Load most annotations, even if they are missing appearances.

Filter out Link and Popup annotations.

Links are not comments, popup annotations are auxiliary information
for other annotations, so neither of these types should be present
in our list of annotations, but all other annotations should be there,
whether they have appearance streams or not.

Ensure has_new_ap is zero when first loaded, and changed if either
the active AP object is changed or the current AP content stream
is updated.

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