fix/deep review improvements

.gitignore

@@ -6,11 +6,15 @@
 bin/
 dist/
 
-# Database / local cache
+# Database / local cache (SQLite main DB + WAL/SHM sidecars)
 elrond*.db
 *.codegraph.db
+*.db-wal
+*.db-shm
+.codegraph/*.db
 
 # Local yaad runtime state (key material + SQLite database + local config — never commit)
+.yaad/
 .yaad/integrity.key
 .yaad/yaad.db
 .yaad/config.toml

compact/compact.go

@@ -5,7 +5,9 @@ package compact
 import (
 	"context"
 	"crypto/sha256"
+	"errors"
 	"fmt"
+	"log/slog"
 	"strings"
 
 	"github.com/GrayCodeAI/yaad/storage"
@@ -93,6 +95,8 @@ func (c *Compactor) Compact(ctx context.Context, project string) (int, error) {
 
 		summary, err := c.summarizer.Summarize(ctx, typ, contents)
 		if err != nil {
+			// Skipping this group is safe — nothing has been mutated yet.
+			slog.Warn("compact: summarize failed, skipping group", "type", typ, "count", len(group), "error", err)
 			continue
 		}
 
@@ -112,61 +116,96 @@ func (c *Compactor) Compact(ctx context.Context, project string) (int, error) {
 			Version:     1,
 		}
 		if err := c.store.CreateNode(ctx, summaryNode); err != nil {
+			// Skipping this group is safe — nothing else has been mutated yet.
+			slog.Warn("compact: create summary node failed, skipping group",
+				"type", typ, "summary_node_id", summaryNode.ID, "error", err)
 			continue
 		}
 
 		// Re-link edges: transfer edges from compacted nodes to the summary node.
+		// From here on the summary node exists, so failures would leave the graph
+		// partially re-linked — abort and propagate instead of silently continuing.
 		compactedIDs := make(map[string]bool, len(ids))
 		for _, id := range ids {
 			compactedIDs[id] = true
 		}
 		for _, id := range ids {
 			// Outbound edges: compacted → other
-			if outEdges, err := c.store.GetEdgesFrom(ctx, id); err == nil {
-				for _, e := range outEdges {
-					if compactedIDs[e.ToID] {
-						continue // skip edges between compacted nodes
-					}
-					_ = c.store.CreateEdge(ctx, &storage.Edge{
-						ID:     uuid.New().String(),
-						FromID: summaryNode.ID,
-						ToID:   e.ToID,
-						Type:   e.Type,
-						Weight: e.Weight,
-					})
+			outEdges, err := c.store.GetEdgesFrom(ctx, id)
+			if err != nil {
+				return compacted, fmt.Errorf("compact: list outbound edges of node %s: %w", id, err)
+			}
+			for _, e := range outEdges {
+				if compactedIDs[e.ToID] {
+					continue // skip edges between compacted nodes
+				}
+				if err := c.relinkEdge(ctx, summaryNode.ID, e.ToID, e); err != nil {
+					return compacted, err
 				}
 			}
 			// Inbound edges: other → compacted
-			if inEdges, err := c.store.GetEdgesTo(ctx, id); err == nil {
-				for _, e := range inEdges {
-					if compactedIDs[e.FromID] {
-						continue
-					}
-					_ = c.store.CreateEdge(ctx, &storage.Edge{
-						ID:     uuid.New().String(),
-						FromID: e.FromID,
-						ToID:   summaryNode.ID,
-						Type:   e.Type,
-						Weight: e.Weight,
-					})
+			inEdges, err := c.store.GetEdgesTo(ctx, id)
+			if err != nil {
+				return compacted, fmt.Errorf("compact: list inbound edges of node %s: %w", id, err)
+			}
+			for _, e := range inEdges {
+				if compactedIDs[e.FromID] {
+					continue
+				}
+				if err := c.relinkEdge(ctx, e.FromID, summaryNode.ID, e); err != nil {
+					return compacted, err
 				}
 			}
 		}
 
