diff --git a/scripts/bootstrap.sh b/scripts/bootstrap.sh
index 1396be7..4553a22 100644
--- a/scripts/bootstrap.sh
+++ b/scripts/bootstrap.sh
@@ -419,10 +419,14 @@ set -e
 # REPO is injected at install time; if it doesn't look like a project, try to
 # find the repo by walking up from the current working directory.
 REPO="__REPO__"
-if [ ! -f "$REPO/CLI.py" ] && [ ! -f "$REPO/pyproject.toml" ] && [ ! -f "$REPO/setup.py" ]; then
+# If the embedded REPO does not contain a canonical project marker, search
+# upward from the current working directory for a project root. Use only
+# explicit project markers (CLI.py or pyproject.toml) to avoid false positives
+# from subdirectories like 'scripts' which may contain their own setup.py.
+if [ ! -f "$REPO/CLI.py" ] && [ ! -f "$REPO/pyproject.toml" ]; then
   CUR="$(pwd -P)"
   while [ "$CUR" != "/" ] && [ "$CUR" != "" ]; do
-    if [ -f "$CUR/CLI.py" ] || [ -f "$CUR/pyproject.toml" ] || [ -f "$CUR/setup.py" ]; then
+    if [ -f "$CUR/CLI.py" ] || [ -f "$CUR/pyproject.toml" ]; then
       REPO="$CUR"
       break
     fi