Checkpointing

TODO:

• Do not overwrite chain files on checkpoint restart
• checkpoint chainCollection random number generator
• checkpoint when ctrl-c is called
• Add timer so that checkpoint checkpoints after set amount of time
• delete chain_file_manager (its unused)
• fix broken tests
• confirm checkpointed output is identical to non-checkpointed output
• Actually this will not work right now because the states of std::distributions must be save to file too, which will get complicated
• We need a design solution
• complain if chains have wrong length on checkpoint
• Move most of logic for chain_collection_file_manager into jsonMaker
• fix memory leak in jsonMaker?
• get rid of jsonMaker and merge jsonManager and jsonMaker
• Add tests for checkpointing