feat: motor stacking, auto-exclude, refined stitching

[FIrgolitsch]

Stacked PR 1/22 — review order: #115 → #97 → #98 → #99 → #100 → #101 → #108 → #106 → #107 → #87 → #116 → #110 → #111 → #40 → #112 → #113 → #117 → #118 → #120 → #121 → #122 → #123 → #124 → #125

Base: main. Retargets to main as upstream PRs merge.

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PR #98 — Motor Stacking & Refined Stitching

Adds motor-based slice stacking and the refined 3D stitching used by the new reconstruction workflow. Two commits: initial feature drop and a follow-up that smooths drift, adds a per-slice reliability flag, and tightens the auto-exclude logic.

New library modules

• linumpy/stitching/motor.py — motor-only stacking. Adds a transform_source column (motor / registered / motor+refined), a per-slice reliable flag, drift smoothing (bounded low-pass on cumulative motor z), and drift / sigma limits used to gate auto-exclude.
• linumpy/stitching/stacking.py — enhanced stacking with confidence gating, z-consistency enforcement between neighbouring slice pairs, and configurable drift limits.

New scripts

• linum_stack_motor_only.py — motor-only stacking CLI
• linum_stack_slices_motor.py — motor-first stacking with optional registration refinement, drift smoothing, rehoming-aware reset (consumes linum_detect_rehoming output from feat: utility modules, preprocessing improvements, galvo correction #97)
• linum_stitch_motor_only.py — motor-only stitch driver
• linum_stitch_3d_refined.py — refined 3D stitching (motor + registration + z-consistency)
• linum_auto_exclude_slices.py — automatic slice exclusion based on drift / sigma / reliability

Updated scripts

• linum_stack_slices_3d.py, linum_stack_slices.py, linum_stitch_3d.py — integrated with the new modules
• linum_align_mosaics_3d_from_shifts.py — consumes the new transform_source column

Tests

• linumpy/tests/test_stitching_motor.py, test_stitching_stacking.py