Add pipeline diagnostics, registration analysis, and quality reporting scripts

[FIrgolitsch]

Summary

A collection of standalone scripts for inspecting, diagnosing, and reporting on any stage of the reconstruction pipeline. None of these scripts are required for the core pipeline — they are investigative and QC tools.

Diagnostics

• linum_diagnose_pipeline.py (~1200 lines) — checks directory layout, file integrity, and common issues across the full pipeline
• linum_diagnose_reconstruction.py — targeted reconstruction diagnostics

Quality Assessment

• linum_assess_slice_quality.py — CPU sharpness/contrast/SNR per slice
• linum_assess_slice_quality_gpu.py — GPU-accelerated version

Analysis

• linum_analyze_acquisition_rotation.py — estimates acquisition rotation from metadata
• linum_analyze_registration_transforms.py — inspects estimated transforms
• linum_analyze_shifts.py — shift distribution analysis and visualisation
• linum_analyze_tile_dilation.py / linum_aggregate_dilation_analysis.py — tile dilation and expansion analysis across subjects

Reporting

• linum_generate_pipeline_report.py (~1700 lines) — generates HTML/JSON quality reports from collected pipeline metrics
• linum_generate_mosaic_aips.py — batch AIP generation for mosaic directories

Utilities

• linum_compare_stitching.py — side-by-side stitching quality comparison
• linum_normalize_z_intensity.py — Z-direction intensity normalisation
• linum_extract_pyramid_levels.py — extract specific OME-Zarr pyramid levels
• linum_screenshot_omezarr_annotated.py — annotated screenshot generation
• linum_aip_png.py — quick-export AIP to PNG
• linum_clean_raw_data.py — raw data directory cleanup and reorganisation
• linum_suggest_params.py — automated parameter suggestions from data characteristics

Dependencies

Depends on PR #85 (thread config module) and PR #86 (utils/metrics.py).

---

Merge order: Merge after PR #85 and PR #86.

[FIrgolitsch]

Closing in favour of #100 (recreated with squashed commits as part of the PR split plan refresh).