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.

internal/tools/links.go

@@ -2,6 +2,7 @@ package tools
 
 import (
 	"context"
+	"fmt"
 	"strings"
 
 	"github.com/modelcontextprotocol/go-sdk/mcp"
@@ -97,9 +98,9 @@ func (t *LinksTool) Related(ctx context.Context, _ *mcp.CallToolRequest, in Rela
 	}
 
 	related := make([]RelatedThought, 0, len(linked)+t.search.DefaultLimit)
-	seen := map[string]struct{}{thought.ID.String(): {}}
+	seen := map[string]struct{}{fmt.Sprint(thought.ID): {}}
 	for _, item := range linked {
-		key := item.Thought.ID.String()
+		key := fmt.Sprint(item.Thought.ID)
 		seen[key] = struct{}{}
 		related = append(related, RelatedThought{
 			ID:        key,
@@ -117,12 +118,12 @@ func (t *LinksTool) Related(ctx context.Context, _ *mcp.CallToolRequest, in Rela
 	}
 
 	if includeSemantic {
-		semantic, err := semanticSearch(ctx, t.store, t.embeddings, t.search, thought.Content, t.search.DefaultLimit, t.search.DefaultThreshold, thought.ProjectID, &thought.ID)
+		semantic, err := semanticSearch(ctx, t.store, t.embeddings, t.search, thought.Content, t.search.DefaultLimit, t.search.DefaultThreshold, thought.ProjectID, &thought.GUID)
 		if err != nil {
 			return nil, RelatedOutput{}, err
 		}
 		for _, item := range semantic {
-			key := item.ID.String()
+			key := fmt.Sprint(item.ID)
 			if _, ok := seen[key]; ok {
 				continue
 			}