Also, adapt code affected by this elsewhere.

* app_results_explorer_cindex: New file.

* app_results_explorer_cindex_controls: New file.

* api: Update with new error variables.

* errors: New file to define error conditions.

* state (init_state, is_metfrag_available, new_runtime_state,
new_empty_project, new_project, ^.*_conf funs): Some updated, some
new.

* test-state: Update with tests for new functionality.

* DESCRIPTION: New version and doc engine.

* NAMESPACE: Adapted.

* man: Updated.

api.R (app): New argument `metfrag_db_dir`.

app: Replaced qa_ms1[2] with qlt_ms1[2], changed how state is handled and fixed extract/prescreen stage in GUI.

api, mix, shiny-ui-base: Introduce the concept of "project" and "data"directories for script-based workflow.