diff --git a/graphify/skill-agents.md b/graphify/skill-agents.md
index 1b3da7c5..6961fa78 100644
--- a/graphify/skill-agents.md
+++ b/graphify/skill-agents.md
@@ -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
         "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
diff --git a/graphify/skill-aider.md b/graphify/skill-aider.md
index 3559b480..5d4f6e0d 100644
--- a/graphify/skill-aider.md
+++ b/graphify/skill-aider.md
@@ -64,7 +64,7 @@ PYTHON=""
 GRAPHIFY_BIN=$(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="$_UV_PY"; fi
 fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
@@ -80,7 +80,7 @@ if [ -z "$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 \
diff --git a/graphify/skill-amp.md b/graphify/skill-amp.md
index 1b3da7c5..6961fa78 100644
--- a/graphify/skill-amp.md
+++ b/graphify/skill-amp.md
@@ -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
         "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
diff --git a/graphify/skill-claw.md b/graphify/skill-claw.md
index a53809df..7985c508 100644
--- a/graphify/skill-claw.md
+++ b/graphify/skill-claw.md
@@ -70,7 +70,7 @@ PYTHON=""
 GRAPHIFY_BIN=$(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 \
diff --git a/graphify/skill-codex.md b/graphify/skill-codex.md
index 36cadce5..e6387fed 100644
--- a/graphify/skill-codex.md
+++ b/graphify/skill-codex.md
@@ -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
         "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
diff --git a/graphify/skill-copilot.md b/graphify/skill-copilot.md
index a53809df..7985c508 100644
--- a/graphify/skill-copilot.md
+++ b/graphify/skill-copilot.md
@@ -70,7 +70,7 @@ PYTHON=""
 GRAPHIFY_BIN=$(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 \
diff --git a/graphify/skill-devin.md b/graphify/skill-devin.md
index 13fb37c8..21a4d1ad 100644
--- a/graphify/skill-devin.md
+++ b/graphify/skill-devin.md
@@ -75,7 +75,7 @@ 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)
@@ -91,7 +91,7 @@ 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
         "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
diff --git a/graphify/skill-droid.md b/graphify/skill-droid.md
index 2bef076d..25d55b23 100644
--- a/graphify/skill-droid.md
+++ b/graphify/skill-droid.md
@@ -70,7 +70,7 @@ PYTHON=""
 GRAPHIFY_BIN=$(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 \
diff --git a/graphify/skill-kilo.md b/graphify/skill-kilo.md
index d3aca08c..da34d0d0 100644
--- a/graphify/skill-kilo.md
+++ b/graphify/skill-kilo.md
@@ -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
         "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
diff --git a/graphify/skill-kiro.md b/graphify/skill-kiro.md
index a53809df..7985c508 100644
--- a/graphify/skill-kiro.md
+++ b/graphify/skill-kiro.md
@@ -70,7 +70,7 @@ PYTHON=""
 GRAPHIFY_BIN=$(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 \
diff --git a/graphify/skill-opencode.md b/graphify/skill-opencode.md
index 2aa66f5b..c40f5278 100644
--- a/graphify/skill-opencode.md
+++ b/graphify/skill-opencode.md
@@ -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
         "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
diff --git a/graphify/skill-pi.md b/graphify/skill-pi.md
index a53809df..7985c508 100644
--- a/graphify/skill-pi.md
+++ b/graphify/skill-pi.md
@@ -70,7 +70,7 @@ PYTHON=""
 GRAPHIFY_BIN=$(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 \
diff --git a/graphify/skill-trae.md b/graphify/skill-trae.md
index c1635cde..fc62552d 100644
--- a/graphify/skill-trae.md
+++ b/graphify/skill-trae.md
@@ -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
         "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
diff --git a/graphify/skill-vscode.md b/graphify/skill-vscode.md
index 30247498..bc303d8e 100644
--- a/graphify/skill-vscode.md
+++ b/graphify/skill-vscode.md
@@ -70,7 +70,7 @@ PYTHON=""
 GRAPHIFY_BIN=$(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 \
diff --git a/graphify/skill.md b/graphify/skill.md
index a53809df..7985c508 100644
--- a/graphify/skill.md
+++ b/graphify/skill.md
@@ -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
         "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
