diff --git a/CHANGELOG.md b/CHANGELOG.md
index a73fed47d..b553094e9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -58,6 +58,7 @@ Full release notes with details on each version: [GitHub Releases](https://githu
 - Fix: a PHP `use` import written with a leading-backslash / fully-qualified prefix now resolves to its target definition instead of being dropped (#2661, thanks @ousamabenyounes).
 - Fix: an unresolved local JS/TS import (to a file absent from the scan) now emits a stable, portable `ref` target id instead of leaking a per-checkout absolute-path slug (#2457, thanks @rohit-jsfreaky).
 - Fix: `graphify benchmark` no longer crashes on a node whose label is `None` (#2674, thanks @Arthuro0103).
+- Fix: the git post-commit hook and skill interpreter probes now strip a shebang argument before using it as a path, so a pipx launcher (`#!/.../python -E`) resolves instead of silently falling back to a `python3` without graphify and printing "could not locate a Python with graphify installed" after every commit (#2629, thanks @hpstr5000).
 
 ## 0.9.40 (2026-08-11)
 
diff --git a/graphify/hooks.py b/graphify/hooks.py
index 5be58d12e..10a584b5b 100644
--- a/graphify/hooks.py
+++ b/graphify/hooks.py
@@ -76,6 +76,11 @@
             */env\\ *) GRAPHIFY_PYTHON="${_SHEBANG#*/env }" ;;
             *)         GRAPHIFY_PYTHON="$_SHEBANG" ;;
         esac
+        # Strip any interpreter argument: pipx writes `#!/.../python -E`, so the
+        # shebang carries a trailing argument that is not part of the path. Keep
+        # the leading word only, else the space trips the allowlist below and the
+        # valid interpreter is discarded (silent python3 fallback, #2629).
+        GRAPHIFY_PYTHON="${GRAPHIFY_PYTHON%% *}"
         # Allowlist: only keep characters valid in a filesystem path to prevent
         # injection if the shebang contains shell metacharacters.
         case "$GRAPHIFY_PYTHON" in
diff --git a/graphify/skill-agents.md b/graphify/skill-agents.md
index 190827d9a..e63ab8669 100644
--- a/graphify/skill-agents.md
+++ b/graphify/skill-agents.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -662,6 +667,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/graphify/skill-amp.md b/graphify/skill-amp.md
index 190827d9a..e63ab8669 100644
--- a/graphify/skill-amp.md
+++ b/graphify/skill-amp.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -662,6 +667,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/graphify/skill-claw.md b/graphify/skill-claw.md
index abd2811d2..a1f8a6a98 100644
--- a/graphify/skill-claw.md
+++ b/graphify/skill-claw.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -665,6 +670,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/graphify/skill-codex.md b/graphify/skill-codex.md
index af3f723c7..36b7542a8 100644
--- a/graphify/skill-codex.md
+++ b/graphify/skill-codex.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -662,6 +667,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/graphify/skill-copilot.md b/graphify/skill-copilot.md
index abd2811d2..a1f8a6a98 100644
--- a/graphify/skill-copilot.md
+++ b/graphify/skill-copilot.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -665,6 +670,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/graphify/skill-droid.md b/graphify/skill-droid.md
index fd148d485..83d82a9e8 100644
--- a/graphify/skill-droid.md
+++ b/graphify/skill-droid.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -662,6 +667,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/graphify/skill-kilo.md b/graphify/skill-kilo.md
index 3e70b050a..c5f6c3162 100644
--- a/graphify/skill-kilo.md
+++ b/graphify/skill-kilo.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -665,6 +670,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/graphify/skill-kiro.md b/graphify/skill-kiro.md
index abd2811d2..a1f8a6a98 100644
--- a/graphify/skill-kiro.md
+++ b/graphify/skill-kiro.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -665,6 +670,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/graphify/skill-opencode.md b/graphify/skill-opencode.md
index 91ced6067..63c223c24 100644
--- a/graphify/skill-opencode.md
+++ b/graphify/skill-opencode.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -657,6 +662,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/graphify/skill-pi.md b/graphify/skill-pi.md
index abd2811d2..a1f8a6a98 100644
--- a/graphify/skill-pi.md
+++ b/graphify/skill-pi.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -665,6 +670,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/graphify/skill-trae.md b/graphify/skill-trae.md
index 050667bc2..b44ab56b4 100644
--- a/graphify/skill-trae.md
+++ b/graphify/skill-trae.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -663,6 +668,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/graphify/skill-vscode.md b/graphify/skill-vscode.md
index 20c7c0835..cf52abe55 100644
--- a/graphify/skill-vscode.md
+++ b/graphify/skill-vscode.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -661,6 +666,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/graphify/skill.md b/graphify/skill.md
index abd2811d2..a1f8a6a98 100644
--- a/graphify/skill.md
+++ b/graphify/skill.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -665,6 +670,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/tests/test_hooks.py b/tests/test_hooks.py
index 9fffb32ba..190658f3f 100644
--- a/tests/test_hooks.py
+++ b/tests/test_hooks.py
@@ -976,3 +976,48 @@ def test_both_hooks_configured(tmp_path):
     for name in ("post-commit", "post-checkout"):
         hook_text = (repo / ".git" / "hooks" / name).read_text()
         assert 'export GRAPHIFY_VIZ_NODE_LIMIT="${GRAPHIFY_VIZ_NODE_LIMIT:-42}"' in hook_text
+
+
+@pytest.mark.skipif(os.name == "nt", reason="POSIX shebang probe")
+def test_hook_probe_resolves_pipx_shebang_with_argument(tmp_path):
+    """#2629: pipx writes `#!/.../python -E` — a shebang *with an argument*.
