From 468646632d36cc8b90f9d521d420c1c4d3141110 Mon Sep 17 00:00:00 2001
From: abhay-codes07 <abhaysingh0293@gmail.com>
Date: Mon, 24 Aug 2026 23:50:06 +0530
Subject: [PATCH 1/2] feat(config): let a project declare what an ambiguous
 extension means (#2961)
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`.inc` is hard-mapped to the Pascal extractor, but it is "include file" in
whatever language a project happens to use: PHP on pfSense, Pascal in a
Delphi tree, SQL or assembly elsewhere. A PHP `.inc` parsed as Pascal does
not fail — it yields a handful of incidental nodes, so the graph looks
populated while the shipped runtime is missing from it (7 nodes instead of
471 on the reporter's file). Hardcoding one more extension (#1042's fix)
cannot generalise, because `.inc` has no single correct global meaning.

`.graphifyrc` gains `language.<ext>=<language | .ext>`:

    language.inc=php
    language.tpl=.ts

The declaration reaches every place graphify keys a decision on the suffix:

  * detect.classify_file          — a declared extension counts as code
  * extract._get_extractor        — dispatch, ahead of the .h/.m sniffs
  * _lang_is_case_insensitive /   — cross-file resolution rules
    _lang_family / the PHP pass
  * resolver_registry             — the declared language's resolvers wake
  * cache.load_cached/save_cached — a `salt` folds the target language
    into the key, so the same bytes cached under the old extractor are
    never served for the new one
  * the extraction pool           — an initializer forwards the mapping to
    workers, which start with empty module state under `spawn`

The parser moves from hooks.py into a dependency-free graphify.rcfile so
detect/extract (and the workers) can read it; hooks._load_graphifyrc keeps
its name and behaviour. detect() and extract() activate `<root>/.graphifyrc`
themselves, so the CLI, `update`/`watch`, the hooks, the MCP server, and the
skill runbook all pick it up with no further wiring. A malformed file is
reported once on stderr and the scan continues with the defaults.
---
 README.md                        |  16 ++
 graphify/cache.py                |  23 +-
 graphify/detect.py               |   8 +-
 graphify/extract.py              |  51 ++++-
 graphify/hooks.py                |  37 +---
 graphify/rcfile.py               | 229 ++++++++++++++++++++
 graphify/resolver_registry.py    |   5 +-
 tests/test_language_overrides.py | 346 +++++++++++++++++++++++++++++++
 8 files changed, 671 insertions(+), 44 deletions(-)
 create mode 100644 graphify/rcfile.py
 create mode 100644 tests/test_language_overrides.py

diff --git a/README.md b/README.md
index d83ea76c0c..ff7d7c4ba6 100644
--- a/README.md
+++ b/README.md
@@ -425,6 +425,22 @@ dist/
 !src/**
 ```
 
+
+## Project configuration
+
+Create a `.graphifyrc` in the scan root for settings that belong to the project rather than to one run. One `key=value` per line, `#` comments.
+
+**Ambiguous extensions.** Some extensions mean different languages in different projects: `.inc` is PHP on pfSense, Pascal in a Delphi tree, SQL or assembly elsewhere; `.h` is C or C++; `.m` is Objective-C or MATLAB. graphify has to pick one global default, and when it picks wrong the file does not fail — it parses as the wrong language and yields a handful of incidental nodes, so the graph looks populated while the real symbols are missing. Declare what the extension means in your repo:
+
+```
+# .graphifyrc
+language.inc=php        # a language name ...
+language.tpl=.ts        # ... or an extension graphify already knows
+viz_node_limit=0        # baked into the git hooks (see Team setup)
+```
+
+The declaration applies everywhere graphify keys a decision on the extension — file classification, extractor dispatch, cross-file resolution, and the AST cache (a file re-parsed under a different language never reuses the old entry). It is read by `graphify extract`, `graphify update`, `watch`, the hooks, the MCP server, and the `/graphify` skill alike. A typo is reported once on stderr and the scan continues with graphify's defaults.
+
 ---
 
 ## Team setup
diff --git a/graphify/cache.py b/graphify/cache.py
index 622ba6cff9..b184c3f2ca 100644
--- a/graphify/cache.py
+++ b/graphify/cache.py
@@ -955,11 +955,19 @@ def cache_dir(root: Path = Path("."), kind: str = "ast",
     return d
 
 
+def _salted_key(h: str, salt: str | None) -> str:
+    """Derive the on-disk key from a content hash plus optional salt."""
+    if not salt:
+        return h
+    return hashlib.sha256(f"{h}:{salt}".encode("utf-8")).hexdigest()
+
+
 def load_cached(path: Path, root: Path = Path("."), kind: str = "ast",
                 cache_root: Path | None = None, prompt: "str | Path | None" = None,
                 prompt_file: "str | Path | None" = None,
                 allow_legacy: bool = True,
-                allow_partial: bool = False) -> dict | None:
+                allow_partial: bool = False,
+                salt: str | None = None) -> dict | None:
     """Return cached extraction for this file if hash matches, else None.
 
     Cache key: SHA256 of file contents.
@@ -988,6 +996,10 @@ def load_cached(path: Path, root: Path = Path("."), kind: str = "ast",
     so :func:`check_semantic_cache` can report N to the user. Callers that must
     not mix vintages within one entry (see :func:`save_semantic_cache`'s
     ``merge_existing``) pass allow_legacy=False.
+    ``salt`` folds extra material into the key for an entry whose validity
+    depends on more than the file's bytes — a file the project remaps to
+    another language (#2961) parses to a different graph from the same
+    content, so it must not hit the entry produced under the old extractor.
     Returns None if no cache entry or file has changed.
     """
     global _legacy_semantic_hits, _corrupt_cache_entries
@@ -996,6 +1008,7 @@ def load_cached(path: Path, root: Path = Path("."), kind: str = "ast",
         h = file_hash(path, root, cache_root=cache_root)
     except OSError:
         return None
+    h = _salted_key(h, salt)
     prompt_fp = _resolve_prompt_fp(prompt, prompt_file)
     entry = cache_dir(location, kind, prompt_fp) / f"{h}.json"
     legacy_hit = False
@@ -1063,9 +1076,13 @@ def load_cached(path: Path, root: Path = Path("."), kind: str = "ast",
 
 def save_cached(path: Path, result: dict, root: Path = Path("."), kind: str = "ast",
                 cache_root: Path | None = None, prompt: "str | Path | None" = None,
-                prompt_file: "str | Path | None" = None) -> None:
+                prompt_file: "str | Path | None" = None,
+                salt: str | None = None) -> None:
     """Save extraction result for this file.
