Stop substituting INPUT_PATH into an interpreted shell command in Step 1

Step 1's own bash and PowerShell fragments both built a command whose
literal text was the resolved scan path, substituted verbatim by the
agent following the instructions before that line ever ran. The bash
form, echo dollar paren cd INPUT_PATH and pwd close paren, still
expands a command substitution even inside the outer double quotes,
and the cd itself was entirely unquoted; the PowerShell form passed
INPUT_PATH as a bare unquoted argument to Resolve Path, exposed to the
same class of problem through a stray semicolon or pipe. A path drawn
from an untrusted source, a malicious readme's suggested command, a
copied value from an untrusted page, executed as code the moment this
line ran, before any Python was ever reached.

Both now capture INPUT_PATH through a construct their own interpreter
guarantees performs no expansion at all: a quoted bash heredoc for the
posix form, a single quoted PowerShell here string for the windows
form. The raw text reaches Python (respectively Resolve Path) only as
inert data on standard input, never as source the shell itself
parses. Verified for the posix form by actually executing the
extracted Step 1 block with a malicious substituted value and
confirming no injected command runs; the PowerShell form could not be
executed in this environment (no interpreter available to install
without an interactive credential prompt), so it was written using
well established, unambiguous here string syntax and reviewed
carefully rather than run.

As a side effect of no longer building the path through an unquoted
cd, a legitimate path containing a space is now handled correctly
too, and a nonexistent path now fails the whole step loudly instead
of silently continuing past a swallowed cd error.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_017qfdzgbA5KedGEjD1AayNh
(cherry picked from commit 9a7e5d0a51)

tools/skillgen/fragments/shell/posix.md

@@ -30,8 +30,14 @@ fi
 # Write interpreter path for all subsequent steps (persists across invocations)
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
-# Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+# Save scan root so `graphify update` (no args) knows where to look next time.
+# INPUT_PATH is passed through a quoted heredoc, never substituted into the
+# command line itself: a bare `cd INPUT_PATH` (or an unquoted heredoc, which
+# still expands $()/backticks in its body) would let a malicious path execute
+# as shell code the moment this line runs.
+"$PYTHON" -c "import os, sys; out_path = os.path.abspath('graphify-out/.graphify_root'); os.chdir(sys.stdin.readline().rstrip('\n')); open(out_path, 'w', encoding='utf-8').write(os.getcwd())" <<'GRAPHIFY_ROOT_EOF'
+INPUT_PATH
+GRAPHIFY_ROOT_EOF
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.

tools/skillgen/fragments/shell/powershell.md

@@ -57,8 +57,15 @@ if (-not $GRAPHIFY_PYTHON) {
 # encoding writes the bytes POSIX writes, and adds no trailing newline.
 $Utf8NoBom = New-Object System.Text.UTF8Encoding $false
 [System.IO.File]::WriteAllText((Join-Path $PWD 'graphify-out\.graphify_python'), [string]$GRAPHIFY_PYTHON, $Utf8NoBom)
-# Save scan root so `graphify update` (no args) knows where to look next time
-[System.IO.File]::WriteAllText((Join-Path $PWD 'graphify-out\.graphify_root'), (Resolve-Path INPUT_PATH).Path, $Utf8NoBom)
+# Save scan root so `graphify update` (no args) knows where to look next time.
+# INPUT_PATH is captured through a single-quoted (literal) here-string, never
+# substituted directly into the command line: an unquoted bareword argument
+# substituted here would let a malicious path (a stray `;`, `|`, or `$(...)`)
+# execute as script code the moment this line runs.
+$InputPathRaw = @'
+INPUT_PATH
+'@
+[System.IO.File]::WriteAllText((Join-Path $PWD 'graphify-out\.graphify_root'), (Resolve-Path $InputPathRaw.Trim()).Path, $Utf8NoBom)
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.