[misc] Better preserve backtraces in several modules

Re-raising inside exception handlers must be done with care in order
to preserve backtraces; even if newer OCaml versions do a better job
in automatically spilling `%reraise` in places that matter, there is
no guarantee for that to happen.

I've done a best-effort pass of places that were re-raising
incorrectly, hopefully I got the logic right.

There is the special case of `Nametab.error_global_not_found` which is
raised many times in response to a `Not_found` error; IMHO this error
should be converted to something more specific, however the scope of
that change would be huge as to do easily...

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