Fix detect.py missing .sh/.json extensions and security harden extractors

- Add .sh, .bash, .json to CODE_EXTENSIONS in detect.py so files reach extractor
- Fix test_detect_incremental manifest path collision with new .json extension
- Update test_watch to reflect .json/.sh are now watched extensions
- B-1: only emit source imports for paths that exist on disk
- J-1: replace stat()+read() with bounded read to eliminate TOCTOU
- J-3: move pair_count cap inside loop so it is honoured exactly
- J-4: namespace $ref/extends refs with "ref_" prefix to prevent ID collision

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

graphify/detect.py

@@ -24,7 +24,7 @@ class FileType(str, Enum):
 
 _MANIFEST_PATH = "graphify-out/manifest.json"
 
-CODE_EXTENSIONS = {'.py', '.ts', '.js', '.jsx', '.tsx', '.mjs', '.ejs', '.go', '.rs', '.java', '.groovy', '.gradle', '.cpp', '.cc', '.cxx', '.c', '.h', '.hpp', '.rb', '.swift', '.kt', '.kts', '.cs', '.scala', '.php', '.lua', '.luau', '.toc', '.zig', '.ps1', '.ex', '.exs', '.m', '.mm', '.jl', '.vue', '.svelte', '.astro', '.dart', '.v', '.sv', '.sql', '.r', '.f', '.F', '.f90', '.F90', '.f95', '.F95', '.f03', '.F03', '.f08', '.F08', '.pas', '.pp', '.dpr', '.dpk', '.lpr', '.inc', '.dfm', '.lfm', '.lpk'}
+CODE_EXTENSIONS = {'.py', '.ts', '.js', '.jsx', '.tsx', '.mjs', '.ejs', '.go', '.rs', '.java', '.groovy', '.gradle', '.cpp', '.cc', '.cxx', '.c', '.h', '.hpp', '.rb', '.swift', '.kt', '.kts', '.cs', '.scala', '.php', '.lua', '.luau', '.toc', '.zig', '.ps1', '.ex', '.exs', '.m', '.mm', '.jl', '.vue', '.svelte', '.astro', '.dart', '.v', '.sv', '.sql', '.r', '.f', '.F', '.f90', '.F90', '.f95', '.F95', '.f03', '.F03', '.f08', '.F08', '.pas', '.pp', '.dpr', '.dpk', '.lpr', '.inc', '.dfm', '.lfm', '.lpk', '.sh', '.bash', '.json'}
 DOC_EXTENSIONS = {'.md', '.mdx', '.qmd', '.txt', '.rst', '.html', '.yaml', '.yml'}
 PAPER_EXTENSIONS = {'.pdf'}
 IMAGE_EXTENSIONS = {'.png', '.jpg', '.jpeg', '.gif', '.webp', '.svg'}

graphify/extract.py

@@ -5696,9 +5696,14 @@ def extract_bash(path: Path) -> dict:
                         line = node.start_point[0] + 1
                         if raw.startswith((".", "/")):
                             resolved = (path.parent / raw).resolve()
-                            tgt_nid = _make_id(str(resolved))
-                            add_edge(file_nid, tgt_nid, "imports_from", line,
-                                     context="import")
+                            # Only emit the edge if the target actually exists on
+                            # disk — prevents graph pollution from crafted paths
+                            # like `source ../../etc/passwd` that traverse outside
+                            # the project tree (B-1).
+                            if resolved.exists():
+                                tgt_nid = _make_id(str(resolved))
+                                add_edge(file_nid, tgt_nid, "imports_from", line,
+                                         context="import")
                         else:
                             tgt_nid = _make_id(raw)
                             if tgt_nid:
@@ -5744,11 +5749,15 @@ def extract_json(path: Path) -> dict:
         return {"nodes": [], "edges": [], "error": "tree-sitter-json not installed"}
 
