diff --git a/deploy/nexus/ensure-genome-vault.sh b/deploy/nexus/ensure-genome-vault.sh
index 42ed105..265c349 100644
--- a/deploy/nexus/ensure-genome-vault.sh
+++ b/deploy/nexus/ensure-genome-vault.sh
@@ -91,6 +91,14 @@ EOF
 grep -qxF 'raw/.stignore' "${vault}/.git/info/exclude" 2>/dev/null \
   || echo 'raw/.stignore' >> "${vault}/.git/info/exclude"
 
+# Syncthing folder marker: must exist on disk (locally, NOT on Git).
+# Without it, Syncthing refuses to scan (“folder marker missing”).
+mkdir -p "${vault}/raw/.stfolder"
+
+# .stfolder must not be included in genome commits
+grep -qxF 'raw/.stfolder' "${vault}/.git/info/exclude" 2>/dev/null \
+|| echo 'raw/.stfolder' >> "${vault}/.git/info/exclude"
+
 # ── 3. Idempotent Syncthing folder configuration (best-effort, does not block the vault) ────────
 folder_state="skipped(no api key)"
 if [[ -n "${SYNCTHING_API_KEY:-}" ]]; then