fix(cli): degrade instead of aborting extraction when --cargo finds no manifest

CHANGELOG.md

@@ -13,6 +13,7 @@ Full release notes with details on each version: [GitHub Releases](https://githu
 - Fix: the incremental rebuild no longer purges AST nodes it just reported as fail-closed "kept" — the eviction pass re-checks the kept set, so a moved-file/symlink layout can't deadlock the shrink guard into refusing every update (#3697, #3695, thanks @hopstreax).
 - Fix: `graph.html` no longer crashes vis-network with a stack overflow on large graphs — nodes are seeded on a spiral before physics runs so overlap-avoidance can't blow the layout recursion (#3699, thanks @sanjaiyan-dev).
 - Fix: node and edge tooltips now show special characters literally (C++ templates like `vector<int>`, generics, `&`, quotes) instead of raw HTML entities, while the HTML sinks that need escaping keep it (#3686, #3664, thanks @hopstreax).
+- Fix: `graphify extract --cargo` no longer aborts the whole extraction, discarding the AST pass that already completed, when no `Cargo.toml` exists at the scan root — an ordinary condition for any repo whose manifest lives in a subdirectory. It now prints a note and continues with an empty cargo result instead, matching the merge step's existing handling of that shape (#3677, thanks @ExhibitJ).
 - Docs: repository links now point at `Graphify-Labs/graphify` instead of the old account (including in generated wiki output), translated READMEs use the current logo, GitHub issue/PR templates were added, and the Enterprise link was corrected (#3692, #3694, #3693, thanks @Abdul535).
 
 ## 0.9.64 (2026-09-18)

graphify/cli.py

@@ -4182,6 +4182,14 @@ def _progress(idx: int, total: int, _result: dict) -> None:
             print("[graphify extract] introspecting Cargo workspace...")
             try:
                 cargo_result = introspect_cargo(target)
+            except FileNotFoundError:
+                # No Cargo.toml at the scan root is an ordinary condition
+                # (e.g. Tauri keeps its manifest under src-tauri/), not a
+                # failure — the AST pass already completed and cargo_result
+                # is already the empty, handled shape the merge below
+                # expects, so degrade instead of discarding that work (#3677).
+                print("[graphify extract] --cargo: no Cargo.toml at scan root, "
+                      "skipping crate edges")
             except (ConnectionError, ImportError, OSError) as exc:
                 print(f"error: {exc}", file=sys.stderr)
                 sys.exit(1)

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)}"
+    )