A little cleanup on the scons build script; build in alternate UART support by default for 2560s except for FF Creator X 2560 (since they may not appreciate the confusion caused by normal, new users seeing that)
Fix microsecond timer.  It would wrap every 71 minutes (32 bits) and MBI tossed in code to make the elapsed print timer deal with that.  Instead, by adding only 8 bits it's possible to have the same basic resolution and to extend the time until it wraps by a factor of 100 * 255.  The 255 from having an 8bit wrap counter and the 100 by not incrementing micros by 100 every time TIMER5 fires.  Instead, increment it by 1 and then have the only consumer -- Timeout objects -- divide their input timeout duration by 100.  Presto: no loss of resolution, and the counter has been further extended by a factor of 100.  So, now instead of wrapping every 71 minutes, i now wraps every 1267.6 days or 3.47 years.  Further, this code removes unneeded functionality from the Timeout object and buys back approximately 250 bytes of SRAM.  Code space savings is -184 bytes on Rep 1's (no savings) and -32 bytes on the Rep 2. Also changes to support new options
Keep simulator compiling
Comment cleanup and other cleanup on Timeout object
Comment cleanup; build system changes
Alignment of new menu items
Work on optional clearing during cancel
Make alternate uart option not visible in MakerWare since setting it over USB would be troublesome anyway; remove unused member variable from Pin object
Another bug introduced by MBI when they copied this code from the G3Firmware code base.  They lost the initialization of bypassing_PID.  Bug is mostly harmless and hence went unnoticed.
bugfix from MBI - endless loop if build time > 10000 hours
Merge pull request #120 from GottfriedSp/master

bugfix from MBI - endless loop if build time > 10000 hours
german: "Zeile" -> "Linie" and formating source code
Merge pull request #121 from GottfriedSp/master

german: "Zeile" -> "Linie" and formating source code
- Added a .gitignore to ignore the simulator build directory.
- Removed debug code from UART.cc
Merge remote-tracking branch 'upstream/master'