I was using Obsidian for a while, but actually switched when I found an awesome open source alternative, SilverBullet. The best comparison would be "Obsidian but for tinkerers/hackers".
Data is stored plaintext the same as obsidian - I actually just copy pasted my vault and it worked with exception of wikilinks being absolute paths only - and haven't looked back
The only downside is that its in early stages of development, but definitely usable
I have an "index" page where I link important pages and files. When I want to move them I rename them. If I do bulk data changes I SSH to my server and move the files in an old fashioned way. Personally I have not tried the filetree plugin, since I did not have the need for it - and probably the author of the project aswell.