fix hook reinstall, CRLF labels, skill-windows missing commands (0.3.28)

CHANGELOG.md

@@ -2,6 +2,12 @@
 
 Full release notes with details on each version: [GitHub Releases](https://github.com/safishamsi/graphify/releases)
 
+## 0.3.28 (2026-04-10)
+
+- Fix: hook installers (Claude Code, Codex, Gemini CLI) now always remove and reinstall the hook on re-run — users upgrading from old versions no longer get stuck with a broken hook format (#182)
+- Fix: rationale node labels no longer contain bare `\r` characters on Windows/WSL CRLF files — breaks Obsidian export was silently producing invalid filenames (#176)
+- Fix: `skill-windows.md` now includes `--wiki`, `--obsidian-dir`, and `--directed` which were missing vs the main skill (#177)
+
 ## 0.3.27 (2026-04-10)
 
 - Fix: graphify install --platform gemini now also copies the skill file to ~/.gemini/skills/graphify/SKILL.md so the /graphify trigger works in Gemini CLI (#174)

graphify/__main__.py

@@ -241,10 +241,8 @@ def _install_gemini_hook(project_dir: Path) -> None:
     except json.JSONDecodeError:
         settings = {}
     before_tool = settings.setdefault("hooks", {}).setdefault("BeforeTool", [])
-    if any("graphify" in str(h) for h in before_tool):
-        print("  .gemini/settings.json  ->  hook already registered (no change)")
-        return
-    before_tool.append(_GEMINI_HOOK)
+    settings["hooks"]["BeforeTool"] = [h for h in before_tool if "graphify" not in str(h)]
+    settings["hooks"]["BeforeTool"].append(_GEMINI_HOOK)
     settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
     print("  .gemini/settings.json  ->  BeforeTool hook registered")
 
@@ -455,11 +453,8 @@ def _install_codex_hook(project_dir: Path) -> None:
         existing = {}
 
     pre_tool = existing.setdefault("hooks", {}).setdefault("PreToolUse", [])
-    if any("graphify" in str(h) for h in pre_tool):
-        print(f"  .codex/hooks.json  ->  hook already registered (no change)")
-        return
-
-    pre_tool.extend(_CODEX_HOOK["hooks"]["PreToolUse"])
+    existing["hooks"]["PreToolUse"] = [h for h in pre_tool if "graphify" not in str(h)]
+    existing["hooks"]["PreToolUse"].extend(_CODEX_HOOK["hooks"]["PreToolUse"])
     hooks_path.write_text(json.dumps(existing, indent=2), encoding="utf-8")
     print(f"  .codex/hooks.json  ->  PreToolUse hook registered")
 
@@ -578,12 +573,8 @@ def _install_claude_hook(project_dir: Path) -> None:
     hooks = settings.setdefault("hooks", {})
     pre_tool = hooks.setdefault("PreToolUse", [])
 
-    # Check if already installed
-    if any(h.get("matcher") == "Glob|Grep" and "graphify" in str(h) for h in pre_tool):
-        print(f"  .claude/settings.json  ->  hook already registered (no change)")
-        return
-
-    pre_tool.append(_SETTINGS_HOOK)
+    hooks["PreToolUse"] = [h for h in pre_tool if not (h.get("matcher") == "Glob|Grep" and "graphify" in str(h))]
+    hooks["PreToolUse"].append(_SETTINGS_HOOK)
     settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
     print(f"  .claude/settings.json  ->  PreToolUse hook registered")
 

graphify/export.py

@@ -463,7 +463,7 @@ def to_obsidian(
     # Map node_id → safe filename so wikilinks stay consistent.
     # Deduplicate: if two nodes produce the same filename, append a numeric suffix.
     def safe_name(label: str) -> str:
-        return re.sub(r'[\\/*?:"<>|#^[\]]', "", label).strip() or "unnamed"
+        return re.sub(r'[\\/*?:"<>|#^[\]]', "", label.replace("\r\n", " ").replace("\r", " ").replace("\n", " ")).strip() or "unnamed"
 
     node_filename: dict[str, str] = {}
     seen_names: dict[str, int] = {}
@@ -699,7 +699,7 @@ def to_canvas(
     CANVAS_COLORS = ["1", "2", "3", "4", "5", "6"]  # red, orange, yellow, green, cyan, purple
 
     def safe_name(label: str) -> str:
-        return re.sub(r'[\\/*?:"<>|#^[\]]', "", label).strip() or "unnamed"
+        return re.sub(r'[\\/*?:"<>|#^[\]]', "", label.replace("\r\n", " ").replace("\r", " ").replace("\n", " ")).strip() or "unnamed"
 
     # Build node_filenames if not provided (same dedup logic as to_obsidian)
     if node_filenames is None:

graphify/extract.py

@@ -1021,7 +1021,7 @@ def _extract_python_rationale(path: Path, result: dict) -> None:
         return None
 
     def _add_rationale(text: str, line: int, parent_nid: str) -> None:
-        label = text[:80].replace("\n", " ").strip()
+        label = text[:80].replace("\r\n", " ").replace("\r", " ").replace("\n", " ").strip()
         rid = _make_id(stem, "rationale", str(line))
         if rid not in seen_ids:
             seen_ids.add(rid)

graphify/skill-windows.md

@@ -15,6 +15,7 @@ Turn any folder of files into a navigable knowledge graph with community detecti
 /graphify <path>                                      # full pipeline on specific path
 /graphify <path> --mode deep                          # thorough extraction, richer INFERRED edges
 /graphify <path> --update                             # incremental - re-extract only new/changed files
+/graphify <path> --directed                            # build directed graph (preserves edge direction: source→target)
 /graphify <path> --cluster-only                       # rerun clustering on existing graph
 /graphify <path> --no-viz                             # skip visualization, just report + JSON
 /graphify <path> --html                               # (HTML is generated by default - this flag is a no-op)
@@ -22,6 +23,8 @@ Turn any folder of files into a navigable knowledge graph with community detecti
 /graphify <path> --graphml                            # export graph.graphml (Gephi, yEd)
 /graphify <path> --neo4j                              # generate graphify-out/cypher.txt for Neo4j
 /graphify <path> --neo4j-push bolt://localhost:7687   # push directly to Neo4j
+/graphify <path> --wiki                               # build agent-crawlable wiki (index.md + one article per community)
+/graphify <path> --obsidian --obsidian-dir ~/vaults/my-project  # write vault to custom path (e.g. existing vault)
 /graphify <path> --mcp                                # start MCP stdio server for agent access
 /graphify <path> --watch                              # watch folder, auto-rebuild on code changes (no LLM needed)
 /graphify add <url>                                   # fetch URL, save to ./raw, update graph

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "graphifyy"
-version = "0.3.27"
+version = "0.3.28"
 description = "AI coding assistant skill (Claude Code, Codex, OpenCode, Cursor, OpenClaw, Factory Droid, Trae) - turn any folder of code, docs, papers, or images into a queryable knowledge graph"
 readme = "README.md"
 license = { file = "LICENSE" }