fix(clone): accept multiple GitHub URLs and reject unknown flags (#2703)

[ousamabenyounes]

graphify clone used to silently drop every URL past the first, which is the exact multi-repo workflow issue #2703 asks about. It now clones each URL in turn and prints each destination path; unknown flags are rejected with a usage message, and --out is refused with multiple URLs to keep destinations unambiguous.

Test verification (RED → GREEN)

With the fix reverted, the new test fails (RED):

            ],
        )
>       with pytest.raises(SystemExit) as exc:
             ^^^^^^^^^^^^^^^^^^^^^^^^^
E       Failed: DID NOT RAISE <class 'SystemExit'>

tests/test_clone_cli.py:94: Failed
----------------------------- Captured stdout call -----------------------------
/tmp/fake/bar
_______________________ test_clone_rejects_unknown_flag ________________________

monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x78e8b1661480>
capsys = <_pytest.capture.CaptureFixture object at 0x78e8b1763360>

    def test_clone_rejects_unknown_flag(monkeypatch, capsys):
        _stub_clone(monkeypatch)
        monkeypatch.setattr(
            sys,
            "argv",
            ["graphify", "clone", "https://github.com/foo/bar", "--nope"],
        )
>       with pytest.raises(SystemExit) as exc:
             ^^^^^^^^^^^^^^^^^^^^^^^^^
E       Failed: DID NOT RAISE <class 'SystemExit'>

tests/test_clone_cli.py:107: Failed
----------------------------- Captured stdout call -----------------------------
/tmp/fake/bar
=============================== warnings summary ===============================
.venv/lib/python3.13/site-packages/_hypothesis_pytestplugin.py:481
  /home/ousama/www/public/ousamabenyounes/graphify/.venv/lib/python3.13/site-packages/_hypothesis_pytestplugin.py:481: UserWarning: Skipping collection of '.hypothesis' directory - this usually means you've explicitly set the `norecursedirs` pytest config option, replacing rather than extending the default ignores.
    warnings.warn(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/test_clone_cli.py::test_clone_multiple_urls_are_all_cloned - Ass...
FAILED tests/test_clone_cli.py::test_clone_branch_flag_applies_to_all - Asser...
FAILED tests/test_clone_cli.py::test_clone_rejects_out_with_multiple_urls - F...
FAILED tests/test_clone_cli.py::test_clone_rejects_unknown_flag - Failed: DID...
==================== 4 failed, 1 passed, 1 warning in 0.32s ====================

With the fix applied, the test passes (GREEN):

Uninstalled 1 package in 1ms
Installed 1 package in 3ms
============================= test session starts ==============================
platform linux -- Python 3.13.12, pytest-9.0.3, pluggy-1.6.0 -- /home/ousama/www/public/ousamabenyounes/graphify/.venv/bin/python
cachedir: .pytest_cache
hypothesis profile 'default'
rootdir: /home/ousama/www/public/ousamabenyounes/graphify
configfile: pyproject.toml
plugins: cov-7.1.0, hypothesis-6.153.0, anyio-4.13.0
collecting ... collected 5 items

tests/test_clone_cli.py::test_clone_multiple_urls_are_all_cloned PASSED  [ 20%]
tests/test_clone_cli.py::test_clone_single_url_still_works PASSED        [ 40%]
tests/test_clone_cli.py::test_clone_branch_flag_applies_to_all PASSED    [ 60%]
tests/test_clone_cli.py::test_clone_rejects_out_with_multiple_urls PASSED [ 80%]
tests/test_clone_cli.py::test_clone_rejects_unknown_flag PASSED          [100%]

=============================== warnings summary ===============================
.venv/lib/python3.13/site-packages/_hypothesis_pytestplugin.py:481
  /home/ousama/www/public/ousamabenyounes/graphify/.venv/lib/python3.13/site-packages/_hypothesis_pytestplugin.py:481: UserWarning: Skipping collection of '.hypothesis' directory - this usually means you've explicitly set the `norecursedirs` pytest config option, replacing rather than extending the default ignores.
    warnings.warn(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
========================= 5 passed, 1 warning in 0.25s =========================

