Add proper "make install" and clean up "--prefix" / "--with-systemwide" handling

We do have a make install, but it currently only (opportunistically) installs bash and zsh completions, and into directories unaffected by --prefix. The rest of its logic is somehow commented out:

install: strip shell-completion
#ifneq ($(prefix), ../run)
#       @echo Copying binaries to $(prefix)
#       $(MKDIR) $(prefix)
#       $(CP) -p -P -R ../run/*.{py,pl,rb} $(PROJ) $(prefix)
#       @echo Copying data and config files to $(prefix)
#       $(MKDIR) $(prefix)
#       $(CP) -p -P -R ../run/*.{chr,conf,lst} $(prefix)
#endif

Other than that, we already handle --prefix mostly similarly to how other typical autoconf'ed software does it:

dnl -DJOHN_SYSTEMWIDE
AC_ARG_WITH(systemwide, [AS_HELP_STRING([--with-systemwide],[install for all users])],,[with_systemwide=no])

AC_PREFIX_DEFAULT([../run])

dnl Handle --prefix -> JOHN_SYSTEMWIDE
dnl A prefix of /usr/local will mean execs in /usr/local/bin and the rest
dnl in /usr/local/share/john
AS_IF([test $prefix != "../run" && test $prefix != "NONE" ],
   [CFLAGS="$CFLAGS -DJOHN_SYSTEMWIDE -DJOHN_SYSTEMWIDE_EXEC='\"$prefix/bin\"' -DJOHN_SYSTEMWIDE_HOME='\"$prefix/share/john\"'"],
   [AS_IF([test $with_systemwide != no], [CFLAGS="$CFLAGS -DJOHN_SYSTEMWIDE"
   prefix=/usr/libexec/john])]
)

I think we should rework the logic around --with-systemwide, though. Do we know of existing users of the present logic?

Start with the existing make install target and the configure logic for --prefix and --with-systemwide shown in the issue. Trace how the current prefix values affect executable, data, and completion destinations. Done means make install consistently installs the project under the selected prefix and the systemwide behavior is clearly defined and tested.