Fix `clean` target

- Fix up `linux/Makefile` so `clean` target works
- Don't copy autoconf files from system; let `autoreconf` take care of that
- Don't overwrite or zap files under version control
- `config.{guess,sub}` are in the `bin/` directory
- Other cleanups
Remove `fix-include-comedilib-h.patch`, accepted upstream
New patches

- Fix for `make distclean`
- Fix for ignored `./configure --includedir`
Fix incorrect arch selection

Correct arch is 'x86', not 'x86_64'.  Who'd've thunk?
Clean up warning building python-rtai pkg
Fix build problem with compressed files

Compressing the ipipe patches in the `binary-indep` section when the
`rtai-source` package is a `binary-arch` package led to a race
condition where `dh_md5sum` failed to process a `.patch` file that had
been converted to `.patch.gz` without its knowledge.
Remove patches:  one upstream, the other irrelevant

fix-make-distclean is upstream

includedir-subdir is irrelevant:  x86_64 arch is obsolete
v. 4.0.2:  update changelog