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Migrate init stage to plugins (#10689)

This commit updates the preset pass manager construction to only use
plugins for the init stage. To accomplish this the previously hard
coded built-in pass manager used for each optimization level are
refactored to be in a plugin named "default". One thing that is changed
in this PR is that the use of `generate_control_flow_options_check()`
is moved to the `pre_init` stage. The reason for this is because the way
the init stage was being constructed in the preset pass managers was to
do initial checking of any methods, and this was unconditionally being
run. This is a more logical fit for pre_init stage because it should run
before any specified plugin.

Fixes: #10687
Fixes: #8661

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