Fix up typos

Ran automated checker for common typos [1]. Most of these changes have
no functional change *except* for `./ci/sim_run.sh` where, previously
the `bootstrap` feature wasn't being selected properly.

I didn't touch anything in the `./ext/` folder as anything in there
should probably be fixed in the upstream repo.

[1] https://github.com/codespell-project/codespell



Signed-off-by: Sam Bristow <sam@bristow.nz>