Added the FIFO interface to the read loop

Modified the read loop to receive the frames sent by the target
and write the first byte of each packet into a FIFO (used with
the Python script that graphs the content of the FIFO as part of
the counter demo)
Added .gitignore
Moved src directory
Modified .gitignore
Added Makefiles to build the project (just temporary solution)
Modified .gitignore
Removed .gitignore
Added autotools specific files
Added error message to configure.ac
GNU specific files maintenance

1) Added README
2) Removed unnecessary GNU specific files
(automake invoked with --foreign flag to ignore
missing files)
Minor code style refactoring
Fixed syntax error
Added paths configuration through env variables

The paths for the named pipe and the command file
are now set through environment variables and they
are managed with config.h
README cleanup
Renamed files (names shortened)