added simple application for testing stk500 over serial port
added executor and logger
added Log.java for output information
updated some references
testing new thread setup
Instancing of protocol class
Fixed threading issue regarding updates of GUI
Minor changes

* Set starting sequence number to 1 to match avrdude practice #9
* Add reminder regarding connection sequence #6
Account for offset, fixes #19
Logging and stream type

* Change from buffered to unbuffered streams to match example #10
* Add interface for logging
* Implement interface in example