thoughts.guid]
-  project_id uuid [ref: > projects.guid]
+  thought_id bigint [ref: > thoughts.id]
+  project_id bigint [ref: > projects.id]
   name text [not null]
   media_type text [not null]
   kind text [not null, default: 'file']
@@ -21,5 +21,5 @@ Table stored_files {
 }
 
 // Cross-file refs (for relspecgo merge)
-Ref: stored_files.thought_id > thoughts.guid [delete: set null]
-Ref: stored_files.project_id > projects.guid [delete: set null]
+Ref: stored_files.thought_id > thoughts.id [delete: set null]
+Ref: stored_files.project_id > projects.id [delete: set null]

schema/meta.dbml

@@ -1,10 +1,11 @@
 Table chat_histories {
-  id uuid [pk, default: `gen_random_uuid()`]
+  id bigserial [pk]
+  guid uuid [unique, not null, default: `gen_random_uuid()`]
   session_id text [not null]
   title text
   channel text
   agent_id text
-  project_id uuid [ref: > projects.guid]
+  project_id bigint [ref: > projects.id]
   messages jsonb [not null, default: `'[]'`]
   summary text
   metadata jsonb [not null, default: `'{}'`]
@@ -29,10 +30,11 @@ Table tool_annotations {
 }
 
 // Cross-file refs (for relspecgo merge)
-Ref: chat_histories.project_id > projects.guid [delete: set null]
+Ref: chat_histories.project_id > projects.id [delete: set null]
 
 Table learnings {
-  id uuid [pk, default: `gen_random_uuid()`]
+  id bigserial [pk]
+  guid uuid [unique, not null, default: `gen_random_uuid()`]
   summary text [not null]
   details text [not null, default: '']
   category text [not null, default: 'insight']
@@ -43,13 +45,13 @@ Table learnings {
   action_required boolean [not null, default: false]
   source_type text
   source_ref text
-  project_id uuid [ref: > projects.guid]
-  related_thought_id uuid [ref: > thoughts.guid]
-  related_skill_id uuid [ref: > agent_skills.id]
+  project_id bigint [ref: > projects.id]
+  related_thought_id bigint [ref: > thoughts.id]
+  related_skill_id bigint [ref: > agent_skills.id]
   reviewed_by text
   reviewed_at timestamptz
-  duplicate_of_learning_id uuid [ref: > learnings.id]
-  supersedes_learning_id uuid [ref: > learnings.id]
+  duplicate_of_learning_id bigint [ref: > learnings.id]
+  supersedes_learning_id bigint [ref: > learnings.id]
   tags "text[]" [not null, default: `'{}'`]
   created_at timestamptz [not null, default: `now()`]
   updated_at timestamptz [not null, default: `now()`]
@@ -68,8 +70,8 @@ Table learnings {
 }
 
 // Cross-file refs (for relspecgo merge)
-Ref: learnings.project_id > projects.guid [delete: set null]
-Ref: learnings.related_thought_id > thoughts.guid [delete: set null]
+Ref: learnings.project_id > projects.id [delete: set null]
+Ref: learnings.related_thought_id > thoughts.id [delete: set null]
 Ref: learnings.related_skill_id > agent_skills.id [delete: set null]
 Ref: learnings.duplicate_of_learning_id > learnings.id [delete: set null]
 Ref: learnings.supersedes_learning_id > learnings.id [delete: set null]

schema/plans.dbml

@@ -1,16 +1,17 @@
 Table plans {
-  id uuid [pk, default: `gen_random_uuid()`]
+  id bigserial [pk]
+  guid uuid [unique, not null, default: `gen_random_uuid()`]
   title text [not null]
   description text [not null, default: '']
   status text [not null, default: 'draft']       // draft, active, blocked, completed, cancelled, superseded
   priority text [not null, default: 'medium']    // low, medium, high, critical
-  project_id uuid [ref: > projects.guid]
+  project_id bigint [ref: > projects.id]
   owner text
   due_date timestamptz
   completed_at timestamptz
   reviewed_by text
   last_reviewed_at timestamptz
-  supersedes_plan_id uuid [ref: > plans.id]
+  supersedes_plan_id bigint [ref: > plans.id]
   tags "text[]" [not null, default: `'{}'`]
   created_at timestamptz [not null, default: `now()`]
   updated_at timestamptz [not null, default: `now()`]
@@ -29,9 +30,9 @@ Table plans {
 
