Consolidate tools.

This is to consolidate the various tools that caffe has into one single binary ("caffe.bin"), and deprecate the multiple binaries hard to remember. In the meantime, we will also switch to the gflags library and get rid of all the argv[4] type hard-coding.

As a result, if you want to do device query, do:

build/tools/caffe.bin devicequery --device_id=0

if you want to do e.g. training with an option of finetuning, do

build/tools/caffe.bin train --solver_proto_file=solver.prototxt [--pretrained_net_file=pretrained.binaryproto]

I have currently deprecated device_query, train_net, finetune_net, net_speed_benchmark. Others could be potentially deprecated in the same way.
Sounds good, I'll change the examples. Not doing the symlinking for now - maybe let's explicitly switch when all the tools are in one binary.