Cleanup: Do not ignore gen directories

The toolchain will complain if they do not exist. Make sure the directories are created, but their contents are ignored.
Cleanup: put accessory_filter.xml in the library

No need to copy it for every project. Thanks, Misha, for the tip!
IOIOLib: small bugs in flow control

The only real bugs here are:
- FlowControlledPacketSender exited the syncronized block before actually removing from the queue.
- FlowControlledPacketSender threw IllegalStateExceptions where IOExceptions are more appropriate.

The rest is some cleanup.
TortureTest: Some fixes

- Prevent test threads from crashing, better handling of timeout
  - Tests thread would exit silently when the UART test threw a ConnectionLostException in response to an IOException. This has now been fixed.
  - Tests exiting with an exception where not counted as failures. They are now.
- Some tweaks to SPITest
  - Print the pins used in a test ordered according to funtion.
  - Open SS and SCLK in open-drain, since they are connected.
- Do not allocate Timer on every iteration
  It is more correct to allocate only a TimerTask and schedule it on a Timer that has already been allocated once.