 
+    ``salt`` must match what the corresponding :func:`load_cached` passes
+    (see there); it namespaces the key, not the directory.
+
     Stores as graphify-out/cache/{kind}/{hash}.json where hash = SHA256 of current file contents.
     result should be a dict with 'nodes' and 'edges' lists.
 
@@ -1112,7 +1129,7 @@ def save_cached(path: Path, result: dict, root: Path = Path("."), kind: str = "a
         # the entry replays portably under any root (#2257). Strictly after the
         # source_file pass, which owns that field's bare-relative format.
         _relativize_ids_in(on_disk, p, root)
-    h = file_hash(p, root, cache_root=cache_root)
+    h = _salted_key(file_hash(p, root, cache_root=cache_root), salt)
     location = cache_root if cache_root is not None else root
     target_dir = cache_dir(location, kind, _resolve_prompt_fp(prompt, prompt_file))
     entry = target_dir / f"{h}.json"
diff --git a/graphify/detect.py b/graphify/detect.py
index 1adad00bbc..cf8faa04d1 100644
--- a/graphify/detect.py
+++ b/graphify/detect.py
@@ -20,6 +20,7 @@
     google_workspace_enabled,
 )
 from graphify.paths import GRAPHIFY_OUT, out_path
+from graphify.rcfile import activate_language_overrides, effective_suffix
 
 
 class FileType(str, Enum):
@@ -511,7 +512,9 @@ def classify_file(path: Path) -> FileType | None:
     # Compound extensions must be checked before simple suffix lookup
     if path.name.lower().endswith(".blade.php"):
         return FileType.CODE
-    ext = path.suffix.lower()
+    # A project may declare what an ambiguous extension means to it
+    # (.graphifyrc `language.inc=php`, #2961); classify by the declared one.
+    ext = effective_suffix(path).lower()
     if not ext:
         return _shebang_file_type(path)
     if ext in CODE_EXTENSIONS:
@@ -1664,6 +1667,9 @@ 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()
+    # The project's extension->language declarations (#2961) shape
+    # classification for this scan.
+    activate_language_overrides(root)
     configured_out_dir = root / GRAPHIFY_OUT
     configured_out_names = {configured_out_dir.name}
     try:
diff --git a/graphify/extract.py b/graphify/extract.py
index e015c9d715..488cbe14d9 100644
--- a/graphify/extract.py
+++ b/graphify/extract.py
@@ -26,6 +26,13 @@
 from .pascal_resolution import resolve_pascal_inherited_calls
 
 # --- migrated to graphify/extractors/ (see graphify/extractors/MIGRATION.md) ---
+from graphify.rcfile import (
+    activate_language_overrides,
+    cache_salt,
+    effective_suffix,
+    get_language_overrides,
+    set_language_overrides,
+)
 from graphify.extractors.base import (  # noqa: F401
     _LANGUAGE_BUILTIN_GLOBALS,
     _file_stem,
@@ -2292,7 +2299,7 @@ def _lang_is_case_insensitive(source_file: object) -> bool:
     """True when the file's language resolves identifiers case-insensitively (#1581)."""
     if not source_file:
         return False
-    return Path(str(source_file)).suffix.lower() in _CASE_INSENSITIVE_EXTS
+    return effective_suffix(str(source_file)).lower() in _CASE_INSENSITIVE_EXTS
 
 
 # Language interop families for cross-file call resolution. A call in one language
@@ -2338,7 +2345,7 @@ def _lang_family(source_file: object) -> str | None:
     """Interop family of the file's language, or None when unknown/not code."""
     if not source_file:
         return None
-    return _LANG_FAMILY_BY_EXT.get(Path(str(source_file)).suffix.lower())
+    return _LANG_FAMILY_BY_EXT.get(effective_suffix(str(source_file)).lower())
 
 
 # A language's own built-in throwable hierarchy, keyed by the interop family of
@@ -5611,6 +5618,12 @@ def _get_extractor(path: Path) -> Any | None:
     # (#1377). apm.yml would otherwise be a .yml document handled by the LLM.
     if is_package_manifest_path(path):
         return extract_package_manifest
+    # A project-declared remap (.graphifyrc `language.inc=php`, #2961) wins
+    # over every sniff below: the user has said what the extension means in
+    # this repo, so a remapped `.h`/`.m` also skips the C++/ObjC probes.
+    remapped = effective_suffix(path)
+    if remapped != path.suffix:
+        return _DISPATCH.get(remapped) or _DISPATCH.get(remapped.lower())
     # `.h` is C/C++/ObjC-ambiguous; route Objective-C headers to extract_objc
     # (the suffix map sends `.h` to extract_c, which can't read @interface etc.).
     # ObjC sniffing has priority over the C++ sniff: an Objective-C++ header can
@@ -5653,6 +5666,13 @@ def _safe_extract_with_xaml_root(extractor, path: Path, root: Path) -> dict:
         _XAML_ACTIVE_EXTRACT_ROOT = previous_root
 
 
+def _worker_init(language_overrides: dict[str, str]) -> None:
+    """Pool initializer. Under ``spawn`` a worker re-imports the package and
+    starts with no overrides; hand it the parent's so `_get_extractor` and the
+    cache key agree across processes (#2961)."""
+    set_language_overrides(language_overrides)
+
+
 def _extract_single_file(args: tuple) -> tuple[int, dict]:
     """Worker function for parallel extraction. Runs in a subprocess.
 
@@ -5681,7 +5701,7 @@ def _extract_single_file(args: tuple) -> tuple[int, dict]:
 
     # Check cache first (avoid re-extraction)
     if not bypass_cache:
-        cached = load_cached(path, root, cache_root=cache_location)
+        cached = load_cached(path, root, cache_root=cache_location, salt=cache_salt(path))
         if cached is not None:
             return idx, cached
 
@@ -5696,7 +5716,7 @@ def _extract_single_file(args: tuple) -> tuple[int, dict]:
     # byte-stable across runs and silently blinds affected/explain to and
     # through the file (#1666); skipping the write lets a rerun self-heal.
     if not bypass_cache and "error" not in result and result.get("nodes"):
-        save_cached(path, result, root, cache_root=cache_location)
+        save_cached(path, result, root, cache_root=cache_location, salt=cache_salt(path))
     return idx, result
 
 
@@ -5762,7 +5782,11 @@ def _extract_parallel(
     failed: list[int] = []  # positions into uncached_work whose future failed
     _PROGRESS_INTERVAL = 100
     try:
-        with concurrent.futures.ProcessPoolExecutor(max_workers=max_workers) as pool:
+        with concurrent.futures.ProcessPoolExecutor(
+            max_workers=max_workers,
+            initializer=_worker_init,
+            initargs=(get_language_overrides(),),
+        ) as pool:
             futures = {
                 pool.submit(_extract_single_file, item): pos
                 for pos, item in enumerate(work_items)
@@ -5861,7 +5885,7 @@ def _extract_sequential(
         result = _safe_extract_with_xaml_root(extractor, path, root)
         # See _extract_single_file: don't cache an anomalous zero-node result (#1666).
         if not bypass_cache and "error" not in result and result.get("nodes"):
-            save_cached(path, result, root, cache_root=cache_location)
+            save_cached(path, result, root, cache_root=cache_location, salt=cache_salt(path))
         per_file[idx] = result
     if total_files >= _PROGRESS_INTERVAL:
         # Consistent denominator with the intermediate lines (#1693).
@@ -5966,6 +5990,17 @@ def extract(
         root = cache_root
     root = root.resolve()
 
+    # Project-level extension->language declarations (#2961). detect() has
+    # usually activated them for this root already; a direct library caller
+    # (the skill runbook, the MCP server, the issue's own repro) gets them here.
+    _overrides = activate_language_overrides(root)
+    if _overrides:
+        print(
+            "  language overrides (.graphifyrc): "
+            + ", ".join(f"{k} -> {v}" for k, v in sorted(_overrides.items())),
+            flush=True,
+        )
+
     # #1774: the cache is an OUTPUT, so when no explicit cache_root is given it is
     # written under the current working directory — never `root` (the inferred
     # common parent of the inputs), which would drop graphify-out/ inside a
@@ -5985,7 +6020,7 @@ def extract(
             continue
         bypass_cache = path.suffix in _JS_CACHE_BYPASS_SUFFIXES
         if not bypass_cache:
-            cached = load_cached(path, root, cache_root=cache_location)
+            cached = load_cached(path, root, cache_root=cache_location, salt=cache_salt(path))
             if cached is not None:
                 per_file[i] = cached
                 continue
@@ -6624,7 +6659,7 @@ def _learn(e: dict) -> None:
     _php_exts = {".php", ".phtml", ".php3", ".php4", ".php5", ".php7", ".phps"}
     _php_sel = [
         (r, p) for r, p in zip(per_file, paths)
-        if p.suffix.lower() in _php_exts and not p.name.lower().endswith(".blade.php")
+        if effective_suffix(p).lower() in _php_exts and not p.name.lower().endswith(".blade.php")
     ]
     if _php_sel:
         try:
diff --git a/graphify/hooks.py b/graphify/hooks.py
index e535e19134..4b0b64a3a0 100644
--- a/graphify/hooks.py
+++ b/graphify/hooks.py
@@ -423,39 +423,14 @@ def _detached_launch(rebuild_body: str) -> str:
 """
 
 
-def _load_graphifyrc(root: Path) -> dict[str, str | int]:
-    """Load key/value options from <root>/.graphifyrc if present.
+def _load_graphifyrc(root: Path) -> dict:
+    """Load ``<root>/.graphifyrc``; the parser lives in :mod:`graphify.rcfile`.
 
-    Supported options:
-      viz_node_limit: integer >= 0 (e.g. viz_node_limit=0)
+    Kept as the hooks-side name so callers and tests need not move. Returns
+    ``viz_node_limit`` (used here) alongside any other option the file sets.
     """
-    rc_path = root / ".graphifyrc"
-    if not rc_path.is_file():
-        return {}
-
-    cfg: dict[str, str | int] = {}
-    content = rc_path.read_text(encoding="utf-8")
-    for line_num, raw in enumerate(content.splitlines(), 1):
-        line = raw.strip()
-        if not line or line.startswith("#"):
-            continue
-        if "=" not in line:
-            raise ValueError(f"Invalid line {line_num} in {rc_path}: {raw!r} (expected key=value)")
-        key, val = line.split("=", 1)
-        key = key.strip()
-        val = val.strip()
-        if key == "viz_node_limit":
-            try:
-                parsed_val = int(val)
-                if parsed_val < 0:
-                    raise ValueError("must be a non-negative integer")
-                cfg["viz_node_limit"] = parsed_val
-            except ValueError as exc:
-                raise ValueError(
-                    f"Invalid viz_node_limit in {rc_path} at line {line_num}: {val!r}. "
-                    f"Must be a non-negative integer."
-                ) from exc
-    return cfg
+    from graphify.rcfile import load_graphifyrc
+    return load_graphifyrc(root)
 
 
 def _git_root(path: Path) -> Path | None:
diff --git a/graphify/rcfile.py b/graphify/rcfile.py
new file mode 100644
index 0000000000..3a7971831a
--- /dev/null
+++ b/graphify/rcfile.py
@@ -0,0 +1,229 @@
+"""Project-level configuration: ``<root>/.graphifyrc``.
+
+One ``key=value`` per line, ``#`` comments, blank lines ignored. Keys:
+
+``viz_node_limit=<int>``
+    Baked into the generated git hooks (see :mod:`graphify.hooks`).
+
+``language.<ext>=<language | .ext>``
+    Treat files with extension ``<ext>`` as the named language for
+    classification, extractor dispatch and cross-file resolution (#2961).