diff --git a/tools/skillgen/expected/graphify__skill-agents.md b/tools/skillgen/expected/graphify__skill-agents.md
index 1b3da7c5..6961fa78 100644
--- a/tools/skillgen/expected/graphify__skill-agents.md
+++ b/tools/skillgen/expected/graphify__skill-agents.md
@@ -70,7 +70,7 @@ PYTHON=""
 GRAPHIFY_BIN=$(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 \
diff --git a/tools/skillgen/expected/graphify__skill-aider.md b/tools/skillgen/expected/graphify__skill-aider.md
index 3559b480..5d4f6e0d 100644
--- a/tools/skillgen/expected/graphify__skill-aider.md
+++ b/tools/skillgen/expected/graphify__skill-aider.md
@@ -64,7 +64,7 @@ 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)
@@ -80,7 +80,7 @@ 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
         "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
diff --git a/tools/skillgen/expected/graphify__skill-amp.md b/tools/skillgen/expected/graphify__skill-amp.md
index 1b3da7c5..6961fa78 100644
--- a/tools/skillgen/expected/graphify__skill-amp.md
+++ b/tools/skillgen/expected/graphify__skill-amp.md
@@ -70,7 +70,7 @@ PYTHON=""
 GRAPHIFY_BIN=$(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 \
diff --git a/tools/skillgen/expected/graphify__skill-claw.md b/tools/skillgen/expected/graphify__skill-claw.md
index a53809df..7985c508 100644
--- a/tools/skillgen/expected/graphify__skill-claw.md
+++ b/tools/skillgen/expected/graphify__skill-claw.md
@@ -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
         "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
diff --git a/tools/skillgen/expected/graphify__skill-codex.md b/tools/skillgen/expected/graphify__skill-codex.md
index 36cadce5..e6387fed 100644
--- a/tools/skillgen/expected/graphify__skill-codex.md
+++ b/tools/skillgen/expected/graphify__skill-codex.md
@@ -70,7 +70,7 @@ PYTHON=""
 GRAPHIFY_BIN=$(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 \
diff --git a/tools/skillgen/expected/graphify__skill-copilot.md b/tools/skillgen/expected/graphify__skill-copilot.md
index a53809df..7985c508 100644
--- a/tools/skillgen/expected/graphify__skill-copilot.md
+++ b/tools/skillgen/expected/graphify__skill-copilot.md
@@ -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
         "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
diff --git a/tools/skillgen/expected/graphify__skill-devin.md b/tools/skillgen/expected/graphify__skill-devin.md
index 13fb37c8..21a4d1ad 100644
--- a/tools/skillgen/expected/graphify__skill-devin.md
+++ b/tools/skillgen/expected/graphify__skill-devin.md
@@ -75,7 +75,7 @@ PYTHON=""
 GRAPHIFY_BIN=$(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="$_UV_PY"; fi
 fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
@@ -91,7 +91,7 @@ if [ -z "$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 \
diff --git a/tools/skillgen/expected/graphify__skill-droid.md b/tools/skillgen/expected/graphify__skill-droid.md
index 2bef076d..25d55b23 100644
--- a/tools/skillgen/expected/graphify__skill-droid.md
+++ b/tools/skillgen/expected/graphify__skill-droid.md
@@ -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
         "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
diff --git a/tools/skillgen/expected/graphify__skill-kilo.md b/tools/skillgen/expected/graphify__skill-kilo.md
index d3aca08c..da34d0d0 100644
--- a/tools/skillgen/expected/graphify__skill-kilo.md
+++ b/tools/skillgen/expected/graphify__skill-kilo.md
@@ -70,7 +70,7 @@ PYTHON=""
 GRAPHIFY_BIN=$(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 \
diff --git a/tools/skillgen/expected/graphify__skill-kiro.md b/tools/skillgen/expected/graphify__skill-kiro.md
index a53809df..7985c508 100644
--- a/tools/skillgen/expected/graphify__skill-kiro.md
+++ b/tools/skillgen/expected/graphify__skill-kiro.md
@@ -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
         "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
diff --git a/tools/skillgen/expected/graphify__skill-opencode.md b/tools/skillgen/expected/graphify__skill-opencode.md
index 2aa66f5b..c40f5278 100644
--- a/tools/skillgen/expected/graphify__skill-opencode.md
+++ b/tools/skillgen/expected/graphify__skill-opencode.md
@@ -70,7 +70,7 @@ PYTHON=""
