--force-overwrite doesn't overwrite intermediate files

Many files such as c1.ntw are not overwritten even when using force overwrite. Since I'm not a huge Python expert I didn't understand what was wrong by the python errors, (KeyError with Achromobacter phage), so I figured something might be wrong with my pandas judging by other issues on this repo. I spent a lot of time changing my gene2genome or raw proteins file before realizing that it still tries to use a c1.ntw from a previous run. I think it is not straightforward to assume that if you switch force overwrite on, some intermediary files are still not overwritten.

I put this in minor because it's not breaking software use but I think it is very misleading

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