Fix phases timing out at 60s during plug calls

Long-running hardware operations — thermal soaks, firmware flashes, slow measurements — were killed after exactly one minute, even when the phase allowed more time.

• Fixed plug method calls dying at 60 seconds: they now run for as long as their phase allows, with no time limit when the phase has none
• Improved timeout errors to name the interrupted plug method instead of a bare "timed out"
• Documented the phase timeout field: duration syntax, bounds, and how the deadline covers plug calls and operator prompts