Reorganize examples

[dyokelson]

Added Alex's BP5 code and reorganized it to fit the structure of the project. There are still ways to make all the examples more consistent with each other, but I will work on those in separate branches. This has all three examples working and documentation for running them.

[dyokelson]

@AlexandreChern If you can pull this code and try running all the examples (see steps below) that would be helpful as verification.

BP1:
localARGS = ["examples/BP1/bp1-qd.dat"]
include("examples/BP1/stripped_qd_driver.jl");

BP6:
localARGS = ["examples/BP6/bp6.dat"]
include("examples/BP6/BP6_driver.jl");

BP5:
include("examples/BP5/BP5-QD.jl");

[AlexandreChern]

Maybe we should delete Manifesto.toml. This file should be generated automatically. Having it here is messing up with dependencies.

[AlexandreChern]

I can run the BP6 as well, but I am not familiar with the problem. Did Brittany formulate this problem?