Fix issue #245

https://github.com/diydrones/apm_planner/issues/245
Linux: Added extra search paths for support files
Linux: Autobuild now working via pbuilder
Added extra build dependencies for Linux branch in readme.md
Addition of pixhawk/px4 reset timer for resetting when the device gets stuck in terminal mode on conection
Changed SerialLink to operate in the UI thread
Added reset timer to reboot device if it is in terminal mode and not responding
Allows for enabling different serial thread methods with an #ifdef
Code cleanup and fixing for timeout based terminal detection
Additional debug output in ArduinoFlash and reduction in time we wait for the bootloader to start