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2 - there are iterators. You can use them or not. There are still directory functions or even glob. Personally, I'd go straight for symfony/finder, but then you've got to figure out composer too.
for simple data structure you can use redis (https://redis.io/) for storage
I’d recommend giving Slim PHP a go. It was a super-easy transition for me (I was in a similar boat to OP a few years ago).
These 2 features are used by (as others have mentioned) the Composer package manager and Packagist package repository that make finding and using libraries easier than ever.
2: Check get_structure() in https://gitlab.com/hsleisink/librarian/-/blob/master/libraries/directory.php.