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Issue #349 was closed, but I still keep getting the same problems: defining new commands in markdown cells with $\newcommand{}{}$ does not seem to work.
I'm using jupyter 4.0.6 ((jupyter --version), installed with Anaconda, on OS X. The cell were the new command is defined has the same strange output and the cells were the newly defined macro is used are not rendered; I just get the command name in red, like an error.
Here is a sample screenshot:
