Upgrading Project Space

Hi,
I am new at this and trying to upgraded 4.5.7 to 4.5.8 .
The below statement is in the update instructions.
I must have selective eyesight to brain connection and have read this in the past, but ignored it.
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Some files in the project space (root, app, public, writable) received updates. 
Due to these files being outside of the system scope they will not be changed without your intervention.
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What does "your intervention "mean?
Does it mean I copy specific file from vendor/codeigniter4/framework into the project space 
and then add my changes if any to the copied file?

If that is the answer and I had not done this for all the previous updates I had done in the past.
What would be the correct way to fix my lack to doing updates correctly?
Maybe, create a new appstarter app and then compare file contents to more the appstarter to my correct application files 
Then copy the changed files and then add my application changes to the copied files?
Thank you for your assitance.
Larry