Initial update with filament sensor and delay

Initial update with all the changes to add the filament sensor with
delay.
Fixed a bug in the temp ISR - was double incrementing
Use SET_INPUT or SET_OUTPUT instead of pinMode

Original used pinMode, which is not a fastio construct, but also used
WRITE, which is a fastio construct.  This caused a problem with the LCD
interface for teensyduino- style boards since the pin numbers are
different for fastio and the usual Arduino IO.