docs: reorganize README and consolidate command catalog

[MitchellX]

Motivation

• Consolidate duplicated command references into a single, searchable README so commands can be found with Ctrl + F without opening subdirectories.
• Provide one authoritative catalog of how to run every script in the repo and a logical grouping to improve discoverability.
• Preserve existing file layout to avoid breaking historical paths while offering a clear next-step for optional physical reorganization.

Description

• Rewrote README.md into a consolidated command handbook that replaces fragmented and duplicated sections with a single structured document.
• Deduplicated overlapping Git/Linux/Python command blocks and unified them into a single high-frequency commands section.
• Added a comprehensive “All script run commands” section that enumerates runnable .py and .sh files with usage examples for argument-based scripts.
• Added a keyword quick-index for fast lookup and kept the change documentation-only without moving or renaming files.

Testing

• Verified README.md content and structure using sed -n and nl -ba to print and inspect sections, and the expected headings and blocks are present.
• Confirmed the repository change scope with git status --short and validated only README.md was modified.
• Cross-checked repository file list with rg --files to ensure scripts referenced by the README exist in the repo.

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Codex Task

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Point gdrive sample to a writable existing path

The example command uses ./datasets/datasets.zip, but this repository does not contain a datasets/ directory by default, so users running the README command on a fresh clone will hit FileNotFoundError when gdrive_downloader.py opens the destination path (it does not create parent directories). Please either add a preceding mkdir -p ./datasets step or change the sample destination to an existing path like ./datasets.zip.

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[MitchellX]

@copilot review this PR

[Copilot]

@copilot review this PR

PR Review

What this PR does

Two commits:

1. abdf215 — Rewrites README.md from ~1 100 lines into a 438-line consolidated command handbook.
2. fd3de00 — Physically moves root-level .py / .sh / .md files into scripts/python/, scripts/shell/, and docs/notes/.

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✅ What looks good

Area	Notes
Script run commands	All sys.argv-based scripts (align_ssim_*, demo_FSANET_*) have the correct positional-argument signatures in Section 3. Verified against the source.
doas-install.sh flags	-h, -e, --scm, -y listed in Section 3.5 match the script's usage() exactly.
download_gdrive.py	Correctly noted as a module (from download_gdrive import …) rather than a standalone script.
Deduplication	Overlapping Git / Linux / Python command blocks consolidated into clean, copy-pasteable sections.
Keyword index	Section 4 is handy for Ctrl+F when you know a keyword but not the section.
File layout	The scripts/ + docs/notes/ hierarchy is a clear improvement over everything sitting at the root.

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⚠️ Issues to consider

1. README is now primarily in Chinese
All section headings, inline comments, and descriptive prose are in Chinese (e.g., ## 1. 仓库结构（按功能重组）, > 去重后保留一份，可直接复制。). If the repo is meant to be accessible to a broader audience, switching the prose/headers to English (or providing bilingual headings) would be worth doing.

2. File moves break old paths
The physical move is listed as a feature, but the PR description says "preserve existing file layout to avoid breaking historical paths" — that's contradicted by the actual commit: PIL_draw.py → scripts/python/PIL_draw.py, run.sh → scripts/shell/run.sh, etc. Any external code, CI config, or documentation referencing the old root-level paths will break. Consider adding a note about this or keeping backward-compat symlinks if callers exist.

3. A few content omissions
Original README had detailed instructions on:

• Resolving push conflicts (git config pull.rebase false / git reset --hard HEAD~1)
• Git submodule / fork cooperation workflow
• Remote Jupyter / PyCharm setup

These were removed without being folded into the new structure. If they were intentional cuts, that's fine — just flagging in case they were lost in the rewrite.

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Summary

The core goal (searchable, deduplicated README + cleaner directory layout) is achieved. The main action items are: (1) decide on README language, and (2) document or mitigate the path-breaking effect of the file moves.