Missing 'story.php' file from published output

When I published my output to upload to my server before, it included a file "story.php''

More recently, when I published a revised version of the module, that file (story.php) is missing and its causing issues with my website.

Any ideas why this is happening or if I am publishing incorrectly ?

I've attached a comparison of my new vs old output files.

Thanks.

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