+    ``<ext>`` may be written with or without its leading dot; the value is
+    either a language name from :data:`LANGUAGE_ALIASES` or an explicit
+    extension graphify already knows (``.php``, ``.pas``, ``.sql``, ...)::
+
+        # pfSense: every .inc under this repo is PHP, not Pascal
+        language.inc=php
+        # a repo whose templates are plain TypeScript
+        language.tpl=.ts
+
+    An ambiguous extension (``.inc`` is PHP, Pascal, SQL or assembly
+    depending on the project; ``.m`` is Objective-C or MATLAB; ``.h`` is C or
+    C++) has no single correct global mapping, so the project declares it.
+
+The parser is deliberately free of heavy imports: :mod:`graphify.detect`
+and :mod:`graphify.extract` consult it on every scan, and the extraction
+worker processes re-import it under ``spawn``.
+"""
+from __future__ import annotations
+
+import sys
+from pathlib import Path
+
+RC_FILENAME = ".graphifyrc"
+
+# Language name -> the canonical extension graphify dispatches it under.
+# Deliberately a short list of names a user is likely to type; any known
+# extension can be given directly instead (``language.inc=.php``).
+LANGUAGE_ALIASES: dict[str, str] = {
+    "php": ".php",
+    "pascal": ".pas", "delphi": ".pas", "freepascal": ".pas",
+    "sql": ".sql",
+    "python": ".py",
+    "javascript": ".js", "js": ".js",
+    "typescript": ".ts", "ts": ".ts",
+    "c": ".c",
+    "cpp": ".cpp", "c++": ".cpp", "cxx": ".cpp",
+    "objc": ".mm", "objective-c": ".mm", "objectivec": ".mm",
+    "java": ".java",
+    "kotlin": ".kt",
+    "scala": ".scala",
+    "groovy": ".groovy",
+    "go": ".go", "golang": ".go",
+    "rust": ".rs",
+    "ruby": ".rb",
+    "csharp": ".cs", "c#": ".cs",
+    "swift": ".swift",
+    "lua": ".lua",
+    "zig": ".zig",
+    "elixir": ".ex",
+    "julia": ".jl",
+    "dart": ".dart",
+    "r": ".r",
+    "fortran": ".f90",
+    "shell": ".sh", "bash": ".sh", "sh": ".sh",
+    "powershell": ".ps1",
+    "verilog": ".v", "systemverilog": ".sv",
+    "terraform": ".tf", "hcl": ".hcl",
+    "ocaml": ".ml",
+    "lisp": ".lisp", "commonlisp": ".lisp",
+    "markdown": ".md",
+    "json": ".json",
+    "yaml": ".yaml",
+    "html": ".html",
+}
+
+
+def _normalise_ext(raw: str) -> str:
+    ext = raw.strip().lower()
+    if not ext.startswith("."):
+        ext = "." + ext
+    return ext
+
+
+def parse_language_value(value: str) -> str:
+    """Resolve the right-hand side of ``language.<ext>=`` to a canonical suffix.
+
+    Accepts a name from :data:`LANGUAGE_ALIASES` (case-insensitive) or an
+    explicit dotted extension. Raises ``ValueError`` for anything else.
+    """
+    v = value.strip()
+    if not v:
+        raise ValueError("empty value")
+    if v.startswith("."):
+        ext = _normalise_ext(v)
+        if len(ext) < 2 or any(ch.isspace() for ch in ext):
+            raise ValueError(f"{value!r} is not an extension")
+        return ext
+    try:
+        return LANGUAGE_ALIASES[v.lower()]
+    except KeyError:
+        known = ", ".join(sorted(LANGUAGE_ALIASES))
+        raise ValueError(
+            f"unknown language {value!r} (use one of: {known}; "
+            f"or an explicit extension such as .php)"
+        ) from None
+
+
+def load_graphifyrc(root: Path) -> dict:
+    """Parse ``<root>/.graphifyrc``. Returns ``{}`` when absent.
+
+    Returned keys: ``viz_node_limit`` (int) and ``languages``
+    (``{".inc": ".php", ...}``) — each present only when the file sets it.
+    Unknown keys are ignored so a newer graphify's options do not break an
+    older one. Malformed lines raise ``ValueError`` naming the line.
+    """
+    rc_path = Path(root) / RC_FILENAME
+    if not rc_path.is_file():
+        return {}
+
+    cfg: dict = {}
+    languages: dict[str, str] = {}
+    content = rc_path.read_text(encoding="utf-8")
+    for line_num, raw in enumerate(content.splitlines(), 1):
+        line = raw.strip()
+        if not line or line.startswith("#"):
+            continue
+        if "=" not in line:
+            raise ValueError(f"Invalid line {line_num} in {rc_path}: {raw!r} (expected key=value)")
+        key, val = line.split("=", 1)
+        key = key.strip()
+        val = val.strip()
+        if key == "viz_node_limit":
+            try:
+                parsed_val = int(val)
+                if parsed_val < 0:
+                    raise ValueError("must be a non-negative integer")
+                cfg["viz_node_limit"] = parsed_val
+            except ValueError as exc:
+                raise ValueError(
+                    f"Invalid viz_node_limit in {rc_path} at line {line_num}: {val!r}. "
+                    f"Must be a non-negative integer."
+                ) from exc
+        elif key.startswith("language."):
+            ext_part = key[len("language."):].strip()
+            if not ext_part or any(ch.isspace() for ch in ext_part):
+                raise ValueError(
+                    f"Invalid language key in {rc_path} at line {line_num}: {key!r} "
+                    f"(expected language.<ext>=<language>)"
+                )
+            try:
+                target = parse_language_value(val)
+            except ValueError as exc:
+                raise ValueError(
+                    f"Invalid {key} in {rc_path} at line {line_num}: {exc}"
+                ) from None
+            languages[_normalise_ext(ext_part)] = target
+    if languages:
+        cfg["languages"] = languages
+    return cfg
+
+
+# ---------------------------------------------------------------------------
+# Active overrides for this process
+# ---------------------------------------------------------------------------
+#
+# detect()/extract() activate the scan root's overrides for the run; the
+# extraction pool forwards them to its workers (they do not inherit module
+# state under ``spawn``). Stored lower-cased on both sides.
+
+_ACTIVE: dict[str, str] = {}
+_warned_roots: set[str] = set()
+
+
+def set_language_overrides(mapping: dict[str, str] | None) -> None:
+    """Replace the process-wide extension overrides (``{".inc": ".php"}``)."""
