How do you mix analog, digital, and boundary scan?

Easily. Unpowered analog testing is performed first, with unit-under-test ground isolated from instrumentation ground. Next, grounds are joined and power is applied. Powered analog testing (checking rails, etc) is performed next. All onboard and offboard boundary scan testing (including digital device testing) is performed next. Power down and ground isolation occur at the end of test. Data logging preserves measurements and test results on a per-serial number basis.

The ScanSuite test environment is intuitive. Debug and integration follow a logical progression. The hardware and software were designed to work in concert.