 // Directional: plan_id cannot proceed until depends_on_plan_id is complete
 Table plan_dependencies {
-  id serial [pk]
-  plan_id uuid [not null, ref: > plans.id]
-  depends_on_plan_id uuid [not null, ref: > plans.id]
+  id bigserial [pk]
+  plan_id bigint [not null, ref: > plans.id]
+  depends_on_plan_id bigint [not null, ref: > plans.id]
   created_at timestamptz [not null, default: `now()`]
 
   indexes {
@@ -43,9 +44,9 @@ Table plan_dependencies {
 
 // Bidirectional: store with plan_a_id < plan_b_id to avoid duplicates
 Table plan_related_plans {
-  id serial [pk]
-  plan_a_id uuid [not null, ref: > plans.id]
-  plan_b_id uuid [not null, ref: > plans.id]
+  id bigserial [pk]
+  plan_a_id bigint [not null, ref: > plans.id]
+  plan_b_id bigint [not null, ref: > plans.id]
   created_at timestamptz [not null, default: `now()`]
 
   indexes {
@@ -56,9 +57,9 @@ Table plan_related_plans {
 }
 
 Table plan_skills {
-  id serial [pk]
-  plan_id uuid [not null, ref: > plans.id]
-  skill_id uuid [not null, ref: > agent_skills.id]
+  id bigserial [pk]
+  plan_id bigint [not null, ref: > plans.id]
+  skill_id bigint [not null, ref: > agent_skills.id]
   created_at timestamptz [not null, default: `now()`]
 
   indexes {
@@ -68,9 +69,9 @@ Table plan_skills {
 }
 
 Table plan_guardrails {
-  id serial [pk]
-  plan_id uuid [not null, ref: > plans.id]
-  guardrail_id uuid [not null, ref: > agent_guardrails.id]
+  id bigserial [pk]
+  plan_id bigint [not null, ref: > plans.id]
+  guardrail_id bigint [not null, ref: > agent_guardrails.id]
   created_at timestamptz [not null, default: `now()`]
 
   indexes {
@@ -80,7 +81,7 @@ Table plan_guardrails {
 }
 
 // Cross-file refs (for relspecgo merge)
-Ref: plans.project_id > projects.guid [delete: set null]
+Ref: plans.project_id > projects.id [delete: set null]
 Ref: plans.supersedes_plan_id > plans.id [delete: set null]
 Ref: plan_dependencies.plan_id > plans.id [delete: cascade]
 Ref: plan_dependencies.depends_on_plan_id > plans.id [delete: cascade]

schema/skills.dbml

@@ -1,5 +1,6 @@
 Table agent_skills {
-  id uuid [pk, default: `gen_random_uuid()`]
+  id bigserial [pk]
+  guid uuid [unique, not null, default: `gen_random_uuid()`]
   name text [unique, not null]
   description text [not null, default: '']
   content text [not null]
@@ -9,7 +10,8 @@ Table agent_skills {
 }
 
 Table agent_guardrails {
-  id uuid [pk, default: `gen_random_uuid()`]
+  id bigserial [pk]
+  guid uuid [unique, not null, default: `gen_random_uuid()`]
   name text [unique, not null]
   description text [not null, default: '']
   content text [not null]
@@ -20,9 +22,9 @@ 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]
+  id bigserial [pk]
+  project_id bigint [not null, ref: > projects.id]
+  skill_id bigint [not null, ref: > agent_skills.id]
   created_at timestamptz [not null, default: `now()`]
 
   indexes {
@@ -32,9 +34,9 @@ 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]
+  id bigserial [pk]
+  project_id bigint [not null, ref: > projects.id]
+  guardrail_id bigint [not null, ref: > agent_guardrails.id]
   created_at timestamptz [not null, default: `now()`]
 
   indexes {
@@ -44,5 +46,7 @@ Table project_guardrails {
 }
 
 // Cross-file refs (for relspecgo merge)
-Ref: project_skills.project_id > projects.guid [delete: cascade]
-Ref: project_guardrails.project_id > projects.guid [delete: cascade]
+Ref: project_skills.project_id > projects.id [delete: cascade]
+Ref: project_skills.skill_id > agent_skills.id [delete: cascade]
+Ref: project_guardrails.project_id > projects.id [delete: cascade]
+Ref: project_guardrails.guardrail_id > agent_guardrails.id [delete: cascade]