+
+    The interpreter probe must strip that argument before using the shebang as a
+    path; otherwise the space trips the character allowlist, the valid pipx
+    interpreter is discarded, and the hook silently falls back to a `python3`
+    that has no graphify (printing 'could not locate a Python with graphify').
+    """
+    import sys
+    from graphify.hooks import _PYTHON_DETECT
+
+    bindir = tmp_path / "bin"
+    bindir.mkdir()
+    launcher = bindir / "graphify"
+    # pipx-style launcher: shebang carries the `-E` argument.
+    launcher.write_text(f"#!{sys.executable} -E\nimport graphify\n", encoding="utf-8")
+    launcher.chmod(0o755)
+
+    script = _PYTHON_DETECT + '\nprintf "%s" "$GRAPHIFY_PYTHON"\n'
+    env = dict(os.environ, PATH=f"{bindir}{os.pathsep}{os.environ['PATH']}")
+    resolved = subprocess.run(
+        ["bash", "-c", script],
+        cwd=tmp_path,
+        env=env,
+        capture_output=True,
+        text=True,
+    ).stdout.strip()
+
+    assert resolved == sys.executable, (
+        f"probe did not resolve the pipx interpreter from a shebang with an "
+        f"argument; got {resolved!r}, expected {sys.executable!r}"
+    )
+
+
+def test_generated_skill_probes_strip_shebang_argument():
+    """#2629: both POSIX probe sites in the rendered skill (step-1 install and the
+    subcommand interpreter guard) must strip a shebang argument, so pipx
+    `#!/.../python -E` launchers resolve instead of silently reverting to python3."""
+    skill = (Path(__file__).resolve().parent.parent / "graphify" / "skill.md").read_text()
+    # Both sites keep only the leading word of the shebang.
+    assert skill.count('_SHEBANG="${_SHEBANG%% *}"') >= 1, "step-1 probe does not strip shebang argument"
+    assert 'PYTHON="${PYTHON%% *}"' in skill, "interpreter guard does not strip shebang argument"
diff --git a/tools/skillgen/expected/graphify__skill-agents.md b/tools/skillgen/expected/graphify__skill-agents.md
index 190827d9a..e63ab8669 100644
--- a/tools/skillgen/expected/graphify__skill-agents.md
+++ b/tools/skillgen/expected/graphify__skill-agents.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -662,6 +667,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/tools/skillgen/expected/graphify__skill-amp.md b/tools/skillgen/expected/graphify__skill-amp.md
index 190827d9a..e63ab8669 100644
--- a/tools/skillgen/expected/graphify__skill-amp.md
+++ b/tools/skillgen/expected/graphify__skill-amp.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -662,6 +667,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/tools/skillgen/expected/graphify__skill-claw.md b/tools/skillgen/expected/graphify__skill-claw.md
index abd2811d2..a1f8a6a98 100644
--- a/tools/skillgen/expected/graphify__skill-claw.md
+++ b/tools/skillgen/expected/graphify__skill-claw.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -665,6 +670,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/tools/skillgen/expected/graphify__skill-codex.md b/tools/skillgen/expected/graphify__skill-codex.md
index af3f723c7..36b7542a8 100644
--- a/tools/skillgen/expected/graphify__skill-codex.md
+++ b/tools/skillgen/expected/graphify__skill-codex.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -662,6 +667,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/tools/skillgen/expected/graphify__skill-copilot.md b/tools/skillgen/expected/graphify__skill-copilot.md
index abd2811d2..a1f8a6a98 100644
--- a/tools/skillgen/expected/graphify__skill-copilot.md
+++ b/tools/skillgen/expected/graphify__skill-copilot.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -665,6 +670,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/tools/skillgen/expected/graphify__skill-droid.md b/tools/skillgen/expected/graphify__skill-droid.md
index fd148d485..83d82a9e8 100644
--- a/tools/skillgen/expected/graphify__skill-droid.md
+++ b/tools/skillgen/expected/graphify__skill-droid.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -662,6 +667,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/tools/skillgen/expected/graphify__skill-kilo.md b/tools/skillgen/expected/graphify__skill-kilo.md
index 3e70b050a..c5f6c3162 100644
--- a/tools/skillgen/expected/graphify__skill-kilo.md
