New function encrqcs::qcs_clean_output.
New function encrqcs::qcs_clean_output_all.
encrqcs::qcs_read_results revamp: it now reads a different and more usable
set of results than before.
encrqcs::qcs_run cleaning of output now more thorough.
Fixed encrqcs::qcs_read_results: it now also reads e.g.
QCS-Incidence-Output-Summary.txt. The regex used to detect files to read
in the results dir was "output([.]txt)|([.]csv)" and is now
"output.*([.]txt)|([.]csv)" (added .*).
encrqcs::qcs_call gains argument optional_steps.
encrqcs::qcs_run now enforces the correct order of columns in dataset.
Replace output element run_log with qcs_call_output, the whole output
object of encrqcs::qcs_call.
encrqcs::qcs_write now enforces the correct order of columns in dataset.
Removed override of system2_arg_list within encrqcs::qcs_run. So now
the user can pass system2_arg_list to the call of encrqcs::qcs_call.
encrqcs::qcs_call simplified. Instead of writing a .bit / .sh and
running that, it now directly calls Java via system2.
Bump dependencies.
[encrqcs::qcs_run] works for the incidence dataset, but the Java
programme seems to fail for the other datasets at this time.
Potentially a protocol id problem.