Cleanup main loop

workflow/qhtcp-workflow

@@ -533,11 +533,12 @@ interactive_header() {
         echo 
         cat <<-EOF
 					Enter project number(s) to analyze:
-					  * A comma-separated list of project numbers (ex. 2,5,12)
+					  * <Enter> for the latest project ($num) (default)
+					  * A comma-separated list of project numbers (2,5,12)
 					  * 0 to add a new project
-					  * <Enter> for the latest project ($num)			  
 				EOF
         ((YES)) || read -r -p "($num): " response
+        echo ""
         if [[ $response == 0 ]]; then 
           ask_pn && PROJECTS+=("${ADD_PROJECTS[@]}")
         else
@@ -568,12 +569,12 @@ interactive_header() {
   if [[ ${#MODULES[@]} -eq 0 && ${#EXCLUDE_MODULES[@]} -eq 0 ]]; then
     cat <<-EOF
 			Enter modules(s) to run:
-			  * A comma-separated list of module numbers
-			  * Example: 2,5,12
+			  * <Enter> for all (default)
+			  * A comma-separated list of module numbers (2,5,12)
 			  * 0 for none	  
-			  * <Enter> for all modules (default)					  
 		EOF
     ((YES)) || read -r -p "(all): " response
+    echo ""
     if [[ -z $response ]]; then
       MODULES=("${ALL_MODULES[@]}")
     elif [[ $response -eq 0 ]]; then
@@ -591,13 +592,14 @@ interactive_header() {
     while :; do
       cat <<-EOF
 				Enter submodules(s) to run followed by its arguments in a comma-separated string
-				  * Quote your string if there are any whitespaces
+				  * <Enter> for none (default)
 				  * A comma-separated list of submodules and their arguments
 				  * Both arguments are required
+				  * Quote the argument string if it contains whitespace
 				  * Example: ${ALL_SUBMODULES[0]},\"arg1,arg2,arg3...\",${ALL_SUBMODULES[1]},\"arg1,arg2,arg3...\"
-				  * <Enter> for none (default)		  
 			EOF
       ((YES)) || read -r -p "(none): " response
+      echo ""
       [[ -z $response ]] && break
       IFS=',' read -ra arr <<< "$response"
       if [[ $((${#arr[@]} % 2)) -eq 0 ]]; then # check if array is even
@@ -1262,10 +1264,17 @@ qhtcp() {
 
   if [[ -d $QHTCP_PROJECT_DIR ]]; then
     # Handle existing output directory
-    echo "A project already exists at $QHTCP_PROJECT_DIR"
-    echo "Would you like to (c)ontinue, (u)pdate it from the template and continue, or (b)ack it up and continue from scratch?"
+    cat <<-EOF
+			A project already exists at $QHTCP_PROJECT_DIR
+			Would you like to 
+			  * (c)ontinue (default)
+			  * (u)pdate it from the template and continue
+			  * (b)ack it up and start from scratch
+		EOF
+
     for i in {1..3}; do # give the user three chances to get it right
-      ((YES)) || read -r -p "Hit [Enter] or c to continue: " response
+      ((YES)) || read -r -p "(c): " response
+      echo ""
       [[ -z $response ]] && break
       case $response in
         u)