fix(storage): add batch ID conflict detection and fix schema indexes

- Add checkForExistingIDs function to detect duplicate IDs within batch
  and conflicts with existing database entries before insert
- Remove thread_id index creation from schema.go since thread_id column
  is added by migration 020_edge_consolidation.go

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

internal/storage/sqlite/batch_ops.go

@@ -4,6 +4,7 @@ import (
 	"context"
 	"database/sql"
 	"fmt"
+	"strings"
 	"time"
 
 	"github.com/steveyegge/beads/internal/types"
@@ -101,6 +102,57 @@ func bulkMarkDirty(ctx context.Context, conn *sql.Conn, issues []*types.Issue) e
 	return markDirtyBatch(ctx, conn, issues)
 }
 
+// checkForExistingIDs verifies that:
+// 1. There are no duplicate IDs within the batch itself
+// 2. None of the issue IDs already exist in the database
+// Returns an error if any conflicts are found, ensuring CreateIssues fails atomically
+// rather than silently skipping duplicates via INSERT OR IGNORE.
+func checkForExistingIDs(ctx context.Context, conn *sql.Conn, issues []*types.Issue) error {
+	if len(issues) == 0 {
+		return nil
+	}
+
+	// Build list of IDs to check and detect duplicates within batch
+	seenIDs := make(map[string]bool)
+	ids := make([]string, 0, len(issues))
+	for _, issue := range issues {
+		if issue.ID != "" {
+			// Check for duplicates within the batch
+			if seenIDs[issue.ID] {
+				return fmt.Errorf("duplicate issue ID within batch: %s", issue.ID)
+			}
+			seenIDs[issue.ID] = true
+			ids = append(ids, issue.ID)
+		}
+	}
+
+	if len(ids) == 0 {
+		return nil
+	}
+
+	// Check for existing IDs in database using a single query with IN clause
+	placeholders := make([]string, len(ids))
+	args := make([]interface{}, len(ids))
+	for i, id := range ids {
+		placeholders[i] = "?"
+		args[i] = id
+	}
+
+	query := fmt.Sprintf("SELECT id FROM issues WHERE id IN (%s) LIMIT 1", strings.Join(placeholders, ","))
+	var existingID string
+	err := conn.QueryRowContext(ctx, query, args...).Scan(&existingID)
+	if err == nil {
+		// Found an existing ID
+		return fmt.Errorf("issue ID %s already exists", existingID)
+	}
+	if err != sql.ErrNoRows {
+		// Unexpected error
+		return fmt.Errorf("failed to check for existing IDs: %w", err)
+	}
+
+	return nil
+}
+
 // CreateIssues creates multiple issues atomically in a single transaction.
 // This provides significant performance improvements over calling CreateIssue in a loop:
 // - Single connection acquisition
@@ -209,6 +261,11 @@ func (s *SQLiteStorage) CreateIssuesWithFullOptions(ctx context.Context, issues
 		return wrapDBError("generate batch IDs", err)
 	}
 
+	// Phase 3.5: Check for conflicts with existing IDs in database
+	if err := checkForExistingIDs(ctx, conn, issues); err != nil {
+		return err
+	}
+
 	// Phase 4: Bulk insert issues
 	if err := bulkInsertIssues(ctx, conn, issues); err != nil {
 		return wrapDBError("bulk insert issues", err)

internal/storage/sqlite/schema.go

@@ -59,8 +59,9 @@ CREATE INDEX IF NOT EXISTS idx_dependencies_issue ON dependencies(issue_id);
 CREATE INDEX IF NOT EXISTS idx_dependencies_depends_on ON dependencies(depends_on_id);
 CREATE INDEX IF NOT EXISTS idx_dependencies_depends_on_type ON dependencies(depends_on_id, type);
 CREATE INDEX IF NOT EXISTS idx_dependencies_depends_on_type_issue ON dependencies(depends_on_id, type, issue_id);
-CREATE INDEX IF NOT EXISTS idx_dependencies_thread ON dependencies(thread_id) WHERE thread_id != '';
+-- NOTE: idx_dependencies_thread and idx_dependencies_thread_type are created by
-CREATE INDEX IF NOT EXISTS idx_dependencies_thread_type ON dependencies(thread_id, type) WHERE thread_id != '';
+-- migration 020_edge_consolidation.go after adding the thread_id column.
+-- They cannot be in the schema because existing databases may not have thread_id yet.
 
 -- Labels table
 CREATE TABLE IF NOT EXISTS labels (