refactor: Split monolithic sqlite.go into focused files (bd-0a43)

Split internal/storage/sqlite/sqlite.go (1050 lines) into focused files
for better maintainability and code discovery:

- store.go (306 lines): SQLiteStorage struct, New() constructor,
  initialization logic, and database utilities (Close, Path, IsClosed,
  UnderlyingDB, UnderlyingConn, CheckpointWAL)

- queries.go (1173 lines): Issue CRUD operations including CreateIssue,
  GetIssue, GetIssueByExternalRef, UpdateIssue, UpdateIssueID,
  CloseIssue, DeleteIssue, DeleteIssues, SearchIssues with all helpers

- config.go (95 lines): Configuration and metadata management (SetConfig,
  GetConfig, GetAllConfig, DeleteConfig, SetMetadata, GetMetadata) plus
  OrphanHandling type definitions

- comments.go (83 lines): Comment operations (AddIssueComment,
  GetIssueComments)

- sqlite.go (31 lines): Package documentation explaining file organization

Additional changes:
- Removed duplicate OrphanHandling definition from ids.go (was causing
  build error with new config.go)

Impact:
- Zero functional changes, all tests pass (2.6s runtime)
- Improved code discovery: easy to locate specific functionality
- Better maintainability: related code grouped logically
- Reduced cognitive load: smaller, focused files

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

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

internal/storage/sqlite/comments.go

@@ -0,0 +1,83 @@
+package sqlite
+
+import (
+	"context"
+	"fmt"
+
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// AddIssueComment adds a comment to an issue
+func (s *SQLiteStorage) AddIssueComment(ctx context.Context, issueID, author, text string) (*types.Comment, error) {
+	// Verify issue exists
+	var exists bool
+	err := s.db.QueryRowContext(ctx, `SELECT EXISTS(SELECT 1 FROM issues WHERE id = ?)`, issueID).Scan(&exists)
+	if err != nil {
+		return nil, fmt.Errorf("failed to check issue existence: %w", err)
+	}
+	if !exists {
+		return nil, fmt.Errorf("issue %s not found", issueID)
+	}
+
+	// Insert comment
+	result, err := s.db.ExecContext(ctx, `
+		INSERT INTO comments (issue_id, author, text, created_at)
+		VALUES (?, ?, ?, CURRENT_TIMESTAMP)
+	`, issueID, author, text)
+	if err != nil {
+		return nil, fmt.Errorf("failed to insert comment: %w", err)
+	}
+
+	// Get the inserted comment ID
+	commentID, err := result.LastInsertId()
+	if err != nil {
+		return nil, fmt.Errorf("failed to get comment ID: %w", err)
+	}
+
+	// Fetch the complete comment
+	comment := &types.Comment{}
+	err = s.db.QueryRowContext(ctx, `
+		SELECT id, issue_id, author, text, created_at
+		FROM comments WHERE id = ?
+	`, commentID).Scan(&comment.ID, &comment.IssueID, &comment.Author, &comment.Text, &comment.CreatedAt)
+	if err != nil {
+		return nil, fmt.Errorf("failed to fetch comment: %w", err)
+	}
+
+	// Mark issue as dirty for JSONL export
+	if err := s.MarkIssueDirty(ctx, issueID); err != nil {
+		return nil, fmt.Errorf("failed to mark issue dirty: %w", err)
+	}
+
+	return comment, nil
+}
+
+// GetIssueComments retrieves all comments for an issue
+func (s *SQLiteStorage) GetIssueComments(ctx context.Context, issueID string) ([]*types.Comment, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT id, issue_id, author, text, created_at
+		FROM comments
+		WHERE issue_id = ?
+		ORDER BY created_at ASC
+	`, issueID)
+	if err != nil {
+		return nil, fmt.Errorf("failed to query comments: %w", err)
+	}
+	defer func() { _ = rows.Close() }()
+
+	var comments []*types.Comment
+	for rows.Next() {
+		comment := &types.Comment{}
+		err := rows.Scan(&comment.ID, &comment.IssueID, &comment.Author, &comment.Text, &comment.CreatedAt)
+		if err != nil {
+			return nil, fmt.Errorf("failed to scan comment: %w", err)
+		}
+		comments = append(comments, comment)
+	}
+
+	if err := rows.Err(); err != nil {
+		return nil, fmt.Errorf("error iterating comments: %w", err)
+	}
+
+	return comments, nil
+}