fix(detect): honor nested .gitignore/.graphifyignore files below the scan root (#1206)

detect() only read .gitignore/.graphifyignore in the scan root and its
ancestor directories (up to the nearest VCS root), loaded once before the
walk began. A .gitignore sitting in a descendant directory — e.g.
vendor/sub/.gitignore — was never read, so files/dirs it excluded leaked
into the graph. Real git (and every other gitignore-aware tool) honors
.gitignore at every directory level, not just the ancestor chain.

Extracts the per-directory read+parse logic into a shared
_load_dir_own_ignore() helper (used by both the existing ancestor-chain
loader and the new call site) and invokes it live inside detect()'s
os.walk loop for every directory visited, before that directory's
children are pruned — so a nested ignore file governs its own subtree
with the same closer-file-wins precedence git uses.

Adds three regression tests: nested file exclude, nested directory prune
(the walk never descends into it), and nested negation overriding a
broader root-level rule.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

graphify/detect.py

@@ -832,6 +832,33 @@ def _git_info_exclude(vcs_root: Path) -> Path | None:
     return exclude if exclude.is_file() else None
 
 
+def _load_dir_own_ignore(d: Path) -> list[tuple[Path, str]]:
+    """Read .gitignore/.graphifyignore directly inside *d* (not its ancestors).
+
+    Merges .gitignore and .graphifyignore for this one directory (#1363):
+    .gitignore is read first and .graphifyignore last, so .graphifyignore
+    patterns (including `!` negations) win on conflict via last-match-wins;
+    adding a .graphifyignore can only ever exclude MORE, never re-include a
+    .gitignore-excluded file (#945 kept: a dir with only a .gitignore still
+    gets sensible defaults).
+
+    Shared by `_load_graphifyignore` (ancestor chain, loaded once before the
+    scan) and the live os.walk loop in `detect()` (called per-directory as
+    each descendant is visited), so nested ignore files *below* the scan
+    root are honored too — previously only the scan root and its ancestors
+    were read, so e.g. `vendor/sub/.gitignore` was silently ignored (#1206).
+    """
+    patterns: list[tuple[Path, str]] = []
+    for fname in (".gitignore", ".graphifyignore"):
+        ignore_file = d / fname
+        if ignore_file.exists():
+            for raw in ignore_file.read_text(encoding="utf-8", errors="ignore").splitlines():
+                line = _parse_gitignore_line(raw)
+                if line:
+                    patterns.append((d, line))
+    return patterns
+
+
 def _load_graphifyignore(root: Path) -> list[tuple[Path, str]]:
     """Read .graphifyignore files and return (anchor_dir, pattern) pairs.
 
@@ -841,6 +868,10 @@ def _load_graphifyignore(root: Path) -> list[tuple[Path, str]]:
 
     Walk ceiling: the nearest VCS root if inside a repo, otherwise the scan
     root itself (hermetic — no leakage across unrelated sibling projects).
+
+    Covers the scan root and its ancestors only — directories *below* the
+    scan root are picked up live during the os.walk in `detect()` instead,
+    since they aren't known until the walk reaches them (#1206).
     """
     root = root.resolve()
     ceiling = _find_vcs_root(root) or root
@@ -869,23 +900,7 @@ def _load_graphifyignore(root: Path) -> list[tuple[Path, str]]:
                 patterns.append((ceiling, line))
 
     for d in dirs:
-        # Merge .gitignore and .graphifyignore for this dir (#1363). Previously
-        # the presence of a .graphifyignore made graphify skip that dir's
-        # .gitignore entirely, so a file excluded only by .gitignore (e.g. a
-        # neutrally-named secret like prod-dump.sql) silently got indexed into
-        # the graph — whose artifacts embed file contents and are often
-        # committed. .gitignore is read first and .graphifyignore last, so
-        # .graphifyignore patterns (including `!` negations) win on conflict via
-        # last-match-wins; adding a .graphifyignore can only ever exclude MORE,
-        # never re-include a .gitignore-excluded file (#945 kept: a project with
-        # only a .gitignore still gets sensible defaults).
-        for fname in (".gitignore", ".graphifyignore"):
-            ignore_file = d / fname
-            if ignore_file.exists():
-                for raw in ignore_file.read_text(encoding="utf-8", errors="ignore").splitlines():
-                    line = _parse_gitignore_line(raw)
-                    if line:
-                        patterns.append((d, line))
+        patterns.extend(_load_dir_own_ignore(d))
     return patterns
 
