diff --git a/setup/generate-modules.sh b/setup/tools/generate-modules.sh
similarity index 97%
rename from setup/generate-modules.sh
rename to setup/tools/generate-modules.sh
index d39a648..7404a69 100755
--- a/setup/generate-modules.sh
+++ b/setup/tools/generate-modules.sh
@@ -11,10 +11,11 @@
 set -euo pipefail
 
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-CONF="$SCRIPT_DIR/modules.conf"
-TUI="$SCRIPT_DIR/tui-install.sh"
-AF="$SCRIPT_DIR/generate-answerfile.sh"
-DOCS="$SCRIPT_DIR/../docs/md/modules.md"
+SETUP_DIR="$(cd "$SCRIPT_DIR/.." && pwd)"
+CONF="$SETUP_DIR/modules.conf"
+TUI="$SETUP_DIR/tui-install.sh"
+AF="$SETUP_DIR/generate-answerfile.sh"
+DOCS="$SETUP_DIR/../docs/md/modules.md"
 
 DRY_RUN=false
 [[ "${1:-}" == "--dry-run" ]] && DRY_RUN=true
diff --git a/setup/sync-modules.sh b/setup/tools/sync-modules.sh
similarity index 88%
rename from setup/sync-modules.sh
rename to setup/tools/sync-modules.sh
index e2cabf1..8101a76 100755
--- a/setup/sync-modules.sh
+++ b/setup/tools/sync-modules.sh
@@ -4,8 +4,9 @@
 set -euo pipefail
 
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-CONF="$SCRIPT_DIR/modules.conf"
-APPS="$SCRIPT_DIR/modules/optional-Modules/apps"
+SETUP_DIR="$(cd "$SCRIPT_DIR/.." && pwd)"
+CONF="$SETUP_DIR/modules.conf"
+APPS="$SETUP_DIR/modules/optional-Modules/apps"
 
 # Read all existing IDs from modules.conf into a set.
 declare -A known