Improve download_bee_download_project to support the update command

[yorkshire-pudding]

As discussed in #299 and #297 we need some improvements to the download_bee_download_project() function to better support the update function.

@hosef said:

As for the download command, I think that it would be a good idea to make a more generic download function that has options passed into it instead of accessing global variables or command line arguments directly. Off the top of my head, I think it would need: project name, download destination, version, if it should replace an existing version, if it should make a backup of the project. While we are at it, we should have other functions that handle getting paths and handling version info. We could then make all the commands that need to download projects wrap these other functions so that they behave consistently.