Cannot run `arara` on TeXworks Linux Mint, two TeX lives present on system

Question

I recently made the switch from Windows 10 to Linux Mint and I am pretty happy so far except arara is not working, it complains Unable to access jarfile when I try and run it through the GUI but arara works when using $ texworks or $ arara on the command line. I seen one of @daleif's comments on this somewhat duplicate (TeXworks doesn't recognize environment variables (Linux Mint 17 KDE)) but I am not sure how to implement the suggestion:

How exactly are you starting texworks? Remember, if you start an editor from a menu, then any setting in bashrc is ignored. You need to add them to .profile, log out and log in again. If you start texworks from the command line it will know the setting from bashrc

I think it is an issue due to Debian having a installed TeXlive being present on the system already (which I was unaware) as can be seen here (I changed my name to user@):

(base) user@user-Aspire-A315-51:~$ whereis latex
latex: /usr/bin/latex /usr/local/texlive/2023/bin/x86_64-linux/latex /usr/share/man/man1/latex.1.gz
(base) user@user-Aspire-A315-51:~$ /usr/bin/latex --version
pdfTeX 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian)
kpathsea version 6.3.4/dev
Copyright 2021 Han The Thanh (pdfTeX) et al.
There is NO warranty.  Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Han The Thanh (pdfTeX) et al.
Compiled with libpng 1.6.37; using libpng 1.6.37
Compiled with zlib 1.2.11; using zlib 1.2.11
Compiled with xpdf version 4.03
(base) user@user-Aspire-A315-51:~$ /usr/local/texlive/2023/bin/x86_64-linux/latex --version
pdfTeX 3.141592653-2.6-1.40.25 (TeX Live 2023)
kpathsea version 6.3.5
Copyright 2023 Han The Thanh (pdfTeX) et al.
There is NO warranty.  Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Han The Thanh (pdfTeX) et al.
Compiled with libpng 1.6.39; using libpng 1.6.39
Compiled with zlib 1.2.13; using zlib 1.2.13
Compiled with xpdf version 4.04

What should I do and what more information should I provide please? tlmgr also doesn't work:

(base) user@user-Aspire-A315-51:~$ sudo tlmgr update --all --self
[sudo] password for user:        
(running on Debian, switching to user mode!)
(see /usr/share/doc/texlive-base/README.tlmgr-on-Debian.md)
TLPDB: not a directory, not loading: /root/texmf
tlmgr: user mode not initialized, please read the documentation!

I have a folder called ~/texmf/ so I am not sure the issue either.

As I am new to Linux, just rm -rf ...'ing preinstalled stuff makes me worry I could compromise my system by breaking dependencies etc. I can compile from the command line so this isn't too much of an issue but as I use TeX everyday, not being able to use TeXworks or TeXmaker from within the application is not ideal, and I use arara in all of my documents. I installed the TeX live 2023 version with the full option after changing over.

When changing the /bin/ path in TeXworks to point to /usr/local/texlive/2023/bin/x86_64-linux/latex it still won't compile.

My $PATH currently looks like this (pretty printed):

/home/user/miniconda3/bin:
/home/user/miniconda3/condabin:
/usr/local/cmake/bin:
/usr/local/pymol:
/usr/local/master-v1.6/bin:
/usr/local/mgltools/bin:
/usr/local/phenix-1.20.1-4487/build/bin:
/usr/local/texlive/2023/bin/x86_64-linux:
/usr/local/texlive/2023:
/usr/local/sbin:
/usr/local/bin:/usr/sbin:
/usr/bin:
/sbin:
/bin:
/usr/games:
/usr/local/games:
/snap/bin:
/usr/local/gv/gview

I have a feeling I might need to purge all TeX live from my system and reinstall.