Sometimes you need to build the binaries for Atmosphère, or you want to change something on the source code, for building your starting point should be: https://github.com/Atmosphere-NX/Atmosphere/blob/master/docs/building.md
On that document you can read:

Building Atmosphère is a very straightforward process that relies almost exclusively on tools provided by the devkitPro organization.
Dependencies:
  • devkitA64
  • devkitARM
  • Python 2 (Python 3 may work as well, but this is not guaranteed)
  • LZ4
  • PyCryptodome (optional)
  • Hactool
Setup a DevKitPro environment: (https://devkitpro.org/wiki/Getting_Started)
Install the following packages via (dkp-)pacman:
  • switch-dev
  • switch-glm
  • switch-libjpeg-turbo
  • devkitARM
  • devkitarm-rules
  • hactool
Install the following library via python's package manager pip, required by exosphere:
  • lz4
Finally, clone the Atmosphère repository and run make under its root directory.

That instructions are a little plain for we the noobs.

First you need Install a MSYS environment:
The latest instructions for install the MSYS environment are on https://gameparadise.org/tutorials/install-msys-environment.171/ if you don't have one working, use them.

After you have the MSYS environment working you need to install DevKitPro
For that you can follow the instructions on the tutorial https://gameparadise.org/tutorials/setup-a-devkitpro-environment-on-windows.172/

Now you can install DevKitPro packages:
Bash: 
pacman -S --noconfirm switch-dev devkitA64 dkp-toolchain-vars libnx switch-tools switch-mesa switch-libdrm_nouveau switch-sdl2

And Atmosphère prerequisites
Bash: 
Pacman -Sy --noconfirm devkitA64 devkitARM devkitarm-rules hactool mingw-w64-x86_64-python mingw-w64-x86_64-python-lz4 mingw-w64-x86_64-python-pycryptodome switch-dev switch-glm switch-libjpeg-turbo mingw-w64-x86_64-python-pip

For me I had to add
zip
package because even if wasn't explicit indicated on the build page, the code needs it.

Additional you need the packages
git make lz4
for all to work, use the command:

Bash: 
Pacman -Sy --noconfirm zip git make lz4

The package hactool need you to copy your own
prod.keys
file on
$HOME/.switch
folder. (
c:\msys64\home\USERNAME\.switch
if you use the default installation folder)

LibNX Dependency
Atmosphère depends heavily on LibNX, generally when a major version of firmware is released or great changes on the code are made, changes to LibNX are also made.
The Atmosphère team works on their own repo of LibNX (https://github.com/Atmosphere-NX/libnx) and forward Pull Request to official SwitchBrew LibNX repo (https://github.com/switchbrew/libnx).

So if there are changes on LibNX you need to build it and install on your setup.

If you haven't done already, setup the environment variables
Bash: 
export DEVKITPRO=/opt/devkitpro
export DEVKITARM=${DEVKITPRO}/devkitARM
export DEVKITPPC=${DEVKITPRO}/devkitPPC
export PATH=${DEVKITPRO}/tools/bin:$PATH

Then go to the Atmosphere-NX/LibNX repo and look what is the new branch for the current firmware, by example, for Firmware 16.0.0 the branch name is "1600_Support"

1711587447593.png


Then go to your MSYS MinGW64 window and clone the Atmosphere-NX/LibNX repo

Bash: 
cd ~
git clone --recursive https://github.com/Atmosphere-NX/libnx.git
cd libnx

And checkout the needed branch:

Bash: 
git checkout 1600_support

Then build and install the new LibNX libraries

Bash: 
make install -j$(nproc)

Now you can build Atmosphère with latest LibNX code; remember if you update the pacman LibNX package the changes get reversed and you need to build LibNX again.

Now is time to build the binaries
Clone the repository:
Bash: 
cd ~
git clone --recursive https://github.com/Atmosphere-NX/Atmosphere

Go to new created Atmosphère folder
Bash: 
cd Atmosphere

Never forget to create the environment variables for DevKitPro
Bash: 
export DEVKITPRO=/opt/devkitpro
export DEVKITARM=/opt/devkitpro/devkitARM
export DEVKITPPC=/opt/devkitpro/devkitPPC

And now you are ready to start the building process:
Bash: 
make -j$(nproc)

I do use the "-j$(nproc)" parameter to "bleed" all the available CPU to run the compiler, without that the whole process could take up to 1 hour.

Remember, as you are getting a new set of binaries, you need new set of sigpatches if you use it. So the great tool from @mrdude comes in hand, the latest release can be downloaded from: https://github.com/mrdude2478/IPS_Patch_Creator/releases/; you use the program to generate a new set of patches for your recently build package3 file.


-Edited: add sigpatches step and clean up a little-
-Edit 2, add LibNX build-