1: Generally the bootstrap is in the "application" directory. It is called from the "public" directory which is in the same level as application (not inside of it). The index.
Php inside the public folder should include the bootstrap. Php and that is where your Document_Root should be set to (note you may need to change / add some include paths for it to work).
Have a look at the singleton pattern. You can double your bootstrap class as a resource container, e.g.
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