Also adapted metfrag subsystem to new data model.

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

* 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.

* 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 .

* 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.

* DESCRIPTION: New version and doc engine.

* NAMESPACE: Adapted.

* man: Updated.

functions which select and define colour palette based on data.

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

But, there is disparity between RT labels and amount of visible
curves. Also, reestablish zooming and double-clicking. Though,
first thing to be done is to re-enable MS2 EIC.

* api.R(report): Updated.

* plotting.R(plot_fname_prefix,plot_save_single): Updated.

* resources.R(REP_TOPDIR): New constant.

* inst/rmd/report_chunk.rmd: New template.

* inst/rmd/report_header.rmd: New template.

* man: Update docs.

app: New dfile_list control

shiny-ui-base(dfile_list): New observer.
(datafiles_b): Updated.

* app (comp_list,set_list): New widgets.

* shiny-ui-base(comp_list_b,set_list_b): New observers.

(setid_b): Removed observer.

* resources.R(MS1_ERR_COARSE,MS1_ERR_FINE): Updated.

(EIC_ERR,RT_EXTR_ERR,RT_SHIFT_ERR): Updated.

(MS2_INT_THOLD): Updated.

* mix.R(presc_conf): Updated.