Use Ref::INVALID more

In this case we have to be a bit more careful since we're changing code that
used to assign to 0,0 and now INVALID is -1, -1 but i'm confident it's

inReplyTo seems to be only used in qt5/src/ and
i've updated the code to use the boolean isInReplyTo instead of checking
the ref number directly

The change in Dict only affects its two callers, one in Annot and one in
Catalog. The one in catalog has been updated, the one in Annot doesn't
seem to need updating (and moreover if you check history before using
the new Dict function was using -1, -1 as ref not initialized)

The change in Array only affects its one caller, in Function, whose code
has been updated

The embFontID change is something that was forgotten in the previous
commit about using Ref::INVALID

The change for iccProfileStreamA is only local to that function and has
been changed to use Ref::INVALID in all its uses
14 files changed