remove binaries
ignore generated files
make native.c cross-platform
fix jist script's reliance on /proc/meminfo
partially fix memprof building, disable it
change build directory to 'build'
fix grid placement

If you placed 2 nodes in a field with X = [0, 10], the nodes would be placed at X=0 and X=5. This commit changes it to X=0 and X=10.
enable assertions
add $JAVA_HOME test and test cases to Makefile

The test cases can be run with "make test".
remove use of proprietary sun HexDumpEncoder

No test scenario seems to trigger the changed method. The use of sun's HexDumpEncoder is commented-out for now, a replacement will be needed if this is actually used.
remove use of proprietary sun GetPropertyAction

The new code will probably work, but since no test case seemed to touch the changed method this is currently untested.
fix exception when the NIC queue gets full

The IP implementation in NetIp.java does not implement any drop logic, so the NIC queue throws an exception when it gets full and an additional insert is attempted.

This commit fixes this issue, by implementing a simple tail drop.