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

* R/shiny-ui-config.R(input$restoreConfB):

Use load_inputs from the command line way of doing things to read all
the inputs. This way, we have the batteries included.

R/shiny-ui-config.R(server_conf): conf is transformed using
rv_lst2lst, file parsing is fixed and so on.

* R/shiny-ui-config.R <shinyFileChoose observers>: Replace vs with volumes.

* R/shiny-ui-base.R(conf2rv_conf,lst2rv_lst): Replace conf2rv_conf
  with lst2rv_lst which is more general and able to work out
  recursively what needs to be change into a reactive values list.

* R/shiny-ui-base.R(rv_conf2conf,rv_lst2lst): Rename rv_conf2conf to
  rv_lst2lst and make it universal. Instead of acting on the fixed set
  of names expected inside conf, crawl through the nested list
  recursively and to the smart thing.

* R/resources.R(REST_TXT_INP): We probably will not need this.

* R/shiny-ui-top.R(launch): fnConf -> fn_conf

R/shiny-ui-base.R(validate1): Fix.

* R/mix.R(new_state): New state (monad).

*R/api.R,R/base.R,R/mix.R <assert>: New function assert. Replaces
 assertthat:assert_that with shiny compatible validation.

* R/api.R (gen_base_ftab,mk_comp_tab,vrfy_conf): Known compounds table
  may also not exist (if, for example, only unknowns are
  inspected). Made changes to reflect that.

* R/api.R(load_inputs): Move m creation to run already.

* R/api.R(gen_base_ftab): Fix return.

* R/api.R(run): gen_base_tab -> gen_base_ftab

* R/api.R(run) <conf>: Detect if run from GUI

(run_in_dir): Change argument from conf to m.

* R/shiny-ui-base.R, NAMESPACE:
  importFrom(shiny,validate) now correct.

* DESCRIPTION:
  File base.R should come before resources.R

* R/shiny-ui-config(fnKnownLCtrl,fnUnkLCtrl,fnSetIdCtrl):
  fnKnownL,fnUnkL,fnSetId buttons.

* R/shiny-ui-config.R<validate>: Change validations of one condition
  to validate1.

* R/shiny-ui-base.R(volumes): Attach the current working directory.

R/shiny-ui-base.R(volumes): New function.

The result for shinyFiles::getVolumes().

* R/shiny-ui-base.R(validate,validate1):

Function validate changed back to shiny original. Introduced validate1
when there is no need for `need'.

* R/resources.R(EMPTY_KNOWN): New variable.

Column headers for trivial known compounds table.

* R/api.R(vrfy_conf): Clearer file.exist messages.

* R/api.R(load_inputs): Load known table only if the file exist,
  because there may be only the unknown compound list.

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

* R/shiny-ui-base.R(conf2rv_conf): New function.
  In order to save config as yaml function, the reactive form of
  config must be converted to a list.

 (input$restoreConfB): New observer.

* R/shiny-ui-base.R(server_conf), R/shiny-ui-top.R(server): Now that
  we update rv inside server_conf, it must return it in some way.

* R/shiny-ui-base.R(obsrv_e,validate,vol_f): New wrappers.

* R/shiny-ui-config.R(saveConfB): Change default filename and
  filetype.

* R/shiny-ui-config.R(input$saveConfB): New observer.

Because we decided to split the server and UI definitions into
separate "modules", we also needed to create a way for different
modules to exchange their reactive values and functions.

In this regard, each module is going to have two server-like
functions, react_module-name_f and react_module-name_v, which will
define and return reactive functions and objects, respectively. Each
such function is server-like, i.e. it will take input, output and
session arguments. The two remaining arguments are rv and rf, for the
input reactive values and functions.

* R/shiny-ui-config.R(react_conf_v): New function.
  Add conf-related reactive values.

  (react_vonf_f): New function. Add conf-related reactive functions.

  (server_conf): Update observers.

* R/shiny-ui-top.R(server): Adapt to the new concept.

* R/shiny-ui-base.R(react_v,react_f,react_e, obsrv, vols): New
  functions.
  Wrap functions that are used a lot.

* R/shiny-ui-base.R(path2vol): New function.

* R/shiny-ui-config.R: New file.
  It will contain everything related to the configuration tab of the
  former shinyUI.R

* R/shiny-ui-top.R: Updated with the config plug-in.

* DESCRIPTION: Updated.

* R/shinyUI.R: Removed.
  A monolithic file that became difficult to maintain.

* R/shiny-ui-top.R: New file. Contains top-level server and interface
  functions.

(mk_ui): New function. Replace old mkUI and serve as a top-level user
interface definition function.

(mk_shinyscreen): Removed most of it. Only the top-level content
remains.

* DESCRIPTION: Updated.

* R/shiny-ui-base.R: New file. Shiny wrappers.

R/api.R (mk_comp_tab): New function.

* R/mix.R(get_set_mode): New function. Replaces and enhances
  getSetMode.

* R/shinyUI.R(getSetMode): Remove getSetMode.

* R/base.R (tab2file,file2tab): Return and write data.table objects.

(print_table): New function. Prints a data frame, or a table nicely.