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Comments should not nest, but the corresponding production rule in Appendix E reads:
_COMMENT ::= '$(' (_WHITECHAR+ (PRINTABLE-SEQUENCE - '$)')* _WHITECHAR+ '$)' _WHITECHAR
which allows for instance $( $( $) as a single comment (whereas metamath.c returns an error). A rule forbidding nesting would be:
_COMMENT ::= '$(' (_WHITECHAR+ (PRINTABLE-SEQUENCE - ('$(' | '$)')))* _WHITECHAR+ '$)' _WHITECHAR
That being said, the above fix is in order to conform to metamath.c. I wouldn't be opposed, if it makes the grammar simpler, to modify the program instead.
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