 GRAPHIFY_BIN=$(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 \
diff --git a/tools/skillgen/expected/graphify__skill-pi.md b/tools/skillgen/expected/graphify__skill-pi.md
index a53809df..7985c508 100644
--- a/tools/skillgen/expected/graphify__skill-pi.md
+++ b/tools/skillgen/expected/graphify__skill-pi.md
@@ -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
         "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
diff --git a/tools/skillgen/expected/graphify__skill-trae.md b/tools/skillgen/expected/graphify__skill-trae.md
index c1635cde..fc62552d 100644
--- a/tools/skillgen/expected/graphify__skill-trae.md
+++ b/tools/skillgen/expected/graphify__skill-trae.md
@@ -70,7 +70,7 @@ PYTHON=""
 GRAPHIFY_BIN=$(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 \
diff --git a/tools/skillgen/expected/graphify__skill-vscode.md b/tools/skillgen/expected/graphify__skill-vscode.md
index 30247498..bc303d8e 100644
--- a/tools/skillgen/expected/graphify__skill-vscode.md
+++ b/tools/skillgen/expected/graphify__skill-vscode.md
@@ -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
         "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
diff --git a/tools/skillgen/expected/graphify__skill.md b/tools/skillgen/expected/graphify__skill.md
index a53809df..7985c508 100644
--- a/tools/skillgen/expected/graphify__skill.md
+++ b/tools/skillgen/expected/graphify__skill.md
@@ -70,7 +70,7 @@ PYTHON=""
 GRAPHIFY_BIN=$(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 \
diff --git a/tools/skillgen/fragments/core/aider.md b/tools/skillgen/fragments/core/aider.md
index 3559b480..5d4f6e0d 100644
--- a/tools/skillgen/fragments/core/aider.md
+++ b/tools/skillgen/fragments/core/aider.md
@@ -64,7 +64,7 @@ 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)
@@ -80,7 +80,7 @@ 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
         "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
diff --git a/tools/skillgen/fragments/core/devin.md b/tools/skillgen/fragments/core/devin.md
index 13fb37c8..21a4d1ad 100644
--- a/tools/skillgen/fragments/core/devin.md
+++ b/tools/skillgen/fragments/core/devin.md
@@ -75,7 +75,7 @@ PYTHON=""
 GRAPHIFY_BIN=$(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="$_UV_PY"; fi
 fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
@@ -91,7 +91,7 @@ if [ -z "$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 \
diff --git a/tools/skillgen/fragments/shell/posix.md b/tools/skillgen/fragments/shell/posix.md
index 717bd800..3534417d 100644
--- a/tools/skillgen/fragments/shell/posix.md
+++ b/tools/skillgen/fragments/shell/posix.md
@@ -4,7 +4,7 @@ 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)
@@ -20,7 +20,7 @@ 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 \
diff --git a/tools/skillgen/gen.py b/tools/skillgen/gen.py
index e742a62c..e6dbbd9b 100644
--- a/tools/skillgen/gen.py
+++ b/tools/skillgen/gen.py
@@ -888,6 +888,20 @@ def _is_obsidian_usage_comment_line(line: str) -> bool:
     return "# full pipeline on current directory" in line
 
 
+def _is_uv_from_interpreter_fix_line(line: str) -> bool:
+    """Whether a line is part of the uv interpreter-detection fix (#1735).
+
+    Step 1's POSIX interpreter probe ran ``uv tool run graphifyy python -c ...``,
+    but ``graphifyy`` exposes its executable as ``graphify``, so uv treated
+    ``python`` as a missing ``graphifyy`` command and the probe silently failed
+    (the ``2>/dev/null`` swallowed uv's "use --from" hint), leaving PYTHON on a
+    graphify-less system interpreter. The probe now runs
+    ``uv tool run --from graphifyy python -c ...``. Both the old (removed) and new
+    (added) forms match here.
+    """
+    return "uv tool run" in line and "graphifyy python" in line
+
+
 # Every line that may differ between a rendered monolith and its pristine v8
 # baseline. Each predicate documents one sanctioned change-class; a blank line is
 # allowed because the multi-line fix blocks insert spacing. Anything else failing
@@ -904,6 +918,7 @@ _SANCTIONED_MONOLITH_DIFFS = (
     _is_no_api_key_fix_line,
     _is_shebang_allowlist_fix_line,
     _is_obsidian_usage_comment_line,
+    _is_uv_from_interpreter_fix_line,
 )