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]