fix(doctor): Preserve parent-child dependencies in child→parent check (GH#750)

The CheckChildParentDependencies detection and ChildParentDependencies fix
were flagging ALL child→parent dependencies, including legitimate
'parent-child' type structural hierarchy relationships.

Now only blocking types (blocks, conditional-blocks, waits-for) are
detected as anti-patterns. The 'parent-child' type is a legitimate
hierarchy marker used for:
- Tracking parent-child relationships
- Transitive block propagation (if parent blocked, children blocked)
- Hierarchy visualization in external tools

Changes:
- Add type filter to SELECT queries (only blocking types)
- Add type filter to DELETE statement (preserve parent-child)
- Add regression test TestChildParentDependencies_PreservesParentChildType

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

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

cmd/bd/doctor/fix/validation.go

@@ -180,11 +180,14 @@ func ChildParentDependencies(path string) error {
 	}
 	defer db.Close()
 
-	// Find child→parent dependencies where issue_id starts with depends_on_id + "."
+	// Find child→parent BLOCKING dependencies where issue_id starts with depends_on_id + "."
+	// Only matches blocking types (blocks, conditional-blocks, waits-for) that cause deadlock.
+	// Excludes 'parent-child' type which is a legitimate structural hierarchy relationship.
 	query := `
-		SELECT d.issue_id, d.depends_on_id
+		SELECT d.issue_id, d.depends_on_id, d.type
 		FROM dependencies d
 		WHERE d.issue_id LIKE d.depends_on_id || '.%'
+		  AND d.type IN ('blocks', 'conditional-blocks', 'waits-for')
 	`
 	rows, err := db.Query(query)
 	if err != nil {
@@ -195,12 +198,13 @@ func ChildParentDependencies(path string) error {
 	type badDep struct {
 		issueID     string
 		dependsOnID string
+		depType     string
 	}
 	var badDeps []badDep
 
 	for rows.Next() {
 		var d badDep
-		if err := rows.Scan(&d.issueID, &d.dependsOnID); err == nil {
+		if err := rows.Scan(&d.issueID, &d.dependsOnID, &d.depType); err == nil {
 			badDeps = append(badDeps, d)
 		}
 	}
@@ -210,10 +214,10 @@ func ChildParentDependencies(path string) error {
 		return nil
 	}
 
-	// Delete child→parent dependencies
+	// Delete child→parent blocking dependencies (preserving parent-child type)
 	for _, d := range badDeps {
-		_, err := db.Exec("DELETE FROM dependencies WHERE issue_id = ? AND depends_on_id = ?",
+		_, err := db.Exec("DELETE FROM dependencies WHERE issue_id = ? AND depends_on_id = ? AND type = ?",
-			d.issueID, d.dependsOnID)
+			d.issueID, d.dependsOnID, d.depType)
 		if err != nil {
 			fmt.Printf("  Warning: failed to remove %s→%s: %v\n", d.issueID, d.dependsOnID, err)
 		} else {

cmd/bd/doctor/fix/validation_test.go

@@ -138,3 +138,66 @@ func TestChildParentDependencies_FixesBadDeps(t *testing.T) {
 		t.Errorf("Expected 2 dirty issues (unique issue_ids from removed deps), got %d", dirtyCount)
 	}
 }
+
+// TestChildParentDependencies_PreservesParentChildType verifies that legitimate
+// parent-child type dependencies are NOT removed (only blocking types are removed).
+// Regression test for GitHub issue #750.
+func TestChildParentDependencies_PreservesParentChildType(t *testing.T) {
+	// Set up test database with both 'blocks' and 'parent-child' type deps
+	dir := t.TempDir()
+	beadsDir := filepath.Join(dir, ".beads")
+	if err := os.MkdirAll(beadsDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	dbPath := filepath.Join(beadsDir, "beads.db")
+	db, err := openDB(dbPath)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	// Create schema with both 'blocks' (anti-pattern) and 'parent-child' (legitimate) deps
+	_, err = db.Exec(`
+		CREATE TABLE issues (id TEXT PRIMARY KEY);
+		CREATE TABLE dependencies (issue_id TEXT, depends_on_id TEXT, type TEXT);
+		CREATE TABLE dirty_issues (issue_id TEXT PRIMARY KEY);
+		INSERT INTO issues (id) VALUES ('bd-abc'), ('bd-abc.1'), ('bd-abc.2');
+		INSERT INTO dependencies (issue_id, depends_on_id, type) VALUES
+			('bd-abc.1', 'bd-abc', 'parent-child'),
+			('bd-abc.2', 'bd-abc', 'parent-child'),
+			('bd-abc.1', 'bd-abc', 'blocks');
+	`)
+	if err != nil {
+		t.Fatal(err)
+	}
+	db.Close()
+
+	// Run fix
+	err = ChildParentDependencies(dir)
+	if err != nil {
+		t.Fatalf("ChildParentDependencies failed: %v", err)
+	}
+
+	// Verify only 'blocks' type was removed, 'parent-child' preserved
+	db, _ = openDB(dbPath)
+	defer db.Close()
+
+	var blocksCount int
+	db.QueryRow("SELECT COUNT(*) FROM dependencies WHERE type = 'blocks'").Scan(&blocksCount)
+	if blocksCount != 0 {
+		t.Errorf("Expected 0 'blocks' dependencies after fix, got %d", blocksCount)
+	}
+
+	var parentChildCount int
+	db.QueryRow("SELECT COUNT(*) FROM dependencies WHERE type = 'parent-child'").Scan(&parentChildCount)
+	if parentChildCount != 2 {
+		t.Errorf("Expected 2 'parent-child' dependencies preserved, got %d", parentChildCount)
+	}
+
+	// Verify only 1 dirty issue (the one with 'blocks' dep removed)
+	var dirtyCount int
+	db.QueryRow("SELECT COUNT(*) FROM dirty_issues").Scan(&dirtyCount)
+	if dirtyCount != 1 {
+		t.Errorf("Expected 1 dirty issue, got %d", dirtyCount)
+	}
+}

cmd/bd/doctor/validation.go

@@ -333,12 +333,14 @@ func CheckChildParentDependencies(path string) DoctorCheck {
 	}
 	defer db.Close()
 
-	// Query for child→parent dependencies where issue_id starts with depends_on_id + "."
+	// Query for child→parent BLOCKING dependencies where issue_id starts with depends_on_id + "."
-	// This uses SQLite's LIKE pattern matching
+	// Only matches blocking types (blocks, conditional-blocks, waits-for) that cause deadlock.
+	// Excludes 'parent-child' type which is a legitimate structural hierarchy relationship.
 	query := `
 		SELECT d.issue_id, d.depends_on_id
 		FROM dependencies d
 		WHERE d.issue_id LIKE d.depends_on_id || '.%'
+		  AND d.type IN ('blocks', 'conditional-blocks', 'waits-for')
 	`
 	rows, err := db.Query(query)
 	if err != nil {