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_config_and_status: Updated. Replaced metfrag controls with inject_inputs.

* app_results_explorer_cindex: New file.

* app_results_explorer_cindex_controls: New file.

* inst/rmd/app_compound_lists_and_sets: 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.

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

* 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.