I ultimately find @dikasp2's solution to work, I ran:

$ xdg-user-dirs-update
to generate and edit a config at
$ vim .config/user-dirs.dirs

and changed to these values:
XDG_DESKTOP_DIR="$HOME/downloads"
XDG_DOWNLOAD_DIR="$HOME/downloads"
XDG_TEMPLATES_DIR="$HOME/downloads"
XDG_PUBLICSHARE_DIR="$HOME/downloads"
XDG_DOCUMENTS_DIR="$HOME/docs"
XDG_MUSIC_DIR="$HOME/music"
XDG_PICTURES_DIR="$HOME/pictures"
XDG_VIDEOS_DIR="$HOME/videos"

Then I ran xdg-user-dirs-update again,

and I find that if you have any user directories removed, then it will assume you don't want them and will start putting things only in the home directory. And will change the config for you, so you could basically do:

XDG_DESKTOP_DIR="$HOME/"
XDG_DOWNLOAD_DIR="$HOME/downloads"
XDG_TEMPLATES_DIR="$HOME/"
XDG_PUBLICSHARE_DIR="$HOME/"
XDG_DOCUMENTS_DIR="$HOME/"
XDG_MUSIC_DIR="$HOME/"
XDG_PICTURES_DIR="$HOME/"
XDG_VIDEOS_DIR="$HOME/"

And now my home folder stays clean! This is a huge win for organization!

i always run iceweasel-uxp inside firejail and i think if you do that it will prevent it from creating any files,
try this command :

firejail --seccomp --noroot --disable-mnt iceweasel-uxp

this will allow your browser to have access to /home/user/Dowloads only it wont allow it to create or have access to other files in your system

OMG! That was on my todo list too -- perfect solution! Thank you

firejail --seccomp --noroot --disable-mnt iceweasel-uxp

this will allow your browser to have access to /home/user/Dowloads only it wont allow it to create or have access to other files in your system

I see @aunta you might be the perfectionist type . is not wrong whatever ideals you might have.
those are standard created by developer for interopability. but of course you are free to make it your way.

maybe try looking into xdg-user-dirs ? you might do some tweaks there

Yes, indeed! Thanks for the tip, I'll try it out

By the way, I can't make an account in the issues.hyperbola.info page, and I was told to hold off on making one for the time being, so sorry if some of my posts should belong in bug reports -- until I eventually can make them

maybe try looking into xdg-user-dirs ? you might do some tweaks there

$ ls -l Desktop/
total 0

wasn't aware of the difference between applications and packages

some packages like iceweasel-uxp create directoriees I don't want or need, how can I prevent it from creating the Desktop directory on every launch?

preferences#general

then click on browse

and you can select wherever you want your downloads to be placed.

as for the .hyperbola folder,

that is where your addons, bookmarks, preferences, etc... are placed.

So its not wise to delete that.

I wasn't sure which you meant, so I thought I should mention both of these things.

Hope this helps.