* R/shiny-ui-base.R(vols,vol_f,volumes): Obsoleted. Removed.

(mk_roots): New function.

* R/shiny-ui-config.R(get_proj_vol,get_proj_path): Obsoleted. Removed.

(server_conf) <shinyFile observers>: Adapt to mk_roots functionality.
<input$switchProjB observer>: Same as above.

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

* R/resources.R(EMPTY_UNK): -> EMPTY_UNKNOWN

* R/api.R(read_conf): The call of vrfy_conf removed due to some
  conflicts. Reinstate verification somewhere else.

* R/api.R(write_conf): Substitute conf with m argument.

(read_conf): Conflicts with the one in R/aip.R, so removed.

* R/api.R(load_data_input): Fix typo.

* R/mix.R(read_conf): Add defaults for mzml, known and unknown. Add
  tab empty list to out in m.

* R/shiny-ui-base.R, R/shiny-ui-base.R (rv_lst2lst, lst2rv_lst,
  rev2list, list2rev): rv_lst2lst -> rev2list, lst2rv_lst -> list2rev

* R/shiny-ui-base.R(isol): New function.
  Alias for isolate.

* R/shiny-ui-config.R(rf$initial_mzml): New reactive function.

(input$mzMLB): New observer.

(rv$conf): Updated.

R/shiny-ui-config.R(rf$get_tags_from_txt): New reactive function.

* R/shiny-ui-config.R(rf$get_compounds): New reactive function.

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

* R/shiny-ui-base.R(txt2tags,combine_tags): New functions.

Needed for shiny UI processing of mzml table.

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

* R/mix.R (read_setid): New assertions.

* R/api.R (load_data_input,load_compound_input): New functions.
  Split the compounds lists loading from data input loading, to better
  adapt to the way this is used in shiny UI.

* R/api.R (load_inputs): Adapted to above

* 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.