Improved file copying (binary handling)

[xoorath]

There are a few things we need to do better for file copying and binary handling.

• Binary files should not use ESD they should just be copied.
• We should wrap file copying to detect if a file has changed or not to allow skipping of those files.
• Not directly related but in a similar part of the code: we should be deleting all temporary files when we're done with them (not just on the next run).