Change timeout, rename semaphore, add comments in config files

Reduce UART synchronous timeout. The timeout of 6 seconds is only
required for some ZigBee protocols. Since NPI Server will be
updated again for ZigBee we change it here to better fit with
RF4CE-only version.

Align client synchronous timeout with maximum synch timeout for
serial interface. Max timeout is for UART which was just reduced
to 2 seconds.

Seeing problems with semaphore posted by _main and timer module. Changing
name and removing extern declaration helped. The problem was that
semaphore was deemed invalid when timer posted to it. It basically
still worked because of the relatively fast poll timeout of 500ms
in _main. (use _main to indicate it's the same for all clients with
a _main.c module. E.g. simple_app_main.c)

Added comments in all configuration files that are still being used.
BeagleBoard is now deprecated.
npi_lnx_ipc.c has been changed to read the modified cfg files.