I suggest to remove the report of what modules are built/not built upon exiting waf shell; this information is relevant to ./waf build, not ./waf shell.

$ ./waf shell
Waf: Entering directory `/path/to/ns-3-dev/build'
Waf: Leaving directory `/path/to/ns-3-dev/build'
$ exit
exit
'shell' finished successfully (2.378s)

Modules built:
aodv                      applications              bridge                   
config-store              core                      csma                     
csma-layout               dsdv                      emu                      
energy                    flow-monitor              internet                 
lr-wpan                   lte                       mesh                     
mobility                  mpi                       netanim                  
network                   nix-vector-routing        ns3tcp                   
ns3wifi                   olsr                      point-to-point           
point-to-point-layout     propagation               spectrum                 
stats                     tap-bridge                template                 
test                      tools                     topology-read            
uan                       virtual-net-device        visualizer               
wifi                      wimax                    

Modules not built:
click                     openflow                 

$