games/vkquake: Improve port

• Replace "${PREFIX}/share/applications" with "${DESKTOPDIR}".
• Use icons from tarball instead of what's in port - remove the binary from the ports tree.
• Remove USES=desktop-file-utils - there is no "MimeType" element in vkquake.desktop.
• Run MKDIR once for all directories.

PR: 288178
Co-authored-by: vvd