Still not working right...

Removed redundant counter while at it.

- All resources are either under src or under resources dirs
- Removed files top level directory
- Move flightgear files to top level dir

Link ids were being used interchangeably with the mavlink channel for
the link. Link ids handed out as a numerically increasing integer. Once
the counter went past MAVLINK_COMM_NUM_BUFFERS all hell would break
loose and cause memory corruption.

Also many LinkManager API changes to further isolate all link
management inside LinkManager.

If it doesn’t exist it will be prefilled with all registered categories
set to false

Changed settings version as the link configurations must be redone (with the new port names)

Also fixed a typo (copy/paste error) in the TCP link settings loading where it was using the UDP port as the default value instead of the TCP port.