docs: add comprehensive project documentation

[FIrgolitsch]

PR #96 — Documentation

Adds and then refreshes the project's long-form documentation so it matches the implementation shipped by PRs #87 and #97–#104.

Files (12)

• docs/PIPELINE_OVERVIEW.md — end-to-end pipeline description
• docs/PIPELINE_PERFORMANCE_ANALYSIS.md — benchmarks and tuning notes
• docs/LIBRARY_MODULES.md — library module reference
• docs/SCRIPTS_REFERENCE.md — CLI scripts reference (every linum_* entry point)
• docs/GPU_ACCELERATION.md — GPU acceleration guide (CuPy / JAX, --use_gpu flag, device detection)
• docs/NEXTFLOW_WORKFLOWS.md — preproc and 3D-reconstruction workflow docs
• docs/MOSAIC_GRID_FORMAT.md — mosaic-grid OME-Zarr layout
• docs/SHIFTS_FILE_FORMAT.md — shifts CSV/JSON schema
• docs/SLICE_CONFIG_FEATURE.md — slice_config.csv schema and lifecycle
• docs/SLICE_INTERPOLATION_FEATURE.md — physical model, zmorph parameters, failure handling
• docs/RECONSTRUCTION_DIAGNOSTICS.md — diagnostics scripts and outputs
• docs/AI_DOCUMENTATION_INDEX.md — index of all docs

Commits

1. docs: add comprehensive project documentation — initial draft
2. docs: update pipeline, GPU, workflow, and script references — synchronises content with the final state of PRs feat: slice interpolation for missing sections (z-morph) #87/feat: utility modules, preprocessing improvements, galvo correction #97–feat: add manual-alignment export, refinement, and global-transform tools #104 (notably SLICE_INTERPOLATION_FEATURE.md, SCRIPTS_REFERENCE.md, NEXTFLOW_WORKFLOWS.md, SLICE_CONFIG_FEATURE.md)

Dependencies

• Stacked on PR build: migrate to uv, add ruff/ty, format all files #95 (build tooling)
• Content describes features shipped by PRs feat: slice interpolation for missing sections (z-morph) #87, feat: utility modules, preprocessing improvements, galvo correction #97–feat: add manual-alignment export, refinement, and global-transform tools #104; safe to merge in any order relative to them since it's pure docs