feat: RepoDiagnoser — clone & analyse any public Git repo via CLI or Python API

[Copilot]

Implements the RepoDiagnoser tool as specified, composing existing toolkit primitives rather than reimplementing them. Also fixes a pre-existing syntax error in cli.py that made the file unparseable.

New package: tools/repo_diagnoser/

• diagnoser.py — RepoDiagnoser class with clone_repo(), analyze(), and diagnose() (clone + analyze in one call). Reuses:
  • toolkit/oe/hasher.hash_file() for per-file SHA-256
  • toolkit/oe/merkle.MerkleTree for fingerprint + inclusion proofs
  • minimal_ai_ide/repository_scanner.RepositoryScanner for structural scan
• cli_diagnose.py — standalone entry point (python -m tools.repo_diagnoser.cli_diagnose)
• README.md — usage docs and integration table

from tools.repo_diagnoser import RepoDiagnoser

result = RepoDiagnoser().diagnose("https://github.com/owner/repo")
print(result["merkle_root"])                        # integrity fingerprint
proof = result["tree"].get_inclusion_proof("README.md")
result["tree"].export_proofs_jsonl(Path("proofs.jsonl"))

cli.py — diagnose subcommand

Adds cmd_diagnose and wires it into main() alongside existing subcommands. Follows the --apply dry-run-by-default pattern. Accepts --url or --local (mutually exclusive), --depth, --ref, --clone-dir, --out-proofs, --json.

# dry-run (no clone)
python cli.py diagnose --url https://github.com/owner/repo

# clone, analyse, export proofs
python cli.py diagnose --url https://github.com/owner/repo --depth 0 --ref main \
    --out-proofs proofs.jsonl --apply

cli.py — pre-existing syntax fixes

The file had two main() bodies merged together with a missing """ opening a bare text block and orphaned argparse.ArgumentParser() kwargs floating in the function body — both causing SyntaxError. Fixed and unified the dispatch to cover all 9 subcommands.

.github/copilot-instructions.md

New file telling Copilot agent mode about the repo's tooling, the diagnose command, and coding conventions (dry-run contract, no bare except, reuse toolkit primitives).

[devin-ai-integration]

Closing as stale (Stage D housekeeping).

This Copilot draft has been open without progress and is superseded by:

• PR PR #139: Universal Aerospace Floor + 35 Polymath Domains + Standards + Upgrades #139 (Universal Aerospace Floor + 35 polymath domains) — landed 2026-04-18
• PR Kimi/pr139 aerospace floor polymath domains #140 (Kimi aerospace-floor polymath follow-up) — landed 2026-04-19
• PR audit(stage-a): hashed investigative taxonomy + gap-analysis JSONL #141 (hashed investigative taxonomy) — landed 2026-04-19
• PR cleanup(stage-b): eliminate float() calls and stubs in production code #142 (production-code cleanup: float() / stubs) — landed 2026-04-19
• PR stage-c: enforce YAML frontmatter on all Markdown files #143 (Markdown frontmatter enforcement) — in review

If the underlying work here is still wanted, re-open a fresh PR rebased on current main; the old branches have substantial drift and CI has moved on. Closing now so the open-PR list reflects reality.