+    _ACTIVE.clear()
+    if mapping:
+        for ext, target in mapping.items():
+            _ACTIVE[_normalise_ext(ext)] = _normalise_ext(target)
+
+
+def get_language_overrides() -> dict[str, str]:
+    return dict(_ACTIVE)
+
+
+def activate_language_overrides(root: Path) -> dict[str, str]:
+    """Load ``<root>/.graphifyrc`` and make its language overrides active.
+
+    A malformed file is reported once per root on stderr and treated as
+    having no overrides — a scan must not die on a config typo, but the
+    user must hear about it, or their ``.inc`` silently stays Pascal.
+    Returns the mapping now active.
+    """
+    try:
+        cfg = load_graphifyrc(Path(root))
+    except (ValueError, OSError) as exc:
+        key = str(root)
+        if key not in _warned_roots:
+            _warned_roots.add(key)
+            print(f"[graphify] warning: ignoring {RC_FILENAME}: {exc}", file=sys.stderr)
+        cfg = {}
+    set_language_overrides(cfg.get("languages"))
+    return get_language_overrides()
+
+
+def effective_suffix(path: Path | str) -> str:
+    """The suffix graphify should treat ``path`` as having.
+
+    Returns the override target when the file's extension is remapped, else
+    the real suffix untouched (case preserved, so callers that distinguish
+    ``.F90`` from ``.f90`` keep doing so).
+    """
+    suffix = Path(path).suffix
+    if not _ACTIVE:
+        return suffix
+    return _ACTIVE.get(suffix.lower(), suffix)
+
+
+def cache_salt(path: Path | str) -> str | None:
+    """Extra cache-key material for a remapped file, else ``None``.
+
+    An AST cache entry is keyed by content, and the same bytes parse to a
+    different graph under a different extractor — so a ``.inc`` cached as
+    Pascal must not be served once the project declares it PHP.
+    """
+    if not _ACTIVE:
+        return None
+    target = _ACTIVE.get(Path(path).suffix.lower())
+    return f"language={target}" if target else None
diff --git a/graphify/resolver_registry.py b/graphify/resolver_registry.py
index b17478a78a..ded758c00c 100644
--- a/graphify/resolver_registry.py
+++ b/graphify/resolver_registry.py
@@ -75,7 +75,10 @@ def run_language_resolvers(
     exercise the driver in isolation.
     """
     active = _REGISTRY if resolvers is None else resolvers
-    suffixes_present = {p.suffix for p in paths}
+    # Honour project-level remaps (#2961): a `.inc` declared PHP must wake
+    # the PHP resolvers, not Pascal's.
+    from graphify.rcfile import effective_suffix
+    suffixes_present = {effective_suffix(p) for p in paths}
     for resolver in active:
         if not (resolver.suffixes & suffixes_present):
             continue
diff --git a/tests/test_language_overrides.py b/tests/test_language_overrides.py
new file mode 100644
index 0000000000..c4cd45e5aa
--- /dev/null
+++ b/tests/test_language_overrides.py
@@ -0,0 +1,346 @@
+"""A project can declare what an ambiguous extension means to it (#2961).
+
+`.inc` is hard-mapped to the Pascal extractor, but it is "include file" in
+whatever language a project uses: PHP on pfSense, Pascal in Delphi, SQL or
+assembly elsewhere. A PHP `.inc` parsed as Pascal does not fail — it yields a
+handful of incidental nodes, so the graph looks populated while the shipped
+runtime is missing from it (7 nodes instead of 471 on the reporter's file).
+
+No global mapping can be right for everyone, so the project says what it
+means in `.graphifyrc`::
+
+    language.inc=php
+
+The declaration has to reach every place graphify keys a decision on the
+suffix — classification, extractor dispatch, the case-folding and interop
+rules for cross-file resolution, the language resolvers, and the AST cache
+key (same bytes parse to a different graph under a different extractor) —
+and it has to survive the trip into the extraction worker processes.
+"""
+from __future__ import annotations
+
+import concurrent.futures
+import io
+from contextlib import redirect_stderr, redirect_stdout
+from pathlib import Path
+
+import pytest
+
+from graphify import rcfile
+from graphify.detect import FileType, classify_file, detect
+from graphify.extract import (
+    _get_extractor,
+    _lang_family,
+    _lang_is_case_insensitive,
+    extract,
+    extract_pascal,
+    extract_php,
+)
+
+try:
+    from graphify.extract import _worker_init
+except ImportError:  # pre-fix tree: the pool had no initializer
+    _worker_init = None
+from graphify.rcfile import (
+    activate_language_overrides,
+    cache_salt,
+    effective_suffix,
+    load_graphifyrc,
+    parse_language_value,
+    set_language_overrides,
+)
+from graphify.resolver_registry import LanguageResolver, run_language_resolvers
+
+PHP_SOURCE = """<?php
+namespace PfBlockerNG;
+
+class RuleSet {
+    public function load(string $path): array { return $this->parse($path); }
+    private function parse(string $path): array { return []; }
+}
+
+function pfb_update_lists(array $cfg): void { $r = new RuleSet(); $r->load('/tmp/x'); }
+function pfb_apply_rules(): void { pfb_update_lists([]); }
+function pfb_cron(): void { pfb_apply_rules(); }
+"""
+
+
+@pytest.fixture(autouse=True)
+def _no_overrides_leak():
+    """Overrides are process state; never let one test's config leak into the next."""
