Description:
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At least starting from 4.3.x, when file is included via include(), it is added to the list of included files, so that the code:
<? include('foo'); include_once('foo'); ?>
woould include 'foo' only once.

However, if you put foo in auto_prepend_file and then do <? include_once('foo'); ?> - 'foo' would be included twice.

I see this behaviour as inconsistent and needing to be fixed, though there can be some BC issues with that. 

Reproduce code:
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1. 
<? include('foo'); include_once('foo'); ?>
foo:
<? echo "Whatever..."; ?>

2.
auto_prepend_file=foo
<? include_once('foo'); ?>

Expected result:
----------------
"Whatever..." once in both cases

Actual result:
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"Whatever..."  once in the first case, twice in the second.