chore(graphify): sync vendored skill 0.9.6 -> 0.9.15

Upstream skill refresh, present in the working tree before this session —
committed here rather than left dangling. Not authored work.

- uv invocation fix: `uv tool run graphifyy python` -> `uv tool run --from
  graphifyy python`. Without --from, uv resolved the command name against
  the package instead of running the interpreter.
- default output is now HTML viz; --obsidian opts into the vault.
- description reworded to trigger on codebase questions generally, not
  only when graphify-out/ already exists.

skills/graphify/.graphify_version

@@ -1 +1 @@
-0.9.6
+0.9.15

skills/graphify/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: graphify
-description: "Use when graphify-out/ exists (or the user asks to build a knowledge graph): questions about the codebase, its architecture, file relationships, or project content are then treated as graphify queries first. Turns any input (code, docs, papers, images, videos) into a persistent knowledge graph with god nodes, community detection, and query/path/explain tools."
+description: "Use for any question about a codebase, its architecture, file relationships, or project content — especially when graphify-out/ exists, where the question should be treated as a graphify query first. Turns any input (code, docs, papers, images, videos) into a persistent knowledge graph with god nodes, community detection, and query/path/explain tools."
 ---
 
 # /graphify
@@ -10,7 +10,7 @@ Turn any folder of files into a navigable knowledge graph with community detecti
 ## Usage
 
 ```
-/graphify                                             # full pipeline on current directory → Obsidian vault
+/graphify                                             # full pipeline on current directory (HTML viz; add --obsidian for a vault)
 /graphify <path>                                      # full pipeline on specific path
 /graphify https://github.com/<owner>/<repo>           # clone repo then run full pipeline on it
 /graphify https://github.com/<owner>/<repo> --branch <branch>  # clone a specific branch
@@ -70,7 +70,7 @@ PYTHON=""
 GRAPHIFY_BIN=$(which graphify 2>/dev/null)
 # 1. uv tool installs — most reliable on modern Mac/Linux
 if [ -z "$PYTHON" ] && command -v uv >/dev/null 2>&1; then
-    _UV_PY=$(uv tool run graphifyy python -c "import sys; print(sys.executable)" 2>/dev/null)
+    _UV_PY=$(uv tool run --from graphifyy python -c "import sys; print(sys.executable)" 2>/dev/null)
     if [ -n "$_UV_PY" ]; then PYTHON="$_UV_PY"; fi
 fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
@@ -86,7 +86,7 @@ if [ -z "$PYTHON" ]; then PYTHON="python3"; fi
 if ! "$PYTHON" -c "import graphify" 2>/dev/null; then
     if command -v uv >/dev/null 2>&1; then
         uv tool install --upgrade graphifyy -q 2>&1 | tail -3
-        _UV_PY=$(uv tool run graphifyy python -c "import sys; print(sys.executable)" 2>/dev/null)
+        _UV_PY=$(uv tool run --from graphifyy python -c "import sys; print(sys.executable)" 2>/dev/null)
         if [ -n "$_UV_PY" ]; then PYTHON="$_UV_PY"; fi
     else
         "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
@@ -313,7 +313,8 @@ from graphify.cache import save_semantic_cache
 from pathlib import Path
 
 new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
-saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
+uncached = [line for line in Path('graphify-out/.graphify_uncached.txt').read_text(encoding=\"utf-8\").splitlines() if line]
+saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH', allowed_source_files=uncached)
 print(f'Cached {saved} files')
 "
 ```