Modernize the build system.

Recent versions of autoconf and automake were giving a lot of warnings. This is
sort of a backport of similar build system changes from the 1.1 banch:

- Fix all autoconf/automake warnings.
- Merge lib/ into src/.
- Don't use symlinks for device.c any more, but use automake conditionals.
- Use explicit paths to local header files.
- Get rid of alloca.c/malloc.c/memcmp.c/realloc.c.