SystemTools: CopyFileAlways: avoid copying file over self

Since commit 228c60b8 (SystemTools: CopyFileAlways: try to create a
cheap CoW clone first, 2018-12-07) on Linux copying a file over itself
by specifying `.` as the destination leaves behind an empty file.  This
has long occurred on Windows too.  Move our existing same-file check
to after we know the real destination file.