Fix critical bugs: bd-169, bd-28, bd-393

- bd-169: Add -q/--quiet flag to bd init command
- bd-28: Improve error handling in RemoveDependency
  - Now checks RowsAffected and returns error if dependency doesn't exist
  - New removeDependencyIfExists() helper for collision remapping
- bd-393: CRITICAL - Fix auto-import skipping collisions
  - Auto-import was LOSING work from other workers
  - Now automatically remaps collisions to new IDs
  - Calls RemapCollisions() instead of skipping

All tests pass.

Amp-Thread-ID: https://ampcode.com/threads/T-cba86837-28db-47ce-94eb-67fade82376a
Co-authored-by: Amp <amp@ampcode.com>

internal/storage/sqlite/collision.go

@@ -466,11 +466,10 @@ func updateDependencyReferences(ctx context.Context, s *SQLiteStorage, idMapping
 
 	// Phase 2: Apply all collected changes
 	for _, update := range updates {
-		// Remove old dependency
-		if err := s.RemoveDependency(ctx, update.oldIssueID, update.oldDependsOnID, "import-remap"); err != nil {
-			// If the dependency doesn't exist (e.g., already removed), that's okay
-			// This can happen if both IssueID and DependsOnID were remapped
-			continue
+		// Remove old dependency - use RemoveDependencyIfExists which doesn't error on missing deps
+		if err := s.removeDependencyIfExists(ctx, update.oldIssueID, update.oldDependsOnID, "import-remap"); err != nil {
+			return fmt.Errorf("failed to remove old dependency %s -> %s: %w",
+				update.oldIssueID, update.oldDependsOnID, err)
 		}
 
 		// Add new dependency with updated IDs

internal/storage/sqlite/dependencies.go

@@ -271,13 +271,65 @@ func (s *SQLiteStorage) RemoveDependency(ctx context.Context, issueID, dependsOn
 	}
 	defer tx.Rollback()
 
-	_, err = tx.ExecContext(ctx, `
+	result, err := tx.ExecContext(ctx, `
 		DELETE FROM dependencies WHERE issue_id = ? AND depends_on_id = ?
 	`, issueID, dependsOnID)
 	if err != nil {
 		return fmt.Errorf("failed to remove dependency: %w", err)
 	}
 
+	// Check if dependency existed
+	rowsAffected, err := result.RowsAffected()
+	if err != nil {
+		return fmt.Errorf("failed to check rows affected: %w", err)
+	}
+	if rowsAffected == 0 {
+		return fmt.Errorf("dependency from %s to %s does not exist", issueID, dependsOnID)
+	}
+
+	_, err = tx.ExecContext(ctx, `
+		INSERT INTO events (issue_id, event_type, actor, comment)
+		VALUES (?, ?, ?, ?)
+	`, issueID, types.EventDependencyRemoved, actor,
+		fmt.Sprintf("Removed dependency on %s", dependsOnID))
+	if err != nil {
+		return fmt.Errorf("failed to record event: %w", err)
+	}
+
+	// Mark both issues as dirty for incremental export
+	if err := markIssuesDirtyTx(ctx, tx, []string{issueID, dependsOnID}); err != nil {
+		return err
+	}
+
+	return tx.Commit()
+}
+
+// removeDependencyIfExists removes a dependency, returning nil if it doesn't exist
+// This is useful during remapping where dependencies may have been already removed
+func (s *SQLiteStorage) removeDependencyIfExists(ctx context.Context, issueID, dependsOnID string, actor string) error {
+	tx, err := s.db.BeginTx(ctx, nil)
+	if err != nil {
+		return fmt.Errorf("failed to begin transaction: %w", err)
+	}
+	defer tx.Rollback()
+
+	result, err := tx.ExecContext(ctx, `
+		DELETE FROM dependencies WHERE issue_id = ? AND depends_on_id = ?
+	`, issueID, dependsOnID)
+	if err != nil {
+		return fmt.Errorf("failed to remove dependency: %w", err)
+	}
+
+	// Check if dependency existed - if not, that's okay, just skip the event
+	rowsAffected, err := result.RowsAffected()
+	if err != nil {
+		return fmt.Errorf("failed to check rows affected: %w", err)
+	}
+	if rowsAffected == 0 {
+		// Dependency didn't exist, nothing to do
+		return nil
+	}
+
 	_, err = tx.ExecContext(ctx, `
 		INSERT INTO events (issue_id, event_type, actor, comment)
 		VALUES (?, ?, ?, ?)