get_summ_subset: Close stale FIXME issues after so many changes.

app_config_and_status: Scale down from TODO/FIXME to TODO.

mk_comp_tab: Remove worked around FIXME.

make_eic_ms1_plot: Removed FIXME related to ms1_rt. This needs a proper rework, but does not have much impact at the moment.

rf_get_cindex: Removed FIXME which seems to not trigger any weird behaviour yet.

output$comp_table: Scale down from TODO/FIXME to TODO for plotting the compound list.

... and others ...