+    set_language_overrides(None)
+    rcfile._warned_roots.clear()
+    yield
+    set_language_overrides(None)
+    rcfile._warned_roots.clear()
+
+
+def _quiet_extract(paths, **kw):
+    with redirect_stdout(io.StringIO()):
+        return extract(paths, **kw)
+
+
+# ---------------------------------------------------------------------------
+# The .graphifyrc parser
+# ---------------------------------------------------------------------------
+
+def test_language_line_maps_an_extension_to_a_canonical_suffix(tmp_path):
+    (tmp_path / ".graphifyrc").write_text("language.inc=php\n", encoding="utf-8")
+    assert load_graphifyrc(tmp_path) == {"languages": {".inc": ".php"}}
+
+
+@pytest.mark.parametrize("key", ["language.inc", "language..inc", "language.INC", "language. inc "])
+def test_the_extension_key_is_normalised(tmp_path, key):
+    (tmp_path / ".graphifyrc").write_text(f"{key}=php\n", encoding="utf-8")
+    assert load_graphifyrc(tmp_path)["languages"] == {".inc": ".php"}
+
+
+@pytest.mark.parametrize("value, expected", [
+    ("php", ".php"), ("PHP", ".php"), ("pascal", ".pas"), ("delphi", ".pas"),
+    ("typescript", ".ts"), ("c++", ".cpp"), (".php", ".php"), (".PHP", ".php"),
+    ("markdown", ".md"),
+])
+def test_values_accept_a_language_name_or_an_explicit_extension(value, expected):
+    assert parse_language_value(value) == expected
+
+
+@pytest.mark.parametrize("value", ["", "klingon", ".", ". php", "php script"])
+def test_an_unknown_language_is_an_error_naming_the_alternatives(value):
+    with pytest.raises(ValueError):
+        parse_language_value(value)
+
+
+def test_a_bad_language_line_reports_its_line_number(tmp_path):
+    (tmp_path / ".graphifyrc").write_text("viz_node_limit=5\nlanguage.inc=klingon\n", encoding="utf-8")
+    with pytest.raises(ValueError, match=r"language\.inc .* line 2.*klingon"):
+        load_graphifyrc(tmp_path)
+
+
+def test_a_bad_language_key_is_an_error(tmp_path):
+    (tmp_path / ".graphifyrc").write_text("language.=php\n", encoding="utf-8")
+    with pytest.raises(ValueError, match="line 1"):
+        load_graphifyrc(tmp_path)
+
+
+def test_the_existing_option_and_unknown_keys_still_behave(tmp_path):
+    (tmp_path / ".graphifyrc").write_text(
+        "# comment\nviz_node_limit=0\nfuture_option=whatever\nlanguage.tpl=.ts\n",
+        encoding="utf-8",
+    )
+    cfg = load_graphifyrc(tmp_path)
+    assert cfg == {"viz_node_limit": 0, "languages": {".tpl": ".ts"}}
+
+
+def test_hooks_still_reads_the_same_file_through_its_old_name(tmp_path):
+    from graphify.hooks import _load_graphifyrc
+    (tmp_path / ".graphifyrc").write_text("viz_node_limit=3\nlanguage.inc=php\n", encoding="utf-8")
+    assert _load_graphifyrc(tmp_path)["viz_node_limit"] == 3
+    (tmp_path / ".graphifyrc").write_text("viz_node_limit=-1\n", encoding="utf-8")
+    with pytest.raises(ValueError, match="Invalid viz_node_limit"):
+        _load_graphifyrc(tmp_path)
+
+
+def test_no_file_means_no_overrides(tmp_path):
+    assert load_graphifyrc(tmp_path) == {}
+    assert activate_language_overrides(tmp_path) == {}
+
+
+# ---------------------------------------------------------------------------
+# Every suffix-keyed decision sees the declared language
+# ---------------------------------------------------------------------------
+
+def test_effective_suffix_is_the_real_one_until_a_project_says_otherwise():
+    assert effective_suffix(Path("x/a.inc")) == ".inc"
+    assert effective_suffix(Path("x/a.F90")) == ".F90"  # case preserved
+    set_language_overrides({".inc": ".php"})
+    assert effective_suffix(Path("x/a.inc")) == ".php"
+    assert effective_suffix(Path("x/a.INC")) == ".php"
+    assert effective_suffix(Path("x/a.F90")) == ".F90"
+
+
+def test_dispatch_goes_to_the_declared_extractor():
+    assert _get_extractor(Path("a.inc")) is extract_pascal
+    set_language_overrides({".inc": ".php"})
+    assert _get_extractor(Path("a.inc")) is extract_php
+    assert _get_extractor(Path("b.pas")) is extract_pascal  # untouched
+
+
+def test_a_remapped_header_skips_the_content_sniff(tmp_path):
+    """`.h` is normally sniffed for C++/ObjC; a declaration makes it definite."""
+    from graphify.extract import extract_cpp
+    h = tmp_path / "plain.h"
+    h.write_text("int add(int a, int b);\n", encoding="utf-8")
+    set_language_overrides({".h": ".cpp"})
+    assert _get_extractor(h) is extract_cpp
+
+
+def test_a_remap_to_an_extension_without_an_extractor_yields_none():
+    set_language_overrides({".inc": ".nosuchlang"})
+    assert _get_extractor(Path("a.inc")) is None
+
+
+def test_classification_follows_the_declaration():
+    assert classify_file(Path("page.tpl")) is None  # unknown extension
+    set_language_overrides({".tpl": ".php", ".txt": ".md"})
+    assert classify_file(Path("page.tpl")) is FileType.CODE
+    assert classify_file(Path("notes.txt")) is FileType.DOCUMENT
+
+
+def test_case_folding_and_interop_family_follow_the_declaration():
+    assert not _lang_is_case_insensitive("lib/a.inc")
+    assert _lang_family("lib/a.inc") is None
+    set_language_overrides({".inc": ".php"})
+    assert _lang_is_case_insensitive("lib/a.inc")  # PHP identifiers fold case
+    assert _lang_family("lib/a.inc") == "php"
+
+
+def test_language_resolvers_wake_for_the_declared_language():
+    ran: list[str] = []
+    resolvers = [
+        LanguageResolver("php", frozenset({".php"}), lambda *a: ran.append("php")),
+        LanguageResolver("pascal", frozenset({".pas", ".inc"}), lambda *a: ran.append("pascal")),
+    ]
+    paths = [Path("a.inc")]
+    run_language_resolvers(paths, [{}], [], [], resolvers=resolvers)
+    assert ran == ["pascal"]
+    ran.clear()
+    set_language_overrides({".inc": ".php"})
+    run_language_resolvers(paths, [{}], [], [], resolvers=resolvers)
+    assert ran == ["php"]
+
+
+# ---------------------------------------------------------------------------
+# The reporter's repro: same bytes, two extensions
+# ---------------------------------------------------------------------------
+
+@pytest.fixture
+def php_pair(tmp_path):
+    (tmp_path / "a.inc").write_text(PHP_SOURCE, encoding="utf-8")
+    (tmp_path / "b.php").write_text(PHP_SOURCE, encoding="utf-8")
+    return tmp_path
+
+
+def _counts(root, name):
+    r = _quiet_extract([root / name], cache_root=root, root=root)
+    return len(r["nodes"]), len(r["edges"])
+
+
+def test_without_a_declaration_the_inc_file_is_nearly_empty(php_pair):
+    """The failure mode: no error, just a graph missing the runtime."""
