jq reformatting decimals in scientific notation -- can this be avoided?

You can't change jq's behavior -- at present date, relevant feature requests are still open -- but you can reformat your numbers after they've been retrieved. For example:

json='{"decimal":0.00001}'
decimal=$(jq '.decimal' <<<"$json")
decimal_f=$(awk -v decimal="$decimal" 'BEGIN { printf("%f\n", decimal) }' </dev/null)

echo "JQ emitted $decimal; reformatted as $decimal_f"

Also, you can reformat your JSON using perl module JSON::PP.

perl -0777 -MJSON::PP -E '$s=<>; $j=JSON::PP->new->ascii->pretty->allow_nonref->allow_bignum;$p=$j->decode($s);say $j->encode($p)'

or nicer:

perl -0777 -MJSON::PP -E '
    $j=JSON::PP->new->ascii->pretty->allow_nonref->allow_bignum;
    $p=$j->decode(<>);
    say $j->encode($p)'

The crucial is the allow_bignum.

Example:

echo '{"decimal":0.00000001}' | perl ....

prints

{
   "decimal" : 0.00000001
}

but without the allow_bignum prints

{
   "decimal" : 1e-08
}

Ps: ... and also, is possible to validate the whole json using perl... :)