Fix state communication issue

First commit to address state communication issue, not yet working.
Attempting to use Verilog task as a solution, however this may not be
the best method of solving this issue.
Added an automated mode

Added in the option to used SW0 to change the mode of the design from
requiring user input at each state to a design that simply runs through
each state. Should y improve speed. Next commit will increase default
fifo size to the maximum allowed.
Cool new gitignore
Updated software

Cleaned up software, comments coming soon.
Updated readme
Added comments to the software.
Threading

Added threading to the auto function in the Python script. Also expanded
the size of the command fifo.
Fixed Software and Firmware Bugs

Modified the software and firmware to actually work in automatic mode.
Cleaned up some software

Changed backed to the manual mode in the software as auto was being
troublesome.
Modified the .ucf for the new adapter card configuration.
Added in HTML T3MAPS manual
Solved data readout

Changed UCF to lvcoms33
Software Change

get rid of pix and chip! Hooray!
Software change

changed output and pulled down command by padding 0s...Have to upload it
because computer crashes a lot...
Added auto method.
Merge branch 'State-Communication'

Conflicts:
	Software/T3MAPSCMD.py