Add make find_missing_links to update-manifest.sh

To avoid problems the script now runs make find_missing_links at the
end. It does it in such a way, though, as to make sure everything is
fine before that. It runs the rule after everything is fine but if it
fails it tells them they do not have to run the script all over again
but they do need to fix the links and then run the appropriate make
rules in order to fix the html file(s). It does note that if you're in
doubt running 'make www' will be the safest bet.

There are two reasons the script does not run make www: first is that it
uses verbosity not used in the make rule and second is it offers to run
the quick-readme2index.sh script to go quicker if one knows that only
a few README.md files were modified. The script now warns that this will
only work if the README.md files have been changed (or timestamp
updated).

tmp/update-manifest.sh

@@ -303,6 +303,10 @@ read -r -n 1 -p "Press any key to continue: "
 echo 1>&2
 
 echo "$(basename "$0"): will now update index.html files." 1>&2
+echo "NOTE: quick-readme2index.sh will not create all index.html" 1>&2
+echo "files: it checks the timestamp of README.md and the respective" 1>&2
+echo "index.html files. Thus if you have not modified all the necessary" 1>&2
+echo "README.md files then you should not use the quick option!" 1>&2
 read -r -p "Do you wish to use quick-readme2index.sh (Y/N)? "
 if [[ "$REPLY" != "Y" && "$REPLY" != "y" ]]; then
     echo "$(basename "$0"): now will run: bin/all-run.sh -v $CAP_D_FLAG bin/readme2index.sh -v $CAP_D_FLAG" 1>&2
@@ -326,7 +330,6 @@ if ! bin/gen-other-html.sh -v "$CAP_D_FLAG"; then
     exit 5
 fi
 
-
 read -r -n 1 -p "Press any key to run: $GIT diff: "
 echo 1>&2
 "$GIT" diff
@@ -337,6 +340,22 @@ if [[ "$REPLY" != "Y" && "$REPLY" != "y" ]]; then
     exit 4
 fi
 
+echo "$(basename "$0"): now will run: make find_missing_links"
+echo "NOTE: this can take a little while." 1>&2
+if ! make find_missing_links; then
+    echo "problem running make find_missing_links, fix and try again." 1>&2
+	echo "NOTE: since everything else was updated, you can just fix the links" 1>&2
+	echo "and then run the appropriate make rules to fix just the affected html" 1>&2
+	echo "files rather than run this script all over again. If you're in doubt," 1>&2
+	echo "you can run:" 1>&2
+	echo
+	echo "		make www" 1>&2
+	echo
+	echo "to be absolutely sure that every html file is updated but this is likely" 1>&2
+	echo "not needed unless a lot of files had broken links." 1>&2
+    exit 5
+fi
+
 if [[ -n "$A_FLAG" ]]; then
     echo "Do you wish to automatically run the commands:" 1>&2
     echo "    git add -u" 1>&2