This was causing unnecessary trouble with loading inputs when running
the command line.

* state(pack_project): New function.

* tests: New tests.

* 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.

* metfrag(summarise_metfrag_results): Update.

* state(new_runtime_state, metfrag_conf): 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 .

* 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.

* 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.

app: Replaced qa_ms1[2] with qlt_ms1[2], changed how state is handled and fixed extract/prescreen stage in GUI.