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Not all metamath term constructors take their arguments in source order. An important example is wal $p A. x ph $., which has x before ph in source order but because wph $f wff ph $. is declared before vx $f setvar x $., the actual argument order is wal(ph, x), which is visible in syntax proofs in the database.
Currently, grammar.rs does not handle this situation correctly, and always adds the arguments to the tree in source order, resulting in ill formed trees of the form wal(x, ph). This is the source of one of the errors reported at digama0/mm-hammer#1 .