[T1.1] Repo structure cleanup SPEC baseline

[DeliciousBuding]

Summary

• Adds the repo-structure-doc-tooling-cleanup SPEC, analysis, task breakdown, dependency graph, milestones, and MASTER progress index.
• Records the reference-graph findings that change the cleanup strategy: external docs is dirty, archive migration must use an isolated receiver, scripts/tests must be wrapper-first, and Desktop readiness script paths are contract-sensitive.
• Creates GitHub tracking resources for [T1.1] Finalize SPEC docs, GitHub tracking, and reference graph #360-[T5.1] Run acceptance and archive cleanup SPEC #367 and milestone refactor(repo): 扁平化仓库结构 #12-M1: 客户端 #16.

Task Issue

closes #360

Tests

• pwsh ./scripts/verify-doc-ssot.ps1 -> doc SSOT ok
• pwsh ./scripts/verify-project-skills.ps1 -> project skill whitelist ok
• pwsh ./scripts/verify-real-e2e-contract.ps1 -> real E2E contract ok
• python -c "import yaml, pathlib; yaml.safe_load(pathlib.Path('api/openapi.yaml').read_text(encoding='utf-8')); print('yaml ok')" -> yaml ok
• git diff --check HEAD -> exit 0
• git diff --cached --check -> exit 0 before amend

Boundaries

• Planning/tracking only; no archive, ADR, script, test, or root artifact deletion in this PR.
• No external TokenDance docs repo write in this PR.

[coderabbitai]

Important

Review skipped

Auto reviews are disabled on base/target branches other than the default branch.

Please check the settings in the CodeRabbit UI or the .coderabbit.yaml file in this repository. To trigger a single review, invoke the @coderabbitai review command.

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro Plus

Run ID: facdc65f-7a7f-4f93-aedb-00b9a79d9bb4

You can disable this status message by setting the reviews.review_status to false in the CodeRabbit configuration file.

Use the checkbox below for a quick retry:

• 🔍 Trigger review

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch docs/repo-structure-doc-tooling-cleanup

---

_{Comment @coderabbitai help to get the list of available commands.}