* 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.

* R/shiny-ui-base.R(txt_file_input): Add new argument `default'.

* R/shiny-ui-config.R(mk_ui_config) <saveConfB,restoreConfB>: Update
  labels.

(mk_ui_config) <saveConfB>: Update filename.

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

R/shiny-ui-gen.R(server-gen): New function.

* R/shiny-ui-top.R(mk_ui) <plugin-ui>: Add plugin-ui field.

(mk_shinyscreen) <plugin-servers>: Add plugin-server field.

* R/shiny-ui-cmpd.R(server_cmpd): New server function.

* R/shiny-ui-sets.R(server_sets): New server function.

* R/shiny-ui-top.R(mk_shinyscreen) <plugin-servers>: Add server_cmpd
  and server_sets.

* R/shiny-ui-top.R(mk_ui) <plugins>: New plugins cmpd, sets, gen.

* R/shiny-ui-gen.R(mk_ui_gen): New function.

* R/shiny-ui-sets.R(mk_ui_sets): New function.

* R/shiny-ui-cmpd.R(mk_ui_cmpd): New function.

* shiny-lessons.org: Update lessons.

* R/shiny-ui-config.R <mzMLtabCtrl>: Updated. Works together with the
  new, updated data files observers.

In the current spirit of naming the observers in the comments, we are
listing the changes under their names inside the contex (angle)
brackets.

Note that some of the observers which were listed as "updated" may, or
may have not been created right now. It was too much to track.

* R/shiny-ui-config.R(server_conf) <update-files-on-restore,update-files-on-mzmlb>:
  New observers. They finally complete the data files modification,
  addition mechanism.

(server_conf) <build-config>: Updated.

(server_conf) <build-compounds>: Updated.