fix(orphan): handle prefixes with dots in orphan detection (GH#508)

The orphan detection was incorrectly flagging issues with dots in their
prefix (e.g., "my.project-abc123") as orphans because it was looking for
any dot in the ID, treating everything before the first dot as the
parent ID.

The fix:
- Add IsHierarchicalID() helper that correctly detects hierarchical IDs
  by checking if the ID ends with .{digits} (e.g., "bd-abc.1")
- Update SQL query in orphan detection migration to use GLOB patterns
  that only match IDs ending with numeric suffixes
- Update all Go code that checks for hierarchical IDs to use the new
  helper function

Test cases added:
- Unit tests for IsHierarchicalID covering normal, dotted prefix, and
  edge cases
- Integration test verifying dotted prefixes do not trigger false
  positives

Fixes: #508

internal/storage/sqlite/migrations_test.go

@@ -620,4 +620,83 @@ func TestMigrateOrphanDetection(t *testing.T) {
 			}
 		}
 	})
+
+	// GH#508: Verify that prefixes with dots don't trigger false positives
+	t.Run("prefix with dots is not flagged as orphan", func(t *testing.T) {
+		store, cleanup := setupTestDB(t)
+		defer cleanup()
+		db := store.db
+
+		// Override the prefix for this test
+		_, err := db.Exec(`UPDATE config SET value = 'my.project' WHERE key = 'issue_prefix'`)
+		if err != nil {
+			t.Fatalf("failed to update prefix: %v", err)
+		}
+
+		// Insert issues with dotted prefix directly (bypassing prefix validation)
+		testCases := []struct {
+			id          string
+			expectOrphan bool
+		}{
+			// These should NOT be flagged as orphans (dots in prefix)
+			{"my.project-abc123", false},
+			{"my.project-xyz789", false},
+			{"com.example.app-issue1", false},
+
+			// This SHOULD be flagged as orphan (hierarchical, parent doesn't exist)
+			{"my.project-missing.1", true},
+		}
+
+		for _, tc := range testCases {
+			_, err := db.Exec(`
+				INSERT INTO issues (id, title, status, priority, issue_type, created_at, updated_at)
+				VALUES (?, ?, ?, ?, ?, datetime('now'), datetime('now'))
+			`, tc.id, "Test Issue", "open", 1, "task")
+			if err != nil {
+				t.Fatalf("failed to insert %s: %v", tc.id, err)
+			}
+		}
+
+		// Query for orphans using the same logic as the migration
+		rows, err := db.Query(`
+			SELECT id
+			FROM issues
+			WHERE
+			  (id GLOB '*.[0-9]' OR id GLOB '*.[0-9][0-9]' OR id GLOB '*.[0-9][0-9][0-9]' OR id GLOB '*.[0-9][0-9][0-9][0-9]')
+			  AND rtrim(rtrim(id, '0123456789'), '.') NOT IN (SELECT id FROM issues)
+			ORDER BY id
+		`)
+		if err != nil {
+			t.Fatalf("query failed: %v", err)
+		}
+		defer rows.Close()
+
+		var orphans []string
+		for rows.Next() {
+			var id string
+			if err := rows.Scan(&id); err != nil {
+				t.Fatalf("scan failed: %v", err)
+			}
+			orphans = append(orphans, id)
+		}
+
+		// Verify only the expected orphan is detected
+		if len(orphans) != 1 {
+			t.Errorf("expected 1 orphan, got %d: %v", len(orphans), orphans)
+		}
+		if len(orphans) == 1 && orphans[0] != "my.project-missing.1" {
+			t.Errorf("expected orphan 'my.project-missing.1', got %q", orphans[0])
+		}
+
+		// Verify non-hierarchical dotted IDs are NOT flagged
+		for _, tc := range testCases {
+			if !tc.expectOrphan {
+				for _, orphan := range orphans {
+					if orphan == tc.id {
+						t.Errorf("false positive: %s was incorrectly flagged as orphan", tc.id)
+					}
+				}
+			}
+		}
+	})
 }