fix(detect): prune only configured output path

graphify/detect.py

@@ -15,7 +15,7 @@
     convert_google_workspace_file,
     google_workspace_enabled,
 )
-from graphify.paths import GRAPHIFY_OUT, GRAPHIFY_OUT_NAME, out_path
+from graphify.paths import GRAPHIFY_OUT, out_path
 
 
 class FileType(str, Enum):
@@ -793,7 +793,7 @@ def count_words(path: Path) -> int:
     "site-packages", "lib64",
     ".pytest_cache", ".mypy_cache", ".ruff_cache",
     ".tox", ".nox", ".eggs", "*.egg-info",  # nox is tox's successor, same .nox/ venv shape (#1804)
-    "graphify-out", GRAPHIFY_OUT_NAME,  # never treat own output as source input (#524); honour GRAPHIFY_OUT (#1423)
+    "graphify-out",  # never treat the default output as source input (#524)
     # Coverage/test-artefact dirs — generated, never architecturally meaningful
     "coverage", "lcov-report",              # Vitest/Istanbul/nyc HTML reports (#870)
     "visual-tests", "visual-test",          # Playwright/visual-regression bundles (#869)
@@ -1182,6 +1182,13 @@ def _resolves_under_root(path: Path, root: Path) -> bool:
 
 def detect(root: Path, *, follow_symlinks: bool | None = None, google_workspace: bool | None = None, extra_excludes: list[str] | None = None, cache_root: Path | None = None, gitignore: bool = True) -> dict:
     root = root.resolve()
+    configured_out_dir = root / GRAPHIFY_OUT
+    configured_out_names = {configured_out_dir.name}
+    try:
+        configured_out_dir = configured_out_dir.resolve()
+    except (OSError, RuntimeError):
+        configured_out_dir = configured_out_dir.absolute()
+    configured_out_names.add(configured_out_dir.name)
     # .graphifyinclude support was removed (#2112): its loader and matchers had
     # no consumers, so the file has been a silent no-op since dot directories
     # became indexed by default (#873). Surface that once per scan so a
@@ -1295,6 +1302,16 @@ def _on_walk_error(err: OSError) -> None:
                 # repos for no correctness gain.
                 kept_dirs: list[str] = []
                 for d in dirnames:
+                    child = dp / d
+                    is_configured_out = False
+                    if d in configured_out_names:
+                        try:
+                            is_configured_out = child.resolve() == configured_out_dir
+                        except (OSError, RuntimeError):
+                            pass
+                    if is_configured_out:
+                        pruned_noise.append(str(child) + os.sep)
+                        continue
                     if _is_noise_dir(d, dp):
                         # Record pruned-as-noise dirs so a wrongly-pruned real
                         # source dir is at least traceable in the output rather

graphify/paths.py

@@ -279,9 +279,8 @@ def disambiguate_ambiguous_candidates(
         {c: candidate_files.get(c, "") for c in survivors},
     )
 
-# Bare directory name even when GRAPHIFY_OUT is an absolute path. Used by the
-# path guards that walk parents looking for the output dir by name, and by the
-# detect scan-exclude so a custom output dir is never re-ingested as source.
+# Bare directory name even when GRAPHIFY_OUT is an absolute path. Used by path
+# guards that walk parents looking for the output directory by name.
 GRAPHIFY_OUT_NAME = os.path.basename(os.path.normpath(GRAPHIFY_OUT))
 
 

tests/test_detect.py

@@ -2192,6 +2192,78 @@ def test_detect_prunes_venv_names_without_markers(tmp_path):
         assert not any(f"{os.sep}{name}{os.sep}" in f for f in all_files), f"{name} must stay pruned"
 
 
+@pytest.mark.parametrize(
+    ("configured_out", "absolute", "symlink_target"),
+    [
+        pytest.param("graphify-out/nlp", False, None, id="default-parent"),
+        pytest.param("artifacts/nlp", False, None, id="custom-parent"),
+        pytest.param("artifacts/nlp", True, None, id="absolute"),
+        pytest.param(
+            "aliases/output-link",
+            False,
+            "artifacts/nlp",
+            id="in-root-symlink",
+        ),
+    ],
+)
+def test_nested_graphify_out_prunes_only_configured_path(
+    tmp_path, configured_out, absolute, symlink_target
+):
+    """#2273: a nested output basename must not prune same-named source dirs."""
+    import json
+    import subprocess
+    import sys
+
+    if absolute:
+        configured_out = str(tmp_path / configured_out)
+
+    source = tmp_path / "src" / "revil" / "nexus" / "nlp" / "core.py"
+    source.parent.mkdir(parents=True)
+    source.write_text("def tokenize(text):\n    return text.split()\n")
+
+    output_dir = (
+        tmp_path / symlink_target
+        if symlink_target is not None
+        else tmp_path / configured_out
+    )
+    if symlink_target is not None:
+        output_dir.mkdir(parents=True)
+        configured_out_link = tmp_path / configured_out
+        configured_out_link.parent.mkdir(parents=True)
+        try:
+            configured_out_link.symlink_to(output_dir, target_is_directory=True)
+        except (OSError, NotImplementedError):
+            pytest.skip("filesystem does not support symlinks")
+
+    generated = output_dir / "generated.py"
+    generated.parent.mkdir(parents=True, exist_ok=True)
+    generated.write_text("SHOULD_NOT_BE_INDEXED = True\n")
+
+    probe = subprocess.run(
+        [
+            sys.executable,
+            "-c",
+            (
+                "import json, sys\n"
+                "from pathlib import Path\n"
+                "from graphify.detect import detect\n"
+                "result = detect(Path(sys.argv[1]))\n"
+                "print(json.dumps(result['files']['code']))\n"
+            ),
+            str(tmp_path),
+        ],
+        cwd=Path(__file__).parents[1],
+        env={**os.environ, "GRAPHIFY_OUT": configured_out},
+        check=True,
+        capture_output=True,
+        text=True,
+    )
+    detected = {Path(p).resolve() for p in json.loads(probe.stdout)}
+
+    assert source.resolve() in detected
+    assert generated.resolve() not in detected
+
+
 def test_detect_records_unclassified_extensionless_files(tmp_path):
     # #1692: extensionless, non-shebang project files (Dockerfile, Makefile, ...)
     # were considered but left no trace. detect() now lists them under