Various bug fixes

This is a bug fix release and includes the following changes

• Fix: Add arduino-mk-vars.md file to RPM SPECfile. (https://github.com/sej7278)
• Fix: Add avr-libc/malloc.c and realloc.c to included core files. Fixes issue #163 (https://github.com/sej7278)
• Fix: Add "gpio" to the list of isp that don't have a port. (Issue #165, #166) (https://github.com/sej7278)
• Fix: Add "-D__PROG_TYPES_COMPAT__" to the avr-g++ compiler flags to match IDE. (https://github.com/sej7278)
• New: Create Makefile-example-mk, a real life Makefile example, to be used as a reference. (https://github.com/tinyladi)
• Tweak: Add OBJDIR to arduino-mk-vars.md (https://github.com/tinyladi)
• Tweak: Beautify arduino-mk-vars.md with code blocks. (https://github.com/tinyladi)
• Fix: AVR tools paths for chipKIT in Linux. (https://github.com/peplin)
• Fix: Consider usb or usb:... to be a valid ISP_PORT (https://github.com/geoffholden)
• Add: Add phony target to run pre-build hook script (https://github.com/jrid)
• Fix: Add BOOTLOADER_PARENT to arduino-mk-vars.md and fixed BOOTLOADER_PATH example. (https://github.com/sej7278)
• Tweak: Replace perl reset script with Python script. (https://github.com/sej7278)
• Tweak: Made choice of Python2/3 interpreter up to the OS. (https://github.com/peplin)
• Tweak: Simplified packaging dependencies. (https://github.com/sej7278)
• Tweak: Tweak AVRDUDE conf detection in windows. (https://github.com/EAGMnor)