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Minor
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Using Eloy's grep trick on the lang files revealed a lot of BOM markers. I assume they don't cause any problems in html files, but I think that the php files can be a problem.
For absolute vi dummies like me, the solution looks like
grep -rl $'\xEF\xBB\xBF' * //Search folder and subfolders for BOM markers
vim filename //opens file in vim
:set nobomb //removes the BOM
:w //saves the file with the same name
:q //quit vim
(credits to Eloy and http://www.tuxfiles.org/linuxhelp/vimcheat.html)
to perform on a *nix or a mac.
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I couldn't find a single corrupted file due to the deletion of the BOM by using Eloy's script. As long as it concerns text files (no binary files) it should be ok to run it and commit to CVS, although being careful is always allowed 
Perhaps, "bom_out.sh" is your script!
MDL-10637Ciao
MDL-10637Ciao