If you're a programmer, you need to move your text (ASCII) files properly from Windows to Linux or else you'll have more headaches than you should. I had that headache today so I'm posting this so you may not have to go through it.
I had some config files for gVim that had an extra "^M" character after every line. I think that's a return carriage in Windows.
To clean files automatically, put them in Subversion, or simpler yet, put it through an FTP server. Make sure though that you upload it as ASCII and the files aren't zipped. Apparently, that does the job!
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