Phase 4: Remove deprecated edge fields from Issue struct (Decision 004)

This is the final phase of the Edge Schema Consolidation. It removes
the deprecated edge fields (RepliesTo, RelatesTo, DuplicateOf, SupersededBy)
from the Issue struct and all related code.

Changes:
- Remove edge fields from types.Issue struct
- Remove edge field scanning from queries.go and transaction.go
- Update graph_links_test.go to use dependency API exclusively
- Update relate.go to use AddDependency/RemoveDependency
- Update show.go with helper functions for thread traversal via deps
- Update mail_test.go to verify thread links via dependencies
- Add migration 022 to drop columns from issues table
- Fix cycle detection to allow bidirectional relates-to links
- Fix migration 022 to disable foreign keys before table recreation

All edge relationships now use the dependencies table exclusively.
The old Issue fields are fully removed.

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

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

internal/storage/sqlite/issues.go

@@ -15,8 +15,6 @@ func insertIssue(ctx context.Context, conn *sql.Conn, issue *types.Issue) error
 		sourceRepo = "." // Default to primary repo
 	}
 
-	// Format relates_to as JSON for storage
-	relatesTo := formatJSONStringArray(issue.RelatesTo)
 	ephemeral := 0
 	if issue.Ephemeral {
 		ephemeral = 1
@@ -28,8 +26,8 @@ func insertIssue(ctx context.Context, conn *sql.Conn, issue *types.Issue) error
 			status, priority, issue_type, assignee, estimated_minutes,
 			created_at, updated_at, closed_at, external_ref, source_repo, close_reason,
 			deleted_at, deleted_by, delete_reason, original_type,
-			sender, ephemeral, replies_to, relates_to, duplicate_of, superseded_by
-		) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+			sender, ephemeral
+		) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
 	`,
 		issue.ID, issue.ContentHash, issue.Title, issue.Description, issue.Design,
 		issue.AcceptanceCriteria, issue.Notes, issue.Status,
@@ -37,7 +35,7 @@ func insertIssue(ctx context.Context, conn *sql.Conn, issue *types.Issue) error
 		issue.EstimatedMinutes, issue.CreatedAt, issue.UpdatedAt,
 		issue.ClosedAt, issue.ExternalRef, sourceRepo, issue.CloseReason,
 		issue.DeletedAt, issue.DeletedBy, issue.DeleteReason, issue.OriginalType,
-		issue.Sender, ephemeral, issue.RepliesTo, relatesTo, issue.DuplicateOf, issue.SupersededBy,
+		issue.Sender, ephemeral,
 	)
 	if err != nil {
 		return fmt.Errorf("failed to insert issue: %w", err)
@@ -53,8 +51,8 @@ func insertIssues(ctx context.Context, conn *sql.Conn, issues []*types.Issue) er
 			status, priority, issue_type, assignee, estimated_minutes,
 			created_at, updated_at, closed_at, external_ref, source_repo, close_reason,
 			deleted_at, deleted_by, delete_reason, original_type,
-			sender, ephemeral, replies_to, relates_to, duplicate_of, superseded_by
-		) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+			sender, ephemeral
+		) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
 	`)
 	if err != nil {
 		return fmt.Errorf("failed to prepare statement: %w", err)
@@ -67,8 +65,6 @@ func insertIssues(ctx context.Context, conn *sql.Conn, issues []*types.Issue) er
 			sourceRepo = "." // Default to primary repo
 		}
 
-		// Format relates_to as JSON for storage
-		relatesTo := formatJSONStringArray(issue.RelatesTo)
 		ephemeral := 0
 		if issue.Ephemeral {
 			ephemeral = 1
@@ -81,7 +77,7 @@ func insertIssues(ctx context.Context, conn *sql.Conn, issues []*types.Issue) er
 			issue.EstimatedMinutes, issue.CreatedAt, issue.UpdatedAt,
 			issue.ClosedAt, issue.ExternalRef, sourceRepo, issue.CloseReason,
 			issue.DeletedAt, issue.DeletedBy, issue.DeleteReason, issue.OriginalType,
-			issue.Sender, ephemeral, issue.RepliesTo, relatesTo, issue.DuplicateOf, issue.SupersededBy,
+			issue.Sender, ephemeral,
 		)
 		if err != nil {
 			return fmt.Errorf("failed to insert issue %s: %w", issue.ID, err)