So after much searching I seem to have found a solution that works, here is what I did. After looking at other Stackoverflow questions I found someone that said this worked for them.

Find the file called copy-www-build-step.sh.

Mine was in
[project_folder]/platforms/ios/cordova/lib/copy-www-build-step.sh

In that file, find the lines beginning rsync -a ...

Add -c to the rsync lines, so they ready rsync -a -c ...

Well I tried that and it did not work on its own. I also tried the answer from Ville and that pulled closer but no cigar. Finally I took what the command from Ville and put it in the copy-www-build-step.sh file

so my top line is now

cd /path/to/your/cordova/project/

cordova prepare



SRC_DIR=www/

DST_DIR=$BUILT_PRODUCTS_DIR/$FULL_PRODUCT_NAME/www

COPY_HIDDEN=

ORIG_IFS=$IFS

IFS=$(echo -en nb)

.....

.....

.....etc etc 

And now I make change , and click run , bam all is updated. I hope this helps someone else.