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The operator frames a good spot, confirms the two DC levels the detector reads there, and the rig then measures its own tilt: step 1.5 mm either side on X and then on Y, and tilt the platform until those levels come back. The correction that fixes an offset point is the correction that levels the whole travel — height error and tilt effect are both proportional to the offset — so the procedure ends by applying it and leaving it applied. Both directions are measured from the same starting tilt and averaged, which makes their disagreement a flatness read-out rather than something averaged away silently. core/auto_align.py holds the geometry and the search, Qt-free. The three T-axes' azimuths are the whole geometry: T1 lies along +X so it alone tilts along X, and T0/T2 move as an equal-and-opposite pair to tilt along Y without touching X (tilt_response derives that, and the tests pin it — an axis map that drifts would still converge, on the wrong axis). The search is a secant null on the split-detector difference: probe once to learn what a microstep is worth, sign included, then step at the null. It refuses to servo on a scope that has not re-triggered, escalates a probe that reads as no response before calling an axis dead, and stops at a per-axis travel limit. gui/align_bridge.py runs it on a worker thread; stopping is a threading.Event rather than a queued command, because the worker is inside a long handler for the whole run. The camera window carries the button and the progress window, and locks the scan panel and the jog pads while a run owns the stage. Adds immediate MEAN measurements and an acquisition count to the scope driver, and read_bias_mv to core/scope_inspect — the one scalar the inspection state was missing. KNOWN_ISSUES.md records what only the rig can settle: the probe step, the travel limit, the hold current, and whether the piston the X phase applies alongside its tilt matters. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>