So you could try grouping icons into sections, labeling the sections, and then clearly delineating the space between said sections. For example, you could have small text in all bold and all caps as the section title. Another user suggested using text with the icons, which is good for accessibility. Also, looking at the first screenshot in your Github, you could completely merge the left icon only nav with the nav directly to its right. This could result in saving some space.

Also, if you really wanted to, you could move back to a more traditional top menu where you have the section title, mousing over the section would open a menu (what is now your icons), and then if needed you could have a submenu underneath (what is your left nav with the words in your first Github photo). Discoverability would potentially take a hit but it's a different way of doing it.

If you have any other questions feel free to reach out, I like doing this stuff.

Edit: Another user suggested using AI enhanced chat to navigate around. This is a sign that the information architecture is WAY too confusing. AI agents shouldn't be utilized for navigation purposes.