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Made `$` match end of line
Since multiline regex option wasn't turned on, `/foo$` only matched the last line of the file. I turned on Multiline mode and realized that `$` still only matches `\n`, so I had to insert a `\r?` pattern before $. I can't think of any cases that might fail this logic, and all the unit tests pass so I'm relatively confident in the strategy. fixes #837
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