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 ...

Also adapted metfrag subsystem to new data model.

* shiny-ui-base(gen_cindex, gen_summ_subset): Adapted. Function
`gen_cindex' now returns less confusing output.

* plotting(get_data_from_key): Argument `outcols' now has a default
NULL value.

Fun unpack_app_state changes gui$paths$data to absolute path now (otherwise dfile_list is not immediately filled).

* state(pack_project): New function.

* tests: New tests.

Also, adapt code affected by this elsewhere.

* shiny-state.R (which_gui_inputs, which_metfrag_inputs,
unpack_app_state, unpack_app_state_metfrag, input2conf_metfrag,
input2conf, app_state2state): Updated. The inputs are defined
in a more structured manner and this resulted in having to update
the entire system of state creation fom GUI.

* shiny-ui-base.R : Updated. Temporary reorganisation while the
app.Rmd is being rebuilt.

* state.R(metfrag_param): New function. Creates MF parameter object.
(metfrag4conf): New function. Creates a conf entry.
(metfrag_conf): Updated.

* inst/rmd/app.Rmd: Under reconstruction.

* app_results_explorer_cindex: New file.

* app_results_explorer_cindex_controls: New file.

* envopts (envopts): Update. Normalise MetFrag paths.

* resources (METFRAG_DATABASE_TYPE, METFRAG_REMOTE_DATABASE_TYPE,
METFRAG_LOCAL_DATABASE_TYPE): Updated. Rearranged for finer control.

* shiny-state (make_metfrag_panel): New function.

* shiny-ui-base (mf-database-type): New observer.
(cando_metfrag, metfrag_panel): New outputs.

* app (MetFrag): Update section header. Delete hardwired controls.
(metfrag_panel): New control which replaced the hardwired controls.

tests: Update with new functionality.

* state.R (encode_ms2_to_line, pack_ms2_w_summ): Functions to pack ms2
data based on selected entries in `summ'.

* app (ms2_spectra_tab_name, ms2_spectra_tab_b): New widgets.

* shiny-ui-base: Added input$ms2_spectra_tab_b observer.

Everything under Measurement Properties refreshes correctly now. The
reason why it did not was the overuse of req functions.