* R/shiny-ui-config.R <input$restoreConfB>: list2rev call removed.

* R/shiny-ui-config.R(ctrl2mzml_df, ctrl2mzml): New functions.

(get_all_sets): New function. Finally stopped recalculating sets.

* R/shiny-ui-config.R(get_tags_from_txt): Isolating input$tagsInp
  prevents fireworks.

* R/shiny-ui-config.R(gen_cmpd_inputs): Fix typo.

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

* R/shiny-ui-config.R(add_mzML_files): Add.

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

* R/api.R(verify_compounds, vrfy_conf): Updated.

* R/api.R(verify_data_df,verify_data): New functions. The first is
  used if the input is only a data frame.

* R/api.R(vrfy_conf,verify_compounds): Updated.

The observers are not really new, but is the policy to name the
observer in the comments for clarity.

* R/shiny-ui-config.R(build-config, build-compounds): New observers.

* (gen_cmd_inputs): New reactive function.

R/shiny-ui-config.R(server_conf) <build observer>: Emulate build
process from the cmd line flow.

* R/api.R <asserts>: file.exists -> isThingFile

* R/shiny-ui-base.R(txt2tags,combine_tags): Move
  to R/shiny-ui-config.R.

* R/shiny-ui-config.R(get_tags_from_txt): Turn into reactive from
  eventReactive. Will it now execute even when button non-pressed?

(server_conf) <rv$m observer>: Add tag handling.

(server_conf) <mzMLtabCtrl render>: Adapt to new tag handling.

shiny-lessons.org: Lessons learned about Shiny while developing
Shinyscreen.

Sorry :)

* 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.