That link takes one to a entry for 3.3 QA. 3.3 is now: $release = '3.3.2+ (Build: 20171027)' in the latest git pull.
The 3 files missing in my experiment were due to how the author of the course put an image next to a Section heading ... if I re-call correctly. Author had created "icons" that had been used in other courses. Author found the URL to the 3 images and provided URL's to them in other courses. Just happened that the one course I choose for the 'clipoof' experiment was one of those. Those 'icons' got lost due to course id changes ... contextual changes ... etc., when restoring the course after 'clipoof'. All the other regularly linked files worked. And legacy no longer required.
Mind you it was just one test backup that I tried 'clipoof' on. Would imagine that other courses run through 'clipoof' might show different results. Still though ... looking at 100's vs a fewer number is a gain. Guess Legacy will be supported in Moodle forever so it's a matter of how much of a perfectionist one is.
Just last week I did a march from 2.6 to 3.3 and when arriving at destination version, discovered they had somehow deleted the admin block (customized theme). Admin block included the course admin block. No way to add the admin block back to courses that were using the clean or more theme, but everything worked with the new boost theme. Looked at tables related to blocks and could never decipher how to get the admin block to appear for all courses regardless of theme chosen.
Had done a run of automated backups of the site right after arriving at 3.3 and saved to a directory outside of Moodle.
So, installed a fresh 3.3.highest then used moosh through a looping bash shell script to restore the majority of the courses. In all courses, course admin menu appeared in any of the stock 3.3 themes ... boost, clean, and more.
Legacy files, however, were still there - in some courses.
The 'customer' was pressing to 'upgrade it' ... to some it's a matter of $ and 'as long as it works' ... ie, didn't want to pursue removing legacy from the site. Granted don't think I've ever seen a Moodle site that was '100% perfect'.
'spirit of sharing', Ken