fix: Make child→parent dep fix opt-in with --fix-child-parent (bd-cuek)

GH#740: bd doctor --fix was auto-removing child→parent dependencies,
calling them an 'anti-pattern'. While these often indicate modeling
mistakes (deadlock), they may be intentional in some workflows.

Changes:
- Add --fix-child-parent flag (required to remove child→parent deps)
- Remove ChildParentDependencies from default --fix set
- Update warning message to reference new flag
- Update comments to reflect more nuanced understanding

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

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

cmd/bd/doctor.go

@@ -48,13 +48,14 @@ type doctorResult struct {
 }
 
 var (
-	doctorFix         bool
-	doctorYes         bool
-	doctorInteractive bool   // bd-3xl: per-fix confirmation mode
-	doctorDryRun      bool   // bd-a5z: preview fixes without applying
-	doctorOutput      string // bd-9cc: export diagnostics to file
-	perfMode          bool
-	checkHealthMode   bool
+	doctorFix            bool
+	doctorYes            bool
+	doctorInteractive    bool   // bd-3xl: per-fix confirmation mode
+	doctorDryRun         bool   // bd-a5z: preview fixes without applying
+	doctorOutput         string // bd-9cc: export diagnostics to file
+	doctorFixChildParent bool   // bd-cuek: opt-in fix for child→parent deps
+	perfMode             bool
+	checkHealthMode      bool
 )
 
 // ConfigKeyHintsDoctor is the config key for suppressing doctor hints
@@ -104,6 +105,7 @@ Examples:
   bd doctor --fix        # Automatically fix issues (with confirmation)
   bd doctor --fix --yes  # Automatically fix issues (no confirmation)
   bd doctor --fix -i     # Confirm each fix individually (bd-3xl)
+  bd doctor --fix --fix-child-parent  # Also fix child→parent deps (opt-in)
   bd doctor --dry-run    # Preview what --fix would do without making changes
   bd doctor --perf       # Performance diagnostics
   bd doctor --output diagnostics.json  # Export diagnostics to file`,
@@ -182,6 +184,7 @@ func init() {
 	doctorCmd.Flags().BoolVarP(&doctorYes, "yes", "y", false, "Skip confirmation prompt (for non-interactive use)")
 	doctorCmd.Flags().BoolVarP(&doctorInteractive, "interactive", "i", false, "Confirm each fix individually (bd-3xl)")
 	doctorCmd.Flags().BoolVar(&doctorDryRun, "dry-run", false, "Preview fixes without making changes (bd-a5z)")
+	doctorCmd.Flags().BoolVar(&doctorFixChildParent, "fix-child-parent", false, "Remove child→parent dependencies (opt-in, bd-cuek)")
 }
 
 // previewFixes shows what would be fixed without applying changes (bd-a5z)
@@ -401,6 +404,11 @@ func applyFixList(path string, fixes []doctorCheck) {
 		case "Orphaned Dependencies":
 			err = fix.OrphanedDependencies(path)
 		case "Child-Parent Dependencies":
+			// bd-cuek: Requires explicit opt-in flag (destructive, may remove intentional deps)
+			if !doctorFixChildParent {
+				fmt.Printf("  ⚠ Child→parent deps require explicit opt-in: bd doctor --fix --fix-child-parent\n")
+				continue
+			}
 			err = fix.ChildParentDependencies(path)
 		case "Duplicate Issues":
 			// No auto-fix: duplicates require user review

cmd/bd/doctor/fix/validation.go

@@ -162,8 +162,9 @@ func OrphanedDependencies(path string) error {
 	return nil
 }
 
-// ChildParentDependencies removes child→parent dependencies (anti-pattern).
-// This fixes the deadlock where children depend on their parent epic.
+// ChildParentDependencies removes child→parent blocking dependencies.
+// These often indicate a modeling mistake (deadlock: child waits for parent, parent waits for children).
+// Requires explicit opt-in via --fix-child-parent flag since some workflows may use these intentionally.
 func ChildParentDependencies(path string) error {
 	if err := validateBeadsWorkspace(path); err != nil {
 		return err

cmd/bd/doctor/validation.go

@@ -308,8 +308,9 @@ func CheckTestPollution(path string) DoctorCheck {
 	}
 }
 
-// CheckChildParentDependencies detects the child→parent dependency anti-pattern.
-// This creates a deadlock: child can't start (parent open), parent can't close (children not done).
+// CheckChildParentDependencies detects child→parent blocking dependencies.
+// These often indicate a modeling mistake (deadlock: child waits for parent, parent waits for children).
+// However, they may be intentional in some workflows, so removal requires explicit opt-in.
 func CheckChildParentDependencies(path string) DoctorCheck {
 	beadsDir := filepath.Join(path, ".beads")
 	dbPath := filepath.Join(beadsDir, beads.CanonicalDatabaseName)
@@ -374,9 +375,9 @@ func CheckChildParentDependencies(path string) DoctorCheck {
 	return DoctorCheck{
 		Name:     "Child-Parent Dependencies",
 		Status:   "warning",
-		Message:  fmt.Sprintf("%d child→parent dependency anti-pattern(s) detected", len(badDeps)),
+		Message:  fmt.Sprintf("%d child→parent dependency detected (may cause deadlock)", len(badDeps)),
 		Detail:   detail,
-		Fix:      "Run 'bd doctor --fix' to remove child→parent dependencies",
+		Fix:      "Run 'bd doctor --fix --fix-child-parent' to remove (if unintentional)",
 		Category: CategoryMetadata,
 	}
 }