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

CHANGELOG.md

@@ -17,6 +17,7 @@ Full release notes with details on each version: [GitHub Releases](https://githu
 - Fix: a PHP `use` import written with a leading-backslash / fully-qualified prefix now resolves to its target definition instead of being dropped (#2661, thanks @ousamabenyounes).
 - Fix: an unresolved local JS/TS import (to a file absent from the scan) now emits a stable, portable `ref` target id instead of leaking a per-checkout absolute-path slug (#2457, thanks @rohit-jsfreaky).
 - Fix: `graphify benchmark` no longer crashes on a node whose label is `None` (#2674, thanks @Arthuro0103).
+- Fix: `graphify clone` now accepts multiple GitHub URLs and clones each one instead of silently dropping every URL past the first, matching the multi-repo workflow (#2703); unknown flags are rejected with a usage message, and `--out` is refused with multiple URLs to keep destinations unambiguous.
 
 ## 0.9.40 (2026-08-11)
 

graphify/cli.py

@@ -2399,28 +2399,46 @@ def _to_simple(g: "_nx.Graph") -> "_nx.Graph":
         print(f"Written to: {out_path}")
 
     elif cmd == "clone":
+        _CLONE_USAGE = (
+            "Usage: graphify clone <github-url> [<github-url> ...] "
+            "[--branch <branch>] [--out <dir>]"
+        )
         if len(sys.argv) < 3:
-            print(
-                "Usage: graphify clone <github-url> [--branch <branch>] [--out <dir>]",
-                file=sys.stderr,
-            )
+            print(_CLONE_USAGE, file=sys.stderr)
             sys.exit(1)
-        url = sys.argv[2]
+        urls: list[str] = []
         branch: str | None = None
         out_dir: Path | None = None
-        args = sys.argv[3:]
+        args = sys.argv[2:]
         i = 0
         while i < len(args):
-            if args[i] == "--branch" and i + 1 < len(args):
+            a = args[i]
+            if a == "--branch" and i + 1 < len(args):
                 branch = args[i + 1]
                 i += 2
-            elif args[i] == "--out" and i + 1 < len(args):
+            elif a == "--out" and i + 1 < len(args):
                 out_dir = Path(args[i + 1])
                 i += 2
+            elif a.startswith("-"):
+                print(f"error: unknown option: {a}", file=sys.stderr)
+                print(_CLONE_USAGE, file=sys.stderr)
+                sys.exit(1)
             else:
+                urls.append(a)
                 i += 1
-        local_path = _clone_repo(url, branch=branch, out_dir=out_dir)
-        print(local_path)
+        if not urls:
+            print(_CLONE_USAGE, file=sys.stderr)
+            sys.exit(1)
+        if out_dir is not None and len(urls) > 1:
+            print(
+                "error: --out is only valid with a single URL; drop --out to clone "
+                "multiple repos into ~/.graphify/repos/<owner>/<repo>",
+                file=sys.stderr,
+            )
+            sys.exit(1)
+        for url in urls:
+            local_path = _clone_repo(url, branch=branch, out_dir=out_dir)
+            print(local_path)
 
     elif cmd == "export":
         subcmd = sys.argv[2] if len(sys.argv) > 2 else ""

graphify/skills/agents/references/github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \

graphify/skills/amp/references/github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \

graphify/skills/claude/references/github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \

graphify/skills/claw/references/github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \

graphify/skills/codex/references/github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \

graphify/skills/copilot/references/github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \

graphify/skills/droid/references/github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \

graphify/skills/kilo/references/github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \

graphify/skills/kiro/references/github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \

graphify/skills/opencode/references/github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \

graphify/skills/pi/references/github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \

graphify/skills/trae/references/github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \

graphify/skills/vscode/references/github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \

graphify/skills/windows/references/github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \

