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I added a <noscript> bit to a hefty javascript section saved the file and (doh!) closed composer. I uploaded the inc section and went to the site to see how my efforts to increase user-friendliness turned out.
Aaaarghh! Composer had totally rewrote major sections of the file so that the page was just one mess of errors. Well, because it was an include file the whole SITE was just a messs of errors :(
Every PHP section was mangled beyond recognition, and there were also </body></html> tags added at the end (what was actually the middle of a page).
It's lucky this site is just personal homepage-ish and definitely the last time I use Composer :)
Because I had closed the program after the edit I couldn't undo the changes. I had a frantic scramble to find older/backed up versions of the code...
Composer: Don't try this at home ;)
The moral of the story:
If we don't change direction, we'll end up where we're headed.