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Issue #277 change to keep original file utf-8 bom. Also fixed a problem where the "replace" added an extra new line to files that did not end with a new line.
I believe this fixes the current problem, but we could use more tests for replace on files with different encodings.
For Issue #210, added an additional fix for regex replace, where the regex contains a $ token. The $ (end of line) token will only match UNIX new line character, so Windows and Mac new lines must be converted to the UNIX new line before calling the replace method.