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InfluxDB
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When it comes to -o i decided to have that one for the output of interpretation and since compilation and interpretation can be done at once, it can have only one meaning (-o edited.text will save the processed input into file edited.txt). Also for it to be less confusing you can use --example-input and --example-output (I've documented these in the wiki and -h gives this as well). But if you have any improvements to this, I'd love to hear them, this is the best I could have come up with. And I plan to make a simple GUI interface for non-programmers so that might help with it as well.
I understand the fear of losing the well-performing phenotypes but what I do is that I keep it as the current best, but remove it from the gene pool. It turns out that it gets recreated many times anyway and my stagnation criteria is when a significant part of the population are identical. FWIW, I solved the adventofcode 2019 day 18 with a GA, https://github.com/tobega/aoc2019/blob/master/a18.tt It's written in my language Tailspin which has a bit different syntax: @ is mutable state, $ is the current value and -> separates pipeline steps that create the next current value from the current value at each step.