* 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.

api, mix, shiny-ui-base: Introduce the concept of "project" and "data"directories for script-based workflow.

* 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.

Values and units have not been read in the GUI template correctly. Now
fixed.

* app<numeric/unit inputs>: Updated. Read in values/units properly.

* base(get_val_unit): New exported function.

* shiny-ui-base<everything related to order_summ table>: Commented
out. Too unstable for now.

* shiny-ui-base (celledit_values, dt_drop_callback, editcell_script,
dropdown_dt): New functions.

(simple_style_dt): Updated.

(rf_get_inp_datafiles): Removed.

(datatab-edit): New observer.

<other observers>: Modified so they work with rv_dfiles, rv_datafiles
and dropdowns.

<renderDT>: Output renders updated.

www: cellEdit javascript and css

app: Updated controls.

commit ad789545c8fab046edc9f97c36c796006d576bf8
Author: Todor Kondić <todor.kondic@uni.lu>
Date:   Thu Dec 10 13:21:13 2020 +0100

    all: Version 0.9.3

    We have redesigned the way the plotting works and how the data
    exploration is situated within the application's interactive document.

    Previously, plots have been generated and stored as tables in the
    m$out$tab sublist of the state object (m). This, however, made it a
    bit more difficult to manipulate plot details which differ between how
    the plots are supposed to be displayed as a part of the application
    and how they look like as individual figures.

    The new approach is to have functions that generate single plots based
    on plot index (see m$conf$figures$grouping) instead of pregenerating
    collections of plots. The same functions are used in parts of the code
    that display this interactively to a user (app.Rmd, the data explorer)
    and those that save figures. The program knows when to apply
    modifications which will make the output suitable to the format of
    display.

    The plot selection table, as well as the plots themselves are now
    hidden in the Data Explorer tab. The plot parameters have been moved
    from the beginning of the document to a side panel. The plots are
    displayed within a well panel next to the side panel.

Prior to this commit, cofiguration consisted of static values and
dynamic variables calculated based on the static values. Changing a
static value meant that those variables had to be recalculated. In a
reactive environment where things change a lot, there was danger that
some parts do not get calculated, or that recalculation leads to
overwriting of other variables. Now, all the dynamic config entries,
such as paths within the project tree are delegated to "accessor"
methods that evaluate their value at the right time.

* R/mix(get_fn_comp,get_fn_extr,get_fn_summ): New functions to
evaluate paths to the comprehensive table, extraction file and the
summary file.

* R/api.R: Corresponding changes in here.

* NAMESPACE: Some updates.

* NAMESPACE: Update exports

* R/api.R(create_plots,save_plots,report): User-level functions to
generate and save plots, as well as generate a report containing them.

* R/mix.R: Supporting functions for above.

* R/resources.R: Supporting params for above.

* R/api.R(sort_spectra): New function to sort the spectral table.

* R/resources.R(DEF_ORDER_SPECTRA): New parameter defining the default
order of the spectral table.

* NAMESPACE: Update exports.

* R/api.R (prescreen): New function. This exported funciton performs a
  range of checks on the spectra in m$extr$ms and produces the initial
  m$out$tab$ftab file table.

* NAMESPACE: exports

* R/mix.R(conf_trans_pres): New function to validate prescreening
  input.

* R/resources.R (CONF_PRES_NUM, CONF_PRES_TU): New parameters holding
  names of dimensionless and time parameters in prescreening list,
  respectively.

* R/api.R(extr_data): New function. Its job will be to extract MS1 and
  MS2 spectra, as well as to store them in m$out$tab$data data table.

* NAMESPACE: Update.

* R/api.R(read_conf): Remove it from api.R .

* R/resources.R(CONF,EMPTY_UNKNOWN,EMPTY_KNOWN): Remove unknown and
  known related parameters. Update the rest accordingly.

* R/mix.R(new_state): Update for multi-compound lists.

* R/api.R(load_compound_input): Update with more column checks.

(load_compound_input): Update with compound list verification.

(verify_compounds): Reduce to checking the existence of files.

NAMESPACE: Update.

* R/api.R(load_compound_input,load_data_input): Exported.

NAMESPACE: Updated.