Full local suite

Command: env -u GEMINI_API_KEY -u GOOGLE_API_KEY -u OPENAI_API_KEY -u ANTHROPIC_API_KEY -u KIMI_API_KEY -u DEEPSEEK_API_KEY -u OLLAMA_HOST uv run --frozen pytest tests/ -q --tb=short && uv run --frozen python -m tools.skillgen --check && uv run --frozen python -m tools.skillgen --audit-coverage && uv run --frozen python -m tools.skillgen --schema-singleton && uv run --frozen python -m tools.skillgen --monolith-roundtrip && uv run --frozen python -m tools.skillgen --always-on-roundtrip

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=============================== warnings summary ===============================
.venv/lib/python3.13/site-packages/_hypothesis_pytestplugin.py:481
  /home/ousama/www/public/ousamabenyounes/graphify/.venv/lib/python3.13/site-packages/_hypothesis_pytestplugin.py:481: UserWarning: Skipping collection of '.hypothesis' directory - this usually means you've explicitly set the `norecursedirs` pytest config option, replacing rather than extending the default ignores.
    warnings.warn(

tests/test_serve_http.py:17
  /home/ousama/www/public/ousamabenyounes/graphify/tests/test_serve_http.py:17: StarletteDeprecationWarning: Using `httpx` with `starlette.testclient` is deprecated; install `httpx2` instead.
    from starlette.testclient import TestClient  # noqa: E402

tests/test_chunking.py::test_checkpoint_scopes_cache_writes_to_chunk_files
tests/test_chunking.py::test_out_of_scope_nodes_are_dropped_from_merged_result
  /home/ousama/www/public/ousamabenyounes/graphify/graphify/llm.py:2354: RuntimeWarning: semantic cache skipped out-of-scope source_file 'B.py'; the file was not dispatched for extraction
    _scs(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
4336 passed, 3 skipped, 4 warnings in 124.85s (0:02:04)
Uninstalled 1 package in 0.70ms
Installed 1 package in 5ms
check OK: 134 artifact(s) match committed output and expected/.
Uninstalled 1 package in 0.99ms
Installed 1 package in 4ms
audit-coverage OK: every per-host v8 heading single-homes in that host's render.
Uninstalled 1 package in 1ms
Installed 1 package in 4ms
schema-singleton OK: the file_type enum is the six-value superset everywhere.
Uninstalled 1 package in 1ms
Installed 1 package in 6ms
monolith-roundtrip OK: each monolith matches v8 modulo the enum unification.
Uninstalled 1 package in 1ms
Installed 1 package in 5ms
always-on-roundtrip OK: each always_on/*.md reproduces its former constant byte for byte.

Fix #2703

[graphify-labs]

Graphify reviewed this change.

Looks safe to merge — no coupling regressions and no blocking issues, checked against the code graph (not a self-assessment).

Formal verification. No changes could be formally verified in this run.

---

Graphify review — findings

This PR updates graphify clone to accept multiple GitHub URLs in a single invocation, looping over each and printing its local path. It also adds argument validation—unknown flags are rejected with a usage message, and --out is disallowed when more than one URL is given. Accompanying changes update the CHANGELOG, the various skill/agent reference docs to reflect the multi-URL syntax, and related tests/generated skill fixtures.

No blocking issues surfaced. 3 lower-confidence candidates did not survive cross-model review.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 495 functions depend on the 327 functions this change touches.

Health — this change adds coupling hotspots:

• worse: dispatch_command() — 7 callers, 117 callees

Verification — 495 functions in the blast radius were not formally verified this run (proofs are advisory here).

Gate & verification

graphify gate

PASS — objectively clean (no health regressions, tests not run — proofs not run this pass (advisory)). Grounded, not self-assessed.

Advisory (not blocking):

• verification_scope: 452 function(s) in the blast radius were not formally verified this run

Formal verification

Could not verify: Could not verify dispatch\_command.

The verifier did not have enough to check dispatch\_command, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: not verifiable: all 23 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous (mostly SystemExit — names the real obstacle, not a sampling gap)

· 1 more finding(s) on lines outside this diff (see the check run).