Add regression tests for cargo extraction with a missing manifest

One test runs extract with the cargo flag against a repo that has no
Cargo.toml at all and confirms it still succeeds and still writes the
graph built from the code already indexed, with a note explaining the
crate edges were skipped. A companion test confirms a repo that does
have a valid manifest still gets its crate node, so the fix only
changes the missing manifest path.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_017qfdzgbA5KedGEjD1AayNh

tests/test_cargo_missing_manifest.py

@@ -0,0 +1,71 @@
+"""`graphify extract --cargo` must degrade, not abort, when no Cargo.toml
+exists at the scan root (#3677).
+
+A missing root manifest is an ordinary condition (e.g. a Tauri app keeps its
+manifest under src-tauri/), not a failure. Before the fix, FileNotFoundError
+(a subclass of OSError) was caught by a handler meant for ImportError/
+ConnectionError and the whole process exited, discarding the AST pass that
+had already completed and never writing graph.json.
+"""
+from __future__ import annotations
+
+import json
+import os
+import subprocess
+import sys
+from pathlib import Path
+
+PYTHON = sys.executable
+_KEY_VARS = ("GEMINI_API_KEY", "GOOGLE_API_KEY", "OPENAI_API_KEY", "OPENAI_BASE_URL",
+             "ANTHROPIC_API_KEY", "MOONSHOT_API_KEY", "DEEPSEEK_API_KEY")
+
+
+def _run(repo: Path, *extra: str):
+    env = {k: v for k, v in os.environ.items() if k not in _KEY_VARS}
+    env["GRAPHIFY_OUT"] = str(repo / "graphify-out")
+    return subprocess.run(
+        [PYTHON, "-m", "graphify", "extract", ".", "--code-only", "--cargo", *extra],
+        cwd=repo, capture_output=True, text=True, env=env,
+    )
+
+
+def test_cargo_flag_without_a_manifest_still_writes_the_graph(tmp_path):
+    repo = tmp_path / "repo"
+    repo.mkdir()
+    (repo / "app.py").write_text("def hello():\n    return 1\n", encoding="utf-8")
+
+    r = _run(repo)
+
+    assert r.returncode == 0, (
+        f"a missing Cargo.toml must not abort the whole extraction: {r.stderr}"
+    )
+    out = r.stdout + r.stderr
+    assert "no Cargo.toml at scan root" in out, (
+        f"the missing manifest should be reported as a skip, not silently dropped: {out}"
+    )
+    graph = repo / "graphify-out" / "graph.json"
+    assert graph.exists(), "the AST work already done must still be written to graph.json"
+    g = json.loads(graph.read_text(encoding="utf-8"))
+    labels = [n.get("label") for n in g["nodes"]]
+    assert any(str(l).startswith("hello") for l in labels), "code was indexed"
+
+
+def test_cargo_flag_with_a_manifest_still_adds_crate_nodes(tmp_path):
+    repo = tmp_path / "repo"
+    repo.mkdir()
+    (repo / "app.py").write_text("def hello():\n    return 1\n", encoding="utf-8")
+    (repo / "Cargo.toml").write_text(
+        '[package]\nname = "app"\nversion = "0.1.0"\nedition = "2021"\n',
+        encoding="utf-8",
+    )
+
+    r = _run(repo)
+
+    assert r.returncode == 0, f"a valid manifest must extract cleanly: {r.stderr}"
+    graph = repo / "graphify-out" / "graph.json"
+    assert graph.exists()
+    g = json.loads(graph.read_text(encoding="utf-8"))
+    node_ids = {n.get("id") for n in g["nodes"]}
+    assert any("app" in str(i) for i in node_ids), (
+        f"a real Cargo.toml should still contribute a crate node; got {sorted(node_ids)}"
+    )