From the PF3 User Guide
8.8.1 Additional Ground Control Monitoring
PF3 also monitors your taxi to/from the runway to ensure you don't enter an active runway without clearance to do so. As in the real world you should not cross any runway unless cleared to do so. With PF3, when reaching a runway intersection, ATC will either clear you to cross or tell you to ‘Hold for traffic’
If you reach a runway intersection and hear nothing from ATC you should HOLD SHORT of the runway! You may then request clearance to continue your taxi by hitting hotkey #0 (zero), but you must be stationary and with TGS ‘active’ for this request to work.