+    inc, php = _counts(php_pair, "a.inc"), _counts(php_pair, "b.php")
+    assert php[0] > 5 and php[1] > 5
+    assert inc[0] < php[0] and inc[1] < php[1]
+
+
+def test_with_the_declaration_the_two_files_yield_the_same_graph(php_pair):
+    (php_pair / ".graphifyrc").write_text("language.inc=php\n", encoding="utf-8")
+    assert _counts(php_pair, "a.inc") == _counts(php_pair, "b.php")
+
+
+def test_a_library_caller_needs_no_setup_beyond_the_file(php_pair):
+    """extract() finds `<root>/.graphifyrc` itself — the skill runbook and the
+    MCP server call it directly, never through the CLI."""
+    (php_pair / ".graphifyrc").write_text("language.inc=php\n", encoding="utf-8")
+    set_language_overrides(None)  # nothing pre-activated
+    assert _counts(php_pair, "a.inc") == _counts(php_pair, "b.php")
+
+
+def test_extract_announces_the_active_overrides(php_pair):
+    (php_pair / ".graphifyrc").write_text("language.inc=php\n", encoding="utf-8")
+    out = io.StringIO()
+    with redirect_stdout(out):
+        extract([php_pair / "a.inc"], cache_root=php_pair, root=php_pair)
+    assert ".inc -> .php" in out.getvalue()
+
+
+def test_detect_counts_a_declared_extension_as_code(tmp_path):
+    (tmp_path / "page.tpl").write_text(PHP_SOURCE, encoding="utf-8")
+    with redirect_stdout(io.StringIO()):
+        before = detect(tmp_path)["files"]
+    (tmp_path / ".graphifyrc").write_text("language.tpl=php\n", encoding="utf-8")
+    with redirect_stdout(io.StringIO()):
+        after = detect(tmp_path)["files"]
+    assert not any(p.endswith("page.tpl") for p in before.get("code", []))
+    assert any(p.endswith("page.tpl") for p in after.get("code", []))
+
+
+# ---------------------------------------------------------------------------
+# The cache must not replay the other language's parse
+# ---------------------------------------------------------------------------
+
+def test_cache_salt_exists_only_for_remapped_files():
+    assert cache_salt(Path("a.inc")) is None
+    set_language_overrides({".inc": ".php"})
+    assert cache_salt(Path("a.inc")) == "language=.php"
+    assert cache_salt(Path("b.php")) is None
+
+
+def test_changing_the_declaration_does_not_serve_the_stale_entry(php_pair):
+    """Extract as Pascal (cached), declare PHP, extract again: the PHP graph,
+    not the Pascal entry keyed by the same bytes."""
+    pascal = _counts(php_pair, "a.inc")
+    (php_pair / ".graphifyrc").write_text("language.inc=php\n", encoding="utf-8")
+    php = _counts(php_pair, "a.inc")
+    assert php == _counts(php_pair, "b.php") != pascal
+    # and back again: the PHP entry must not be served for the Pascal parse
+    (php_pair / ".graphifyrc").write_text("language.inc=pascal\n", encoding="utf-8")
+    assert _counts(php_pair, "a.inc") == pascal
+
+
+# ---------------------------------------------------------------------------
+# Worker processes
+# ---------------------------------------------------------------------------
+
+@pytest.mark.skipif(_worker_init is None, reason="pre-fix tree")
+def test_worker_init_installs_the_parents_overrides():
+    _worker_init({".inc": ".php"})
+    assert _get_extractor(Path("a.inc")) is extract_php
+
+
+@pytest.mark.skipif(_worker_init is None, reason="pre-fix tree")
+def test_the_pool_hands_its_workers_the_overrides(php_pair, monkeypatch):
+    """Under `spawn` a worker starts with empty module state; the pool must
+    forward the mapping through its initializer."""
+    seen: dict = {}
+
+    class RecordingPool(concurrent.futures.ThreadPoolExecutor):
+        def __init__(self, max_workers=None, initializer=None, initargs=(), **kw):
+            seen["initializer"] = initializer
+            seen["initargs"] = initargs
+            super().__init__(max_workers=max_workers, initializer=initializer, initargs=initargs)
+
+    monkeypatch.setattr(concurrent.futures, "ProcessPoolExecutor", RecordingPool)
+    for i in range(25):  # past _PARALLEL_THRESHOLD
+        (php_pair / f"f{i}.inc").write_text(PHP_SOURCE, encoding="utf-8")
+    (php_pair / ".graphifyrc").write_text("language.inc=php\n", encoding="utf-8")
+    files = sorted(php_pair.glob("f*.inc"))
+    result = _quiet_extract(files, cache_root=php_pair, root=php_pair, parallel=True)
+    assert seen["initializer"] is _worker_init
+    assert seen["initargs"] == ({".inc": ".php"},)
+    # and every file came back as PHP, not Pascal
+    per_file = {}
+    for n in result["nodes"]:
+        per_file.setdefault(n.get("source_file"), 0)
+        per_file[n.get("source_file")] += 1
+    assert len(per_file) == 25 and min(per_file.values()) > 5
+
+
+# ---------------------------------------------------------------------------
+# A config typo must be loud, not fatal
+# ---------------------------------------------------------------------------
+
+def test_a_malformed_rc_warns_once_and_scans_without_overrides(php_pair):
+    (php_pair / ".graphifyrc").write_text("language.inc=klingon\n", encoding="utf-8")
+    err = io.StringIO()
+    with redirect_stderr(err):
+        first = _counts(php_pair, "a.inc")
+        _counts(php_pair, "a.inc")
+    assert first == _counts(php_pair, "a.inc")  # Pascal, as before
+    assert err.getvalue().count("ignoring .graphifyrc") == 1
+    assert "klingon" in err.getvalue()
+
+
+def test_activating_a_root_without_rc_clears_a_previous_roots_overrides(tmp_path):
+    set_language_overrides({".inc": ".php"})
+    activate_language_overrides(tmp_path)
+    assert effective_suffix(Path("a.inc")) == ".inc"

From ee776c6a08f8a223f68254e3b2975729b41a0dd0 Mon Sep 17 00:00:00 2001
From: Andre Brait <andrebrait@gmail.com>
Date: Thu, 3 Sep 2026 06:53:44 +0000
Subject: [PATCH 2/2] feat: enable native Leiden on modern Python

The Graphify clustering path already imports graspologic_native directly, but the leiden extra still installed the Python graspologic package, whose metadata excludes Python 3.13+. Use graspologic-native's cp39-abi3 wheels instead so the extra works on current Python versions without a compiler or a rustworkx fork.
