Side-channel analysis has been proven effective at detecting hardware Trojans in integrated circuits (ICs). However, most detection techniques rely on large external probes and antennas for data collection and require a long measurement time to detect Trojans. Such limitations make these techniques impractical for run-time deployment and ineffective in detecting small Trojans with subtle side-channel signatures. To overcome these challenges, we propose a Programmable Sensor Array (PSA) for run-time hardware Trojan detection, localization, and identification. PSA is a tampering-resilient integrated on-chip magnetic field sensor array that can be re-programmed to change the sensors' shape, size, and location. Using PSA, EM side-channel measurement results collected from sensors at different locations on an IC can be analyzed to localize and identify the Trojan. The PSA has better performance than conventional external magnetic probes and state-of-the-art on-chip single-coil magnetic field sensors. We fabricated an AES-128 test chip with four AES Hardware Trojans. They were successfully detected, located, and identified with the proposed on-chip PSA within 10 milliseconds using our proposed cross-domain analysis.