+++ b/tools/skillgen/expected/graphify__skill-kilo.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -665,6 +670,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/tools/skillgen/expected/graphify__skill-kiro.md b/tools/skillgen/expected/graphify__skill-kiro.md
index abd2811d2..a1f8a6a98 100644
--- a/tools/skillgen/expected/graphify__skill-kiro.md
+++ b/tools/skillgen/expected/graphify__skill-kiro.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -665,6 +670,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/tools/skillgen/expected/graphify__skill-opencode.md b/tools/skillgen/expected/graphify__skill-opencode.md
index 91ced6067..63c223c24 100644
--- a/tools/skillgen/expected/graphify__skill-opencode.md
+++ b/tools/skillgen/expected/graphify__skill-opencode.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -657,6 +662,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/tools/skillgen/expected/graphify__skill-pi.md b/tools/skillgen/expected/graphify__skill-pi.md
index abd2811d2..a1f8a6a98 100644
--- a/tools/skillgen/expected/graphify__skill-pi.md
+++ b/tools/skillgen/expected/graphify__skill-pi.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -665,6 +670,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/tools/skillgen/expected/graphify__skill-trae.md b/tools/skillgen/expected/graphify__skill-trae.md
index 050667bc2..b44ab56b4 100644
--- a/tools/skillgen/expected/graphify__skill-trae.md
+++ b/tools/skillgen/expected/graphify__skill-trae.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -663,6 +668,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/tools/skillgen/expected/graphify__skill-vscode.md b/tools/skillgen/expected/graphify__skill-vscode.md
index 20c7c0835..cf52abe55 100644
--- a/tools/skillgen/expected/graphify__skill-vscode.md
+++ b/tools/skillgen/expected/graphify__skill-vscode.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -661,6 +666,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/tools/skillgen/expected/graphify__skill.md b/tools/skillgen/expected/graphify__skill.md
index abd2811d2..a1f8a6a98 100644
--- a/tools/skillgen/expected/graphify__skill.md
+++ b/tools/skillgen/expected/graphify__skill.md
@@ -76,6 +76,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
@@ -665,6 +670,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/tools/skillgen/fragments/shell/interpreter-guard-posix.md b/tools/skillgen/fragments/shell/interpreter-guard-posix.md
index f7e344881..2b31e2bcc 100644
--- a/tools/skillgen/fragments/shell/interpreter-guard-posix.md
+++ b/tools/skillgen/fragments/shell/interpreter-guard-posix.md
@@ -3,6 +3,11 @@ if [ ! -f graphify-out/.graphify_python ]; then
     GRAPHIFY_BIN=$(which graphify 2>/dev/null)
     if [ -n "$GRAPHIFY_BIN" ]; then
         PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+        # Resolve `/usr/bin/env python` and strip any shebang argument (pipx
+        # writes `.../python -E`) before the allowlist check, else the space
+        # forces the unverified python3 fallback into .graphify_python (#2629).
+        case "$PYTHON" in */env\ *) PYTHON="${PYTHON#*/env }" ;; esac
+        PYTHON="${PYTHON%% *}"
         case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
     else
         PYTHON="python3"
diff --git a/tools/skillgen/fragments/shell/posix.md b/tools/skillgen/fragments/shell/posix.md
index 3534417d2..978409a13 100644
--- a/tools/skillgen/fragments/shell/posix.md
+++ b/tools/skillgen/fragments/shell/posix.md
@@ -10,6 +10,11 @@ fi
 # 2. Read shebang from graphify binary (pipx and direct pip installs)
 if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
     _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
+    # Resolve `/usr/bin/env python` to the interpreter, then strip any argument
+    # (pipx writes `.../python -E`) so a shebang argument is not mistaken for the
+    # path and rejected by the allowlist below (silent python3 fallback, #2629).
+    case "$_SHEBANG" in */env\ *) _SHEBANG="${_SHEBANG#*/env }" ;; esac
+    _SHEBANG="${_SHEBANG%% *}"
     case "$_SHEBANG" in
         *[!a-zA-Z0-9/_.@-]*) ;;
         *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;