Right now the nature of the autoformat plugins could potentially allow major damage to be caused to an entry's data, because they write changes directly to the entry's file. Regular expressions have to be carefully constructed to protect the content. I've been toying with the possibility of filtering the data applied to the output files instead. The auto_break plugin did this in versions prior to 2.7, but because of it, updating an entire site could take a real long time. To speed things up it made since to apply the auto formatting to an entry only when it's been changed. I'm still thinking along those lines of course, but instead of storing the filtered version in the entry's file, I would make use of the the formatted/filtered bits that get stored to the parts directory.
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