swaps work for graphviz; code cleanup to gmakefile.c

Finally broke some of the more awefully long functions into more readable
size functions in preraporation for swap support and other non-c files.

Some configure fixes and cleanups.

Added the --buildprefix= option to adjust the build prefix at configure time.
swaps is probably working now

some swaps tests exist, but need more
various code cleanups
fixed configure problems
Fixed much with the INPUT model.

Trying to get the test case examples.customwithnativetool hot. It works
except for the graphviz plot.

This has also broken a bunch of stuff again.
Fixed regression caused by last commit.