There has been significant progress in reverse engineering bitstream formats of some FPGAs which has allowed the development of open source FPGA workflows. If you want to know more, take a look at:
At work I use Vivado. It's proprietary but I've never had any problems using it on Linux. I believe there are free editions as well. It has the same problems all FPGA tooling has (bloated, slow build times, not user friendly). Maybe some of the open source tooling improves on that, but I've never heard of anyone using it for real projects. Last I checked the open source stuff also only supported Verilog (not sure if it supports SystemVerilog too). Not the end of the world, but a lot of projects use VHDL or are mixed language.
Edit: Mostly people just use whatever software the FPGA vendor provides. So for Xilinx you use Vivado. For Intel/Altera people use Quartus. Some people do development in an IDE like Sigasi (which I've heard is much better than the vendor specific IDE's, but I've never used it), but they still build with the vendor tooling.
As an enthusiast, that's what I use too.. also on my home Linux system. The tooling is generic enough that you can actually instrument a build system with Makefiles and the Vivado command line programs. If you have the right FPGA board you can also instrument the bitstream upload as well.
I do most of my development like any other programming language and never have to touch the custom GUIs.
Icestorm http://www.clifford.at/icestorm/
Yosys http://www.clifford.at/yosys/
NextPNR https://github.com/YosysHQ/nextpnr
SymbiFlow https://symbiflow.github.io/