     try:
-        if path.stat().st_size > _JSON_MAX_BYTES:
+        # Bounded read instead of stat()+read() to eliminate TOCTOU (J-1):
+        # read one byte beyond the limit so we can detect oversized files even
+        # if the file grows between stat and read.
+        with path.open("rb") as _f:
+            source = _f.read(_JSON_MAX_BYTES + 1)
+        if len(source) > _JSON_MAX_BYTES:
             return {"nodes": [], "edges": [], "error": "json file too large to index"}
         language = Language(tsjson.language())
         parser = Parser(language)
-        source = path.read_bytes()
         tree = parser.parse(source)
         root = tree.root_node
     except Exception as e:
@@ -5805,11 +5814,13 @@ def extract_json(path: Path) -> dict:
 
     def walk_object(obj_node, parent_nid: str, parent_key: str | None,
                     depth: int, pair_count: list) -> None:
-        if depth > 6 or pair_count[0] > 500:
+        if depth > 6:
             return
         for child in obj_node.children:
             if child.type != "pair":
                 continue
+            if pair_count[0] >= 500:  # check per-pair so the cap is honoured exactly (J-3)
+                return
             pair_count[0] += 1
             key = _key_text(child)
             if not key:
@@ -5829,13 +5840,15 @@ def extract_json(path: Path) -> dict:
                 walk_object(val, key_nid, key, depth + 1, pair_count)
 
             elif val.type == "array":
-                # For "extends" arrays (tsconfig, eslint): each string element
+                # For "extends" arrays (tsconfig, eslint): each string element.
+                # Prefix with "ref_" so external refs don't collide with real
+                # code/file node IDs that share the same collapsed _make_id (J-4).
                 for item in val.children:
                     if item.type == "string":
                         content = item.child_by_field_name("string_content")
                         ref = _read_text(content, source) if content else _read_text(item, source).strip('"\'')
                         if ref:
-                            ref_nid = _make_id(ref)
+                            ref_nid = _make_id("ref", ref)
                             if ref_nid:
                                 add_edge(key_nid, ref_nid, "extends", line, context="import")
 
@@ -5844,12 +5857,14 @@ def extract_json(path: Path) -> dict:
                 val_text = _read_text(content, source) if content else _read_text(val, source).strip('"\'')
 
                 if key == "extends" and val_text:
-                    ref_nid = _make_id(val_text)
+                    # Namespace external refs to avoid ID collision with file nodes (J-4)
+                    ref_nid = _make_id("ref", val_text)
                     if ref_nid:
                         add_edge(file_nid, ref_nid, "extends", line, context="import")
 
                 elif key == "$ref" and val_text:
-                    ref_nid = _make_id(val_text)
+                    # Namespace $ref values to prevent edge hijacking into code nodes (J-4)
+                    ref_nid = _make_id("ref", val_text)
                     if ref_nid:
                         add_edge(parent_nid, ref_nid, "references", line)
 

tests/test_detect.py

@@ -230,7 +230,11 @@ def test_detect_incremental_propagates_follow_symlinks(tmp_path, monkeypatch):
     (real_dir / "note.md").write_text("# real note\n\nsome content")
     (tmp_path / "linked_corpus").symlink_to(real_dir)
 
-    manifest_path = str(tmp_path / "manifest.json")
+    # Store manifest inside graphify-out/ so it is pruned by _SKIP_DIRS
+    # and doesn't get re-detected as a code file now that .json is indexed.
+    manifest_dir = tmp_path / "graphify-out"
+    manifest_dir.mkdir()
+    manifest_path = str(manifest_dir / "manifest.json")
 
     # Without following symlinks, the symlinked dir contents are invisible.
     no_link = detect_incremental(tmp_path, manifest_path, follow_symlinks=False)

tests/test_watch.py

@@ -47,7 +47,9 @@ def test_watched_extensions_includes_images():
     assert ".jpg" in _WATCHED_EXTENSIONS
 
 def test_watched_extensions_excludes_noise():
-    assert ".json" not in _WATCHED_EXTENSIONS
+    # .json is now indexed (bash/JSON extractors added in #866)
+    assert ".json" in _WATCHED_EXTENSIONS
+    assert ".sh" in _WATCHED_EXTENSIONS
     assert ".pyc" not in _WATCHED_EXTENSIONS
     assert ".log" not in _WATCHED_EXTENSIONS