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.

Cleaned some more erroneous MS2 spectra (for precid) by removing intensity NAs from cgram_ms1 when using cgram_ms1 for preserving fine results.

analyse_extracted_data: Adapted to db inputs. Also fixed sec/mins conversions in a couple of places.

Also, adapt code affected by this elsewhere.

* app_results_explorer_cindex: New file.

* app_results_explorer_cindex_controls: New file.

* api: Update with new error variables.

* errors: New file to define error conditions.

* state (init_state, is_metfrag_available, new_runtime_state,
new_empty_project, new_project, ^.*_conf funs): Some updated, some
new.

* test-state: Update with tests for new functionality.

* DESCRIPTION: New version and doc engine.

* NAMESPACE: Adapted.

* man: Updated.

api.R (app): New argument `metfrag_db_dir`.