The solution is simply "tidy"/Tidy-HTML.  It will take your poorly formatted HTML code (and I mean files that span just a few lines that are unreadable) and fix it up.

Note the command below does everything in place.  *Make sure you take a backup of all .html files*

It also seems to break html5 code/templates so beware.

tidy -im yourfile.html

An automated way in bash:

cd /your/website/directory


for html in `find .|grep ".html$"`; do


tidy -im $html


done

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