[Docs] Overview of SPIMquant Workflows and Output Types

[Copilot]

Adds the missing narrative documentation for SPIMquant's pipeline — previously most reference pages were stubs with <!-- TODO --> placeholders.

New: docs/reference/workflow_overview.md

"How SPIMquant Works" end-to-end narrative. Covers all 8 major stages (import → masking → registration → segmentation → region props → quantification → heatmaps → group stats) plus optional vessel/patch/MRI stages. Each stage includes:

• A Mermaid flow diagram
• Explanation of what happens and why
• Table of key output files

Updated: docs/reference/outputs.md

Full output file reference replacing the stub:

• Directory layout diagram
• Per-stage BIDS path patterns with wildcard explanations
• Column definitions for TSV/Parquet tables
• File format summary table (.nii.gz, .ozx, .parquet, .tsv, .html, etc.)

Updated: docs/reference/rules.md

Full Snakemake rules reference replacing the stub — all rules grouped by .smk file with inputs, outputs, tools, and resource notes.

Updated: docs/howto/segmentation.md

Practical segmentation guide replacing the stub — covers bias correction methods, threshold vs otsu+k3i2, object filtering config, and the 0/100 mask scaling convention.

Navigation / cross-links

• mkdocs.yml: adds Workflow Overview, Output Files, Workflow Rules, DAG Visualization to Reference nav; Segmentation Methods to How-To Guides
• docs/index.md: adds Quick Links to the new overview and output pages
• docs/workflow_visualization.md: adds tip admonition pointing to the new narrative overview

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[akhanf]

closing this since out of date with naming refactor