promote aliases and flags, to ensure they have priority over config files add Application.flatten_flags() method, which adjusts the alias and flag dicts, such that they point to the subclass in the Application.classes list when passed to the argv parser. This prevents TerminalInteractiveShell.colors in a config file overriding `--colors` on the command-line, which points to InteractiveShell.colors. Flattening is only done when the answer is unambiguous, so multiply inherited classes (e.g. Launchers in ipcluster) are not touched. also remove now-obsolete manual workaround for this in IPClusterStart closes gh-849