[cleanup] Replace uses of UserError constructor, clarify exception names.

We replace some uses of `raise (UserError ...)` with
`CErrors.user_err`, ideally we would like to make the error raising
API not depend on the exception themselves, but that's still a long
way to go.

We also rename the `Timeout` exception as to clarify purpose in the
codebase, given that it has 3 different ones as of today.

cc: #7560

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