4
If you correctly put in 301 redirects and update your sitemap, the site will be fine. However...
What are you trying to gain from this change?
The Stack Exchange-style hierarchy doesn't make sense for what it seems you're trying to accomplish (a Wikipedia-style website?). What you currently have makes more sense in terms of organizing the information:
...
3
There is a risk with URL changes of SEO problems, ranking loss, and traffic declines. When correctly implemented with 301 redirects, it can go perfectly fine, but it doesn't always do so.
I recommend changing URLs only when there is an overwhelming need. If you do want to change URLs you should consider gentler changes as well:
Chang the URL structure ...
2
What you are seeing is default behaviour on Apache.
when I enter random subdirectories, such as /index.php/asdfghjk
/asdfghjk is an additional path-segment in the URL. It's not strictly a "subdirectory". (Directories and subdirectories relate to a filesystem. The URL does not necessarily map directly to the filesystem.)
When additional path segments ...
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