Fix Windows build due to line ending changes in sed

Fix Windows build due to line ending changes in sed

The recent sed update in cygwin [1] changed the way sed handles
carriage returns. This meant that every .in file we processed
still contained CR, which doesn't work for .sh files.

Force LF line endings for those files (and also other shell scripts).

[1] https://cygwin.com/ml/cygwin-announce/2017-02/msg00036.html