Fixed a couple of things in update_versions script
diff --git a/update_versions b/update_versions
index 8073da1..af28ca6 100644
--- a/update_versions
+++ b/update_versions
@@ -2,7 +2,7 @@
 #
 # Script to update PTP versions
 #
-# Usage: user_id update_versions ptp_version photran_version [branch]
+# Usage: user_id update_versions ptp_version [branch]
 #
 # user_id - user id to use to clone repo
 # ptp_version - new version string for PTP and Photran (e.g. "5.0.1")
@@ -10,6 +10,11 @@
 #
 # Note: as of 9.1, PTP and Photran versions will be kept in sync
 #
+# Manual update is required for:
+# - the target version in org.eclipse.photran/pom.xml and org.eclipse.ptp/pom.xml
+# - MANIFEST.MF in core/org.eclipse.ptp.doc.user
+# - pom.xml in core/org.eclipse.ptp.doc.user
+#
 # A "qualifier" suffix will automatically be added to the version where appropriate
 #
 # If version numbers are updated on a branch other than master, it is recommended to run
@@ -29,11 +34,11 @@
 user_id=$1
 ptp_version=$2
 
-if [ $# -gt 3 ]; then
-	BRANCH=$4
+if [ $# -gt 2 ]; then
+	BRANCH=$3
 fi
 
-if [ -f fix_ptp_versions ]; then
+if [ -d fix_ptp_versions ]; then
 	echo "please remove fix_ptp_versions first"
 	exit 1
 fi