This makes code easier to read and more consistent between C++ and Java.
Also update clang-format settings to always add a line break (even if no braces are used).
Also added scripts for EOF newline management and for removing trailing whitespace. configure.bat was rewritten to use CRLF line endings. Documentation for the existing scripts was also improved.
* Replaced include guards with #pragma once
* All source files now have exactly one newline appended
Some files had either two newlines at the end or none (which isn't POSIX compliant). This patch fixes that.
