cells.csv and cell_rules.csv in output folder

[elmbeech]

I have a basic question of what is copied to the output folder.

1. the cell seeding file cells.csv or what ever it's name is, is so far not copied into the output folder. should we do that? might the cells.csv be needed for downstream analysis?

2. the cell_rules.csv file is actually not a copy of the cell_rules.csv file in the in the config folder (which is nowadays a version 2). it is generated, and it is a rules version 1 file.

The big question behind all of this is:

• What is the intent of the files that are copied into the output folder?
• Should there be only files that are of use for down stream data analysis (e.g. with physicell data loader)?
• Should there be all the files needed to be able to rerun?
• nothing of all above but something else?

PS: the calls to handle all of this are currently downstream of the custom.cpp / create_cell_types function, which is called from the main.cpp / main function.