 
@@ -1194,6 +1209,14 @@ def detect(root: Path, *, follow_symlinks: bool | None = None, google_workspace:
                     dirnames.clear()
                     continue
             if not in_memory_tree:
+                # dp == root was already loaded by _load_graphifyignore (root is
+                # the last entry in its ancestor chain); every other directory
+                # reached by the walk is a descendant below the scan root, whose
+                # own .gitignore/.graphifyignore is unknown until we get here.
+                # Load it now, before pruning dp's children, so a nested ignore
+                # file governs its own subtree the same way git honors it (#1206).
+                if dp != root:
+                    ignore_patterns.extend(_load_dir_own_ignore(dp))
                 # Prune noise dirs in-place so os.walk never descends into them.
                 # Dot dirs are allowed — users often want .github/, .claude/, etc.
                 # Framework caches (.next, .nuxt, …) are caught by _is_noise_dir.

tests/test_detect.py

@@ -227,6 +227,67 @@ def test_graphifyignore_at_git_root_is_included(tmp_path):
     assert result["graphifyignore_patterns"] == 1
 
 
+def test_gitignore_nested_below_root_excludes_file(tmp_path):
+    """A .gitignore in a subdirectory below the scan root is honored too (#1206).
+
+    Previously only the scan root and its ancestors were read, so a
+    .gitignore sitting inside e.g. vendor/sub/ was silently skipped.
+    """
+    (tmp_path / ".gitignore").write_text("*.log\n")
+    sub = tmp_path / "vendor" / "sub"
+    sub.mkdir(parents=True)
+    (sub / ".gitignore").write_text("secret.txt\n")
+    (tmp_path / "root.py").write_text("x = 1")
+    (tmp_path / "root.log").write_text("noise")
+    (sub / "keep.py").write_text("y = 2")
+    (sub / "secret.txt").write_text("shh")
+
+    result = detect(tmp_path)
+    code_files = result["files"]["code"]
+    assert any("root.py" in f for f in code_files)
+    assert any("keep.py" in f for f in code_files)
+    assert not any("root.log" in f for f in code_files)
+    assert not any("secret.txt" in f for f in code_files)
+    assert result["graphifyignore_patterns"] == 2
+
+
+def test_gitignore_nested_below_root_prunes_whole_directory(tmp_path):
+    """A nested .gitignore excluding a directory prevents descending into it."""
+    sub = tmp_path / "vendor" / "sub"
+    sub.mkdir(parents=True)
+    (sub / ".gitignore").write_text("build/\n")
+    build = sub / "build"
+    build.mkdir()
+    (build / "generated.py").write_text("x = 1")
+    (sub / "keep.py").write_text("y = 2")
+
+    result = detect(tmp_path)
+    code_files = result["files"]["code"]
+    assert any("keep.py" in f for f in code_files)
+    assert not any("generated.py" in f for f in code_files)
+
+
+def test_gitignore_nested_negation_overrides_broader_root_rule(tmp_path):
+    """A closer (nested) .gitignore's `!` re-include wins over a root exclude,
+    matching git's closer-file-wins precedence."""
+    (tmp_path / ".gitignore").write_text("*.txt\n")
+    sub = tmp_path / "vendor" / "sub"
+    sub.mkdir(parents=True)
+    (sub / ".gitignore").write_text("!important.txt\n")
+    (tmp_path / "root.txt").write_text("a")
+    (sub / "important.txt").write_text("b")
+    (sub / "other.txt").write_text("c")
+
+    result = detect(tmp_path)
+    # .txt is not a code extension so check the document bucket instead
+    doc_files = result["files"]["document"] if "document" in result["files"] else []
+    unclassified = result.get("unclassified", [])
+    all_seen = doc_files + unclassified
+    assert any("important.txt" in f for f in all_seen)
+    assert not any(f.endswith("root.txt") for f in all_seen)
+    assert not any(f.endswith("other.txt") for f in all_seen)
+
+
 def test_detect_handles_circular_symlinks(tmp_path):
     sub = tmp_path / "a"
     sub.mkdir()