ci: Replace exec-with-shell wrapper with "plain bash"

Also, promote defaults.run.shell from inside only the primary jobs to
the top level.

The src/ci/exec-with-shell.py wrapper script was formerly used to change
out the shell mid-job by intercepting a CI_OVERRIDE_SHELL environment
variable.  Now, instead, we just set `bash` as the global default across
all jobs, and we also delete the exec-with-shell.py script.

Signed-off-by: Kristofer Rye <kristofer.rye@gmail.com>

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