Before this change, `app.booting` was set by Application plugin as part
of regular phase invocation, which executes individual plugins in
subsequent turns of the event loop. As a result, `app.booting` was
initially `undefined` despite the fact that the booting process was
already in progress.
This patch moves manipulation of `app.booting` flag directly to
`Bootstrapper#run` method, to ensure it's set early enough and always
properly cleared at the end.
c10e8225bb