Move Makefile to Makefile.in, add a distclean.

The clean command should now remove all generated files and dirs
from the build directory; the distclean will also purge Makefile
and .config.status.

For simplification, and to avoid the problem of running make before
configure, Makefile is now Makefile.in, and will only be copied by configure.

.gitignore got restructured a bit.