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2) xshell makes the common tasks of shelling out to other processes and massaging file system simpler
Check out the execvr Jupyter kernel.
I actually just did that earlier today: https://github.com/ssokolow/trunc_filenames
1) In "serous" projects, there's always a need for some amount of scripting. Rather than crating a scripts directory with .sh files and worrying how grep on mac is different from grep on linux, it is much better for the team's velocity to write the thing in Rust (https://twitter.com/id_aa_carmack/status/989951283900514304). The xtask pattern (I stress that this is a pattern, rather than a library or a cargo subcomand) helps achieve nice UX for this.
3) xflags is my preferred way to parse CLI arguments for such scripts. It's not good at all, but, for me, it's the best for the task at the moment.
4) For scripts you put for everyday use in ~/bin, I've found busybox style multipurpose binary invaluable. You put all your scripts into a single Rust binary, and than hard-link this binary under different names in PATH, so that the first argv is actually the name of subcommand. Here's how the infra works for my scripts, and here's an example script.