These files are intended to be used with HTMLE and compiled for touchscreen devices. They will not work on desktop (unless you're using touch emulation).
Copy everything in the section that looks like:
<script type="bitsyGameData" id="exportedGameData">
...
</script>
From your game file into the "bitsy_modded.html" file.
Copy everything in the section that looks like:
<script>var sourceCode=".........";compile(["restart"],sourceCode);</script>
From your game file into the "puzzlescript_modded.html" file.