Add a copy of the Chisel JAR file

This allows me to run tests just from a Scala file.  This has
advantages and disadvantages: it allows me to test that I still
actually work with the Flo backend, but it also requires that the C++
backend for Chisel works.

The testing infastructure is kind of a mess...  I really need to
figure out what I'm doing here.
Support running Scala tests

The test harness now checks for Scala files and runs them.
Run clock_lo before clock_hi

I don't know how I managed to get this wrong...  The code now runs
clok_lo BEFORE running clock_hi, which results in the correct values
being computed from IOs.

There are also some tests for this behavior.

In additon, a number of chisel-tutorial tests now run.
Fix race in tests named "test"

I had the line

  $ cat test.stdin | ./opt

which would both read from and overwrite test.stdin, causing a race
condition.  This only happened for tests named "test", which is why I
hadn't noticed it before.

The fix is to just copy and run

  $ cat test.stdin.copy | ./opt

I also remove a workaround for this overwriting, though the removed
workaround just helps me read stdin (not the computer).