Remove 'warning:' string from configure.in message

Buildbot detects warnings by grepping output for '[Ww]arning:';
instead, use 'caution:'.
machinetalk/Submakefile:  fix protobuf C++ include list

With `../include` already prepended to the header file path, the later
substitution in `MT_INSTALL_INCS` adds `../include/` to the list, causing
the later error message in `make clean`:

    rm: cannot remove ‘../include/’: Is a directory
Silence make jobserver warnings

    make[2]: warning: jobserver unavailable: using -j1.  Add `+' to parent
    make rule.
silence 'ldconfig' warning when building Debian packages

    ldconfig /tmp/machinekit/machinekit/src/../debian/tmp/usr/lib
    /sbin/ldconfig.real: Can't create temporary cache file
        /etc/ld.so.cache~: Permission denied
    make[1]: [install-kernel-indep] Error 1 (ignored)
debian/rules.in:  dpkg-shlibdeps warning exclusions

Add patterns to the `$(SHLIBDEPS_X)` variable that will be prefixed by
`-X` and appended to the `dh_shlibdeps` command.

Remove old, nonsensical `-l` argument (`/usr/lib` is in the default
list already, and `/debian/machinekit/usr/lib` is not a standard path
on any system!)

Conflicts:
	debian/rules.in
configure.in:  silence warning about libxenomai useless dependency

`libxenomai` symbols aren't directly used; silence this warning during
Debian package builds:

    dpkg-shlibdeps: warning: package could avoid a useless dependency
    if debian/machinekit-xenomai/usr/lib/linuxcnc/xenomai/rtapi.so
    debian/machinekit-xenomai/usr/lib/linuxcnc/ulapi-xenomai.so were
    not linked against libxenomai.so.0 (they use none of the library's
    symbols)