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Are you running $system.OBJ.Load("name of file") without specifying any qualifiers? If so, I believe the default qualifiers are "CUK" (compile, update only, keep source). You might want to try $system.OBJ.Load("name of file", "CK") and see if that helps.

You can run a query like SELECT * FROM someTable ORDER BY %ID and it will order by the row ID without including it as part of the result set. Ultimately we would need more information (like the query you're running) to provide additional answers, but ORDER BY %ID sounds like what you want to use.

$system.OBJ.IsUpToDate()might fit the bill for your first question.

set sc = $system.OBJ.GetClassList(.classes)
set cls="", outdated=""
for {
    set cls = $order(classes(cls))
    quit:(cls="")
    if '$system.OBJ.IsUpToDate(cls) set outdated = outdated _ $lb(cls)
}
for i=1:1:$listlength(outdated) {
    write $listget(outdated, i)
}

should work for your 2nd question (documentation here: https://docs.intersystems.com/irislatest/csp/documatic/%25CSP.Documatic....)

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