* 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/base.R(file2tab): Updated. Different NA defaults.

* R/base.R(gen_uniq_lab): New function.

* R/mix.R(read_conf): Moved from api.R and updated. Now generates
  random names for the files in compound lists. This was needed
  because in its reactive form, a list of reactives needs names.

* R/resources.R(EMPTY_CONF): New parameter. Skeleton conf object.

* 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.

Loading only two lists of rigid layout became is a bit
unflexible. Introducing the option to load instead multiple compound
lists that must conform to a certain format.

* R/api.R(load_compound_input): Updated. Now reads multiple compound
  CSVs, if provided.

* R/mix.R(read_set_id): Updated.

* R/mix.R(verify_cmpd_l): New function.

* R/resources.R(EMPTY_CMPD_LIST): New parameter. The layout of a
  compound list.

* R/mix.R(calc_mz_from_smiles): New function.

* resources.R(ADDUCTS,ISOTOPES): New parameters. Reimports of enviPat
  data.

* mix.R(calc_mz_from_smiles): New function. Inspired by one of the
RChemMass functions.

* resources.R(ADDUCTMAP): Updated.

* extraction.R(gen_mz_range,gen_rt_range): Updated. Rownames are not
  IDs anymore.

(gen_ms1_chrom): Updated.

* R/shiny-ui-top.R(launch): Update.

* R/api.R(run): Update function.

* R/api.R(mk_tol_funcs): New function.

* R/api.R(concurrency): New function.

* R/resources.R(NO_WORKERS): New parameter.

* R/api.R(run): Update.

* R/extraction.R(centroided1,centroided): New functions.

R/shiny-ui-top(mk_shinyscreen): Add server_gen to server.

* R/shiny-ui-gen.R(server-gen): New observer. This one is to test the
  workflow.

* R/shiny-ui-config.R(mzml2disp): Consider set mismatch case.

* R/shiny-ui-config.R <update-files-on-mzmlb>: Drop unnecessary lines.

* R/resources.R(TAG_DEF,TAG_NA,SET_NA): Add _NA tags to represent NA
  in tag and set columns of the data table control and define TAG_DEF
  in terms of TAG_NA.

(COMP_NAME_FIRST): Order of columns in the comprehensive table.

* R/mix.R(add_wd_to_mzml_old): Removed.

* R/mix.R(gen_sup_ftab): Removed.

(add_wd_to_mzml): Updated.

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

NAMESPACE: Updated.

* R/api.R(gen_base_ftab): Remove. Function mk_comp_tab took over.

* NAMESPACE: Update.

* R/api.R(mk_comp_tab): More data.table friendly.

* R/api.R(load_compound_input): Works properly if tables are not
  truthy.

* R/shiny-ui-config.R <everywhere>: Adapt to m_conf,m_input_cmpds,
  m_input and m usage.

(rv$m$conf$project): Replaced with rv$project_path

* R/shiny-ui-config.R(gen_cmpd_inputs): Obsolete function removed.

(get_all_sets): Adapt to using the m_input_cmpds function.

From the beginning, the intention was to follow the simple signal
passing paradigm, where a single state object is being passed from
function to function. With a GUI this is complicated by continuously
changing state and in a reactive paradigm of Shiny, additional
complication arises from inability to distinguish between different
inputs for the same destination observer, or reactive function.

But, now that the problem has been solved by adding new reactive state
variables for the project path and the data file control, it was
possible to emulate the streamlined signal processing flow by adding a
few new reactive functions.

Here they are.

* R/shiny-ui-config.R(m_conf,m_input,m): New reactive functions. Each
  builds its part of the m object. Each calls the preceeding one.

* R/shiny-ui-config.R(mk_ui_config): New output fnDataFilesCtrl. New
  button impDataFilesB.

<shinyFiles observers>: New observer impDataFilesB

<restore-conf>: Do not modify the rv state for all conf
parameters. Instead, just do that for rv$m$conf$project. The rest will
be taken care of in <build-config>.

Also, update the new `datafiles' input.

<update-files-on-restore>: Add dependency on rv$m$input$tab$setid.

<build-config>: Update rv$m$conf$data from the new input.

<fnDataFilesCtrl>: New render.