 		// Archive compacted nodes
 		for _, id := range ids {
-			old, _ := c.store.GetNode(ctx, id)
-			if old != nil {
-				_ = c.store.SaveVersion(ctx, old.ID, old.Content, "compactor", "compacted into "+summaryNode.ID[:8])
-				old.Confidence = 0
-				_ = c.store.UpdateNode(ctx, old)
-				compacted++
+			old, err := c.store.GetNode(ctx, id)
+			if err != nil {
+				if errors.Is(err, storage.ErrNodeNotFound) {
+					// Node disappeared concurrently — nothing to archive.
+					slog.Warn("compact: node vanished before archival", "node_id", id)
+					continue
+				}
+				return compacted, fmt.Errorf("compact: load node %s for archival: %w", id, err)
+			}
+			if old == nil {
+				continue
 			}
+			if err := c.store.SaveVersion(ctx, old.ID, old.Content, "compactor", "compacted into "+summaryNode.ID[:8]); err != nil {
+				return compacted, fmt.Errorf("compact: save version of node %s: %w", old.ID, err)
+			}
+			old.Confidence = 0
+			if err := c.store.UpdateNode(ctx, old); err != nil {
+				return compacted, fmt.Errorf("compact: archive node %s: %w", old.ID, err)
+			}
+			compacted++
 		}
 	}
 	return compacted, nil
 }
 
+// relinkEdge transfers an edge onto the summary node. Duplicate edges are
+// benign (the link already exists) and are logged at debug level; any other
+// failure is propagated so the compaction pipeline can abort.
+func (c *Compactor) relinkEdge(ctx context.Context, fromID, toID string, orig *storage.Edge) error {
+	err := c.store.CreateEdge(ctx, &storage.Edge{
+		ID:     uuid.New().String(),
+		FromID: fromID,
+		ToID:   toID,
+		Type:   orig.Type,
+		Weight: orig.Weight,
+	})
+	if err == nil {
+		return nil
+	}
+	if errors.Is(err, storage.ErrDuplicateEdge) {
+		slog.Debug("compact: re-linked edge already exists", "from", fromID, "to", toID, "type", orig.Type)
+		return nil
+	}
+	return fmt.Errorf("compact: re-link edge %s→%s (%s): %w", fromID, toID, orig.Type, err)
+}
+
 func buildCompactSummary(typ string, contents []string) string {
 	// Take first 5 items as representative
 	limit := 5

temporal/backbone.go

@@ -10,6 +10,7 @@ package temporal
 
 import (
 	"context"
+	"log/slog"
 	"sync"
 
 	"github.com/GrayCodeAI/yaad/storage"
@@ -105,21 +106,30 @@ func (b *Backbone) recoverTail(ctx context.Context, project string) string {
 }
 
 // persistTail saves the tail node ID as a metadata node for O(1) recovery.
+// It is best-effort (often invoked from a goroutine): failures degrade tail
+// recovery to the slow scan path, so they are logged rather than propagated —
+// but never silently discarded.
 func (b *Backbone) persistTail(ctx context.Context, project, nodeID string) {
 	key := "_temporal_tail"
 	if existing, err := b.store.GetNodeByKey(ctx, key, project); err == nil && existing != nil {
-		_ = b.store.UpdateNodeContent(ctx, existing.ID, nodeID)
+		if uerr := b.store.UpdateNodeContent(ctx, existing.ID, nodeID); uerr != nil {
+			slog.Warn("temporal: failed to update tail marker (recovery will fall back to scan)",
+				"project", project, "marker_id", existing.ID, "tail_node_id", nodeID, "error", uerr)
+		}
 		return
 	}
-	_ = b.store.CreateNode(ctx, &storage.Node{
+	if cerr := b.store.CreateNode(ctx, &storage.Node{
 		ID:      uuid.New().String(),
 		Type:    "meta",
 		Content: nodeID,
 		Key:     key,
 		Project: project,
 		Scope:   "system",
 		Tier:    1,
-	})
+	}); cerr != nil {
+		slog.Warn("temporal: failed to create tail marker (recovery will fall back to scan)",
+			"project", project, "tail_node_id", nodeID, "error", cerr)
+	}
 }
 
 // Timeline returns nodes in chronological order for a project,