Handle existing qhtcp project dir gracefully

workflow/qhtcp-workflow

@@ -267,14 +267,16 @@ random_words() {
   printf "%s_" "${arr[@]}" | sed 's/_$//'
 }
 # @description Backup one or more files to an incremented .bk file
+# @exitcode backup iterator max 255
 backup() {
   debug "Running: ${FUNCNAME[0]}" "$@"
   for f in "$@"; do
     [[ -e $f ]] || continue
     count=1
     while [[ -f $f.bk.$count ]]; do
-      count=$((count+1))
+      count=$((count++))
     done
+    echo "Backing up $f to $f.bk.$count"
     debug "rsync -a $f $f.bk.$count"
     rsync -a "$f" "$f.bk.$count"
   done
@@ -811,17 +813,34 @@ qhtcp() {
   debug "Running: ${FUNCNAME[0]}"
 
   if [[ -d $QHTCP_PROJECT_DIR ]]; then
+    # Handle existing output directory
     echo "A project already exists at $QHTCP_PROJECT_DIR"
-    ask "Safely update $QHTCP_PROJECT_DIR from the $QHTCP_TEMPLATE_DIR template?"
-    if ! ((YES)) && ask "Back up $QHTCP_PROJECT_DIR to $QHTCP_PROJECT_DIR.bk first and start fresh?"; then
-      mv "$QHTCP_PROJECT_DIR" "$QHTCP_PROJECT_DIR.bk" || (echo "Backup unsuccessful, exiting"; exit 1)
+    echo "Would you like to (c)ontinue, (u)pdate it from the template and continue, or (b)ack it up and continue from scratch?"
+    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
+      [[ -z $response ]] && break
+      case $response in
+        u)
+          echo "Updating project from template"
+          echo "Only files that are newer in the template will be overwritten"
+          if rsync --archive --update "$QHTCP_TEMPLATE_DIR"/ "$QHTCP_PROJECT_DIR"; then
+            echo "Project updated with template"
           fi
-  fi
-
-  # Copy template to QHTCP project directory
+          ;;
+        b)
+          backup "$QHTCP_PROJECT_DIR" && rm -rf "$QHTCP_PROJECT_DIR"
           if rsync --archive --update "$QHTCP_TEMPLATE_DIR"/ "$QHTCP_PROJECT_DIR"; then
             echo "New project created at $QHTCP_PROJECT_DIR"
           fi
+          ;;
+        *)
+          err "Invalid response, please try again"
+          continue
+          ;;
+      esac
+      break
+    done
+  fi
 
   # Sets STUDIES_NUMS and NUM_STUDIES (yes this makes sense)
   get_studies "$STUDY_INFO_FILE"
@@ -832,7 +851,7 @@ qhtcp() {
 
   # If the next Exp dir already exists don't use it
   while [[ -d $QHTCP_PROJECT_DIR/Exp$next_study_num ]]; do
-    (( next_study_num=next_study_num+1 ))
+    (( next_study_num++ ))
   done
 
   # Use initials from project not whoami