More cleanup.
Changed to a first word fall through fifo.

This also ensures the correct timing of signals sent by the bulk transfer.
Only send out (and increase) the package count header for bulk packages.
Add a dedicated input for the spill identifier signal.
Add a board ID to the returning JDRS header.
Updated the To Do list after the recent beam test experiences.
Corrected the start of MMCM configuration.

This starts after the last register has been written, not with the first one.
Updated the point with software structure to be more precise.
LVTTL is not supported by the ML605.
The order of modules in the project's file of the firmware changed.

This shouldn't imply any visible change in the project, the .xise file is automatically generated thus the change of order.