Daniel Bergman

the example already existed. just making it `make`-able and renaming it. Oh, I did also complete the rule for transform to exhausted T cell so that can happen now.

initialize total_attack_time to 0.0

1

Previously, it was unset and so it seems one cell (the first placed?) would have an arbitrary value.

handle abspath for output folder creation

1

any path starting with the path separator (indicating an absolute path) will cause an error with the current implementation _even if the path already exists_. This is because it attempts...

conserve internalized substrates on transform

2

much like we chose to preserve volume on transform (#284) we should at least consider preserving internalized substrates on transform. within `Cell::convert_to_cell_definition` we could go with something like the following...

apply rules BEFORE checking for transformation

2

Everything else (in phenotype updates) is after applying the rules. with it ordered previously (transform then apply rules), it is possible for cells at the beginning of a sim to...