---
 README.md                     |   2 +-
 pyproject.toml                |   4 +-
 tests/test_wheel_packaging.py |   8 +
 uv.lock                       | 915 ++--------------------------------
 4 files changed, 54 insertions(+), 875 deletions(-)

diff --git a/README.md b/README.md
index ff7d7c4ba6..223ad485e9 100644
--- a/README.md
+++ b/README.md
@@ -255,7 +255,7 @@ Codex users also need `multi_agent = true` under `[features]` in `~/.codex/confi
 | `neo4j` | Neo4j push support | `uv tool install "graphifyy[neo4j]"` |
 | `falkordb` | FalkorDB push support | `uv tool install "graphifyy[falkordb]"` |
 | `svg` | SVG graph export | `uv tool install "graphifyy[svg]"` |
-| `leiden` | Leiden community detection (Python < 3.13 only) | `uv tool install "graphifyy[leiden]"` |
+| `leiden` | Leiden community detection via the native abi3 wheel (Python 3.10+) | `uv tool install "graphifyy[leiden]"` |
 | `ollama` | Ollama local inference | `uv tool install "graphifyy[ollama]"` |
 | `openai` | OpenAI / OpenAI-compatible APIs | `uv tool install "graphifyy[openai]"` |
 | `gemini` | Google Gemini API | `uv tool install "graphifyy[gemini]"` |
diff --git a/pyproject.toml b/pyproject.toml
index 7fd891dc85..3a0dbda725 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -62,7 +62,7 @@ falkordb = ["falkordb"]
 pdf = ["pypdf>=6.12.0", "markdownify"]
 watch = ["watchdog"]
 svg = ["matplotlib", "numpy>=2.0; python_version >= '3.13'"]
-leiden = ["graspologic; python_version < '3.13'"]
+leiden = ["graspologic-native>=1.2.1"]
 office = ["python-docx", "openpyxl"]
 google = ["openpyxl"]
 # --postgres reconstructs DDL and feeds it to extract_sql(), which needs the
@@ -98,7 +98,7 @@ commonlisp = ["tree-sitter-commonlisp"]
 # every platform, no C toolchain; optional because Robot Framework corpora are
 # QA-automation specific.
 robot = ["robotframework>=4.0"]
-all = ["mcp>=1,<3", "starlette>=1.3.1,<2", "neo4j", "falkordb", "pypdf>=6.12.0", "markdownify", "watchdog", "graspologic; python_version < '3.13'", "python-docx", "openpyxl", "faster-whisper; python_version >= '3.11'", "yt-dlp>=2026.6.9", "matplotlib", "numpy>=2.0; python_version >= '3.13'", "openai", "tiktoken", "boto3", "anthropic", "tree-sitter-sql", "jieba", "tree-sitter-dm", "tree-sitter-hcl", "tree-sitter-pascal", "tree-sitter-ocaml", "tree-sitter-commonlisp", "robotframework>=4.0"]
+all = ["mcp>=1,<3", "starlette>=1.3.1,<2", "neo4j", "falkordb", "pypdf>=6.12.0", "markdownify", "watchdog", "graspologic-native>=1.2.1", "python-docx", "openpyxl", "faster-whisper; python_version >= '3.11'", "yt-dlp>=2026.6.9", "matplotlib", "numpy>=2.0; python_version >= '3.13'", "openai", "tiktoken", "boto3", "anthropic", "tree-sitter-sql", "jieba", "tree-sitter-dm", "tree-sitter-hcl", "tree-sitter-pascal", "tree-sitter-ocaml", "tree-sitter-commonlisp", "robotframework>=4.0"]
 
 [project.scripts]
 graphify = "graphify.__main__:main"
diff --git a/tests/test_wheel_packaging.py b/tests/test_wheel_packaging.py
index 0c93bb8344..169d2b7c56 100644
--- a/tests/test_wheel_packaging.py
+++ b/tests/test_wheel_packaging.py
@@ -8,6 +8,7 @@
 from __future__ import annotations
 
 import subprocess
+import tomllib
 import sys
 import zipfile
 from pathlib import Path
@@ -82,3 +83,10 @@ def test_skill_artifact_ships_in_wheel(artifact: Path, wheel_namelist: set[str])
         f"`graphify install` would hard-exit for this host. Check the "
         f"[tool.setuptools.package-data] globs in pyproject.toml."
     )
+
+def test_leiden_extra_installs_the_native_backend_on_new_python() -> None:
+    extras = tomllib.loads((REPO / "pyproject.toml").read_text(encoding="utf-8"))["project"][
+        "optional-dependencies"
+    ]
+    assert any(dep.startswith("graspologic-native") for dep in extras["leiden"])
+    assert all("python_version" not in dep for dep in extras["leiden"])
diff --git a/uv.lock b/uv.lock
index 888412e056..2ac55b7502 100644
--- a/uv.lock
+++ b/uv.lock
@@ -6,10 +6,10 @@ resolution-markers = [
     "python_full_version >= '3.14' and sys_platform == 'emscripten'",
     "python_full_version >= '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'",
     "python_full_version == '3.13.*' and sys_platform == 'win32'",
-    "python_full_version >= '3.11' and python_full_version < '3.13' and sys_platform == 'win32'",
     "python_full_version == '3.13.*' and sys_platform == 'emscripten'",
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