Developers on various platforms can often unknowingly introduce encoding issues on files. Here is a solution to one problem.
Simple one liner to remove all ^M line returns from files in a directory. I use this on an Open Source project I work on mainly for PHP files. Type "CTRL v" then "CTRL m" to get the system ^M char. The character will not copy and paste. The filter for SVN is optional and insert CVS or git for your SCM of choice.
grep -IUrl "^M" * | grep -v svn | xargs sed -i 's/^M$//'
Easy! Search the directory recursively. Filter out the SVN files. Run SED against the files in the list.