Download the repo (zip link or git clone)
Run custominstall.py with boot9.bin, movable.sed, path to the SD root, and CIA files to install (see Usage section).
Download and use custom-install-finalize on the 3DS system to finish the install.

Setup

Linux users must build wwylele/save3ds and place save3ds_fuse in bin/linux. Just install rust using rustup, then compile with: cargo build. Your compiled binary is located in target/debug/save3ds_fuse, copy it to bin/linux.

movable.sed is required and can be provided with -m or --movable.

boot9 is needed:

-b or --boot9 argument (if set)
BOOT9_PATH environment variable (if set)
%APPDATA%\3ds\boot9.bin (Windows-specific)
~/Library/Application Support/3ds/boot9.bin (macOS-specific)
~/.3ds/boot9.bin
~/3ds/boot9.bin

A SeedDB is needed for newer games (2015+) