* 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.

* inputs_metfrag: New file.

* app_results_explorer_cindex: New file.

* app_results_explorer_cindex_controls: New file.

* inst/rmd/app_compound_lists_and_sets: New file.

* metfrag(summarise_metfrag_results): Update.

* state(new_runtime_state, metfrag_conf): Update.

DESCRIPTION: Depends: Add readxl and sort alphabetically. Change order of contributors to (mostly) alphabetical.

Last author is going to be the leader of the group, the first is the
most important contributor (author, creator).

* metfrag(metrag_run): Update.

* envopts: New option `java_bin'.

* resources: New parameter METFRAG_DB_SEARCH_RELDEV.

* state (new_runtime_state, metfrag_conf, get_metfrag_targets,
write_metfrag_config, metfrag_run_many): Update. Running many configs
now works.

* tests: Update.

* state (base_conf): Update. Decorates the return object with class
`state'. New class `state'.
(get_metfrag_targets, metfrag_on_state): New functions.
(write_metfrag_config): Update. Add checks for ion_mz and adduct not
being more, or less than one. Also, make filenames nicer and fix the
spectral separator.

(metfrag_run_many, metfrag_run_many_w_futures): New functions to run
metfrag.

tests: New tests and snapshots.

* base.R (write_keyval_file): New function.

* resources.R (METFRAG_ADDUCT_SWITCHES): Fix a typo.

* state.R (new_runtime_state): Update results with the new field
`subpaths'. Also, opted for relative vs absolute paths, because the
latter do not play well with tests in (stochastic) temporary
directories.

(base_conf): Update result to have a class `conf' signature.

(metfrag_conf): Update with new parameters.

(new_conf): Update with a call to `metfrag_conf'.

(write_metfrag_config): New function which writes the MetFrag config
file.

* tests/testthat/test-metfrag.R: New file with MetFrag tests.

* tests/testthat/_snaps/metfrag.md: New file .