The compiler also fails if a multi-line comment doesn't end at the end of a line.

  <!-- a comment --> and more text

It outputs an empty compiled file.

My honest opinion is that you should consider rewriting the compiler in a classic tokenize-parse-compile style. Several projects (like mustache.js) have had to go through this evolution. Your current solution -- line-by-line with regexes and state flags -- will only get hairier and hairier.