fix: wiki encoding+collisions, hook rebase guard, detect path resolve, readme gitignore docs

- wiki.py: add encoding="utf-8" to all write_text() calls (fixes Windows cp1252 crash #496)
- wiki.py: deduplicate filenames with _unique_slug() to prevent silent article overwrites (#497)
- hooks.py: skip post-commit/post-checkout during rebase/merge/cherry-pick (#485)
- detect.py: resolve root path at detect() entry so .graphifyignore patterns match consistently (#495)
- README.md: document manifest.json, cost.json gitignore and .graphifyignore platform file examples (#369)

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

README.md

@@ -164,8 +164,10 @@ Think of it this way: the always-on hook gives your assistant a map. The `/graph
 
 **Recommended `.gitignore` additions:**
 ```
-# commit graph outputs, ignore the extraction cache
-graphify-out/cache/
+# keep graph outputs, skip heavy/local-only files
+graphify-out/cache/            # optional: commit for shared extraction speed, skip to keep repo small
+graphify-out/manifest.json     # mtime-based, invalid after git clone — always gitignore this
+graphify-out/cost.json         # local token tracking, not useful to share
 ```
 
 **Shared setup:**
@@ -176,6 +178,16 @@ graphify-out/cache/
 
 **Excluding paths** — create `.graphifyignore` in your project root (same syntax as `.gitignore`). Files matching those patterns are skipped during detection and extraction.
 
+```
+# .graphifyignore example
+AGENTS.md          # graphify install files — don't extract your own instructions as knowledge
+CLAUDE.md
+GEMINI.md
+.gemini/
+.opencode/
+docs/translations/ # generated content you don't want in the graph
+```
+
 ## Using `graph.json` with an LLM
 
 `graph.json` is not meant to be pasted into a prompt all at once. The useful

graphify/detect.py

@@ -334,6 +334,7 @@ def _is_ignored(path: Path, root: Path, patterns: list[tuple[Path, str]]) -> boo
 
 
 def detect(root: Path, *, follow_symlinks: bool = False) -> dict:
+    root = root.resolve()
     files: dict[FileType, list[str]] = {
         FileType.CODE: [],
         FileType.DOCUMENT: [],

graphify/hooks.py

@@ -44,6 +44,13 @@ _HOOK_SCRIPT = """\
 # Auto-rebuilds the knowledge graph after each commit (code files only, no LLM needed).
 # Installed by: graphify hook install
 
+# Skip during rebase/merge/cherry-pick to avoid blocking --continue with unstaged changes
+GIT_DIR=$(git rev-parse --git-dir 2>/dev/null)
+[ -d "$GIT_DIR/rebase-merge" ] && exit 0
+[ -d "$GIT_DIR/rebase-apply" ] && exit 0
+[ -f "$GIT_DIR/MERGE_HEAD" ] && exit 0
+[ -f "$GIT_DIR/CHERRY_PICK_HEAD" ] && exit 0
+
 CHANGED=$(git diff --name-only HEAD~1 HEAD 2>/dev/null || git diff --name-only HEAD 2>/dev/null)
 if [ -z "$CHANGED" ]; then
     exit 0
@@ -93,6 +100,13 @@ if [ ! -d "graphify-out" ]; then
     exit 0
 fi
 
+# Skip during rebase/merge/cherry-pick
+GIT_DIR=$(git rev-parse --git-dir 2>/dev/null)
+[ -d "$GIT_DIR/rebase-merge" ] && exit 0
+[ -d "$GIT_DIR/rebase-apply" ] && exit 0
+[ -f "$GIT_DIR/MERGE_HEAD" ] && exit 0
+[ -f "$GIT_DIR/CHERRY_PICK_HEAD" ] && exit 0
+
 """ + _PYTHON_DETECT + """
 echo "[graphify] Branch switched - rebuilding knowledge graph (code files)..."
 $GRAPHIFY_PYTHON -c "

graphify/wiki.py

@@ -190,12 +190,23 @@ def to_wiki(
     god_nodes_data = god_nodes_data or []
 
     count = 0
+    used_slugs: set[str] = set()
+
+    def _unique_slug(base: str) -> str:
+        slug = base
+        n = 2
+        while slug in used_slugs:
+            slug = f"{base}_{n}"
+            n += 1
+        used_slugs.add(slug)
+        return slug
 
     # Community articles
     for cid, nodes in communities.items():
         label = labels.get(cid, f"Community {cid}")
         article = _community_article(G, cid, nodes, label, labels, cohesion.get(cid))
-        (out / f"{_safe_filename(label)}.md").write_text(article)
+        slug = _unique_slug(_safe_filename(label))
+        (out / f"{slug}.md").write_text(article, encoding="utf-8")
         count += 1
 
     # God node articles
@@ -203,12 +214,14 @@ def to_wiki(
         nid = node_data.get("id")
         if nid and nid in G:
             article = _god_node_article(G, nid, labels)
-            (out / f"{_safe_filename(node_data['label'])}.md").write_text(article)
+            slug = _unique_slug(_safe_filename(node_data['label']))
+            (out / f"{slug}.md").write_text(article, encoding="utf-8")
             count += 1
 
     # Index
     (out / "index.md").write_text(
-        _index_md(communities, labels, god_nodes_data, G.number_of_nodes(), G.number_of_edges())
+        _index_md(communities, labels, god_nodes_data, G.number_of_nodes(), G.number_of_edges()),
+        encoding="utf-8",
     )
 
     return count

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "graphifyy"
-version = "0.4.25"
+version = "0.4.26"
 description = "AI coding assistant skill (Claude Code, Codex, OpenCode, Cursor, Gemini CLI, Aider, OpenClaw, Factory Droid, Trae, Hermes, Kiro, Google Antigravity) - turn any folder of code, docs, papers, images, or videos into a queryable knowledge graph"
 readme = "README.md"
 license = { file = "LICENSE" }