tests/test_clone_cli.py

@@ -0,0 +1,110 @@
+"""`graphify clone` multi-URL support (#2703).
+
+The clone command used to silently swallow every URL after the first: a user
+who typed `graphify clone url1 url2` got only url1 cloned and no indication
+that url2 was dropped. Multi-repo analysis is the exact workflow issue #2703
+asks about, so extra URLs are now cloned in turn and each destination path is
+printed on its own line. Unknown flags are rejected instead of skipped.
+"""
+from __future__ import annotations
+
+import sys
+from pathlib import Path
+
+import pytest
+
+from graphify import cli
+
+
+def _stub_clone(monkeypatch):
+    calls: list[tuple[str, str | None, Path | None]] = []
+
+    def fake(url, branch=None, out_dir=None):
+        calls.append((url, branch, out_dir))
+        return Path(f"/tmp/fake/{url.rsplit('/', 1)[-1]}")
+
+    monkeypatch.setattr(cli, "_clone_repo", fake)
+    return calls
+
+
+def test_clone_multiple_urls_are_all_cloned(monkeypatch, capsys):
+    calls = _stub_clone(monkeypatch)
+    monkeypatch.setattr(
+        sys,
+        "argv",
+        [
+            "graphify",
+            "clone",
+            "https://github.com/foo/bar",
+            "https://github.com/baz/qux",
+        ],
+    )
+    cli.dispatch_command("clone")
+    assert [c[0] for c in calls] == [
+        "https://github.com/foo/bar",
+        "https://github.com/baz/qux",
+    ]
+    out = capsys.readouterr().out.splitlines()
+    assert "/tmp/fake/bar" in out
+    assert "/tmp/fake/qux" in out
+
+
+def test_clone_single_url_still_works(monkeypatch, capsys):
+    calls = _stub_clone(monkeypatch)
+    monkeypatch.setattr(
+        sys, "argv", ["graphify", "clone", "https://github.com/foo/bar"]
+    )
+    cli.dispatch_command("clone")
+    assert calls == [("https://github.com/foo/bar", None, None)]
+    assert "/tmp/fake/bar" in capsys.readouterr().out
+
+
+def test_clone_branch_flag_applies_to_all(monkeypatch):
+    calls = _stub_clone(monkeypatch)
+    monkeypatch.setattr(
+        sys,
+        "argv",
+        [
+            "graphify",
+            "clone",
+            "https://github.com/foo/bar",
+            "https://github.com/baz/qux",
+            "--branch",
+            "dev",
+        ],
+    )
+    cli.dispatch_command("clone")
+    assert [c[1] for c in calls] == ["dev", "dev"]
+
+
+def test_clone_rejects_out_with_multiple_urls(monkeypatch, capsys):
+    _stub_clone(monkeypatch)
+    monkeypatch.setattr(
+        sys,
+        "argv",
+        [
+            "graphify",
+            "clone",
+            "https://github.com/foo/bar",
+            "https://github.com/baz/qux",
+            "--out",
+            "/tmp/dest",
+        ],
+    )
+    with pytest.raises(SystemExit) as exc:
+        cli.dispatch_command("clone")
+    assert exc.value.code == 1
+    assert "--out" in capsys.readouterr().err
+
+
+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:
+        cli.dispatch_command("clone")
+    assert exc.value.code == 1
+    assert "--nope" in capsys.readouterr().err

tools/skillgen/expected/graphify__skills__agents__references__github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \

tools/skillgen/expected/graphify__skills__amp__references__github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \

tools/skillgen/expected/graphify__skills__claude__references__github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \

tools/skillgen/expected/graphify__skills__claw__references__github-and-merge.md

@@ -12,9 +12,8 @@ LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
 
 **Multiple repos (cross-repo graph):**
 ```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Clone each repo (one call or many — both work), run the full pipeline on each, then merge
+graphify clone <url1> <url2>   # → ~/.graphify/repos/<owner1>/<repo1> and .../<owner2>/<repo2>
 # Run /graphify on each local path to produce their graph.json files
 # Then merge:
 graphify merge-graphs \