Better document "slow" options that should be avoided

(Zhang, 2019) used -a (the option is now --out-reads), that is far from optimal, taking time to output all reads vdj#919

Since !434 (merged), options were renamed and are more explicit. However, we should ensure that the non-recommended options are clearly docuemted as such:

in -h / -H (we could also move options from -h to advanced usage -H)
with Warning for non-optimal use on stdout (we have already some)
in doc/vidjil-algo.md

Edited Oct 23, 2019 by Mathieu Giraud

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