[plugin_handler] Initilialise PluginHandler before phase 3.

From the CLI, if the user run a plugin, it happens that the PluginHandler is
not initiliased yet when accessing phase_3 of components inits (#FIXME: change
the names!).

This commit moves the PluginHandler init before the phase_3.
[ptp] Ensure that output is not None before iterating.