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Replaced the comment regex with a filter that easier to understand and doesn't have this issue:

However. This is an edge-case but could happen:

It seems to me from https://neo4j.com/docs/2.2.2/cypher-comments.html that cypher supports comments, any reason why we need to "clean the command"? Could it not simply be removed (perhaps some version stuff with cypher?).
From some initial looks this

Doesn't work if we let cypher handle the comments because then the second statement is evaluated as cypher instead of a command. So perhaps leaving the cleaning as it is is preferable? The current implementation has that awkward edgecase but at least the syntax highlighting indicates the something might be wrong.
changelog: Fix comment issue in multi statement commands