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.

I understand the intent when this was first created but nobody is using it and it no longer fits the context. If and when a need to abstract the serial link comes back, we can revisit this.

Also converted qDebug statements to logging category

I noticed that some times, the disconnect signal would get to the updateConnect button (tool bar) before the link was physically disconnected. That would cause it to count it as a still connected link and get the connect button logic out of sync.
While at it, added an interface to the UDP link to return its configuration instance. That allows the LinkManager to unlink it when disconnecting it.

This came through google groups and as the change is right where I'd been working, I added it here to avoid collision.