Why not just save a lot of time and trouble and use the vendor supplied IDE? I'm not aware of any viable alternative. ISE and Quartus are both available for Linux.
There are various reasons:
1) FPGA IDE’s lag noticeably behind everything else on the planet (even VS code is significantly ahead of every fpga ide) in term of everything, especially dependency management
That's because nobody actually uses the IDE for code development, only for synthesis and place-and-route.
2) the integrated editor in fpga tools are almost at notepad level of sucking, using an external editor takes away the I in IDE and thus the things don’t make sense
You are correct -- they do suck. Which is why those of us who do this for a living choose another editor (I prefer emacs, see that long thread about it) but everyone has their own preference. There is absolutely no reason to use the Xilinx/Altera/Microsemi/Lattice tools' built-in editor.
Code entry is a separate process from simulation and from the back end synthesis and place-and-route.
3) altera hasn’t even managed to integrate a modelsim front end and waveform viewer in the crappy mess they call An IDE
And so what? I use ModelSim standalone. That's a lot more flexible and actually straightforward than pushing a button in the fitter project manager. My ModelSim projects have more than one top-level and simulation configuration.
And not having the simulator integrated into the IDE means you can choose any simulator you like. I've been using GHDL and it's fine and a lot more lightweight than ModelSim.
4) using VCS with gui projects is a nightmare, as the bloody things spread the settings and everything else among so many directories it isn’t even funny
I've been using a version-control system with FPGAs for 20 years. All you need to put into your repo are the sources, the synthesis constraint files and the simulation project file (for ModelSim that's the .mpf). Keep your sources separate from the other two things. You can re-create the entire GUI project for Vivado if you use their script.
Microsemi's Libero is annoying as hell and I stopped using it. Once I realized that you can run the designer place-and-route standalone, I just did that. Synplify runs standalone, too.
I mean, I agree that FPGA tool usability sucks in general. Xilinx finally got religion late in the ISE cycle and got rid of the binary project file format and replaced it with VCS-friendly XML. Then they went backwards for Vivado. And it's not like they actually listen to their users.