Fix #676 #678 #681: graphifyignore negation, Antigravity slash command, Gemini hook Windows

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

graphify/__main__.py

@@ -252,9 +252,13 @@ _GEMINI_HOOK = {
         {
             "type": "command",
             "command": (
-                "[ -f graphify-out/graph.json ] && "
-                r"""echo '{"decision":"allow","additionalContext":"graphify: Knowledge graph exists. Read graphify-out/GRAPH_REPORT.md for god nodes and community structure before searching raw files."}' """
-                r"""|| echo '{"decision":"allow"}'"""
+                'python -c "'
+                "import sys,pathlib,json;"
+                "e=pathlib.Path('graphify-out/graph.json').exists();"
+                "d={'decision':'allow'};"
+                "e and d.update({'additionalContext':'graphify: Knowledge graph exists. Read graphify-out/GRAPH_REPORT.md for god nodes and community structure before searching raw files.'});"
+                "sys.stdout.write(json.dumps(d))"
+                '"'
             ),
         }
     ],
@@ -448,11 +452,13 @@ Rules:
 """
 
 _ANTIGRAVITY_WORKFLOW = """\
+---
+name: graphify
+description: Turn any folder of files into a navigable knowledge graph
+---
+
 # Workflow: graphify
-**Command:** /graphify
-**Description:** Turn any folder of files into a navigable knowledge graph
 
-## Steps
 Follow the graphify skill installed at ~/.agents/skills/graphify/SKILL.md to run the full pipeline.
 
 If no path argument is given, use `.` (current directory).

graphify/detect.py

@@ -656,11 +656,14 @@ def detect(root: Path, *, follow_symlinks: bool = False) -> dict:
                 # Prune noise dirs in-place so os.walk never descends into them.
                 # Hidden dirs are allowed through if they could contain an
                 # explicitly included path (.graphifyinclude allowlist).
+                # When negation patterns (!) exist, skip directory-level ignore
+                # pruning so negated files inside can still be reached.
+                has_negation = any(p.startswith("!") for _, p in ignore_patterns)
                 dirnames[:] = [
                     d for d in dirnames
                     if (not d.startswith(".") or _could_contain_included_path(dp / d, root, include_patterns))
                     and not _is_noise_dir(d)
-                    and not _is_ignored(dp / d, root, ignore_patterns)
+                    and (has_negation or not _is_ignored(dp / d, root, ignore_patterns))
                 ]
             for fname in filenames:
                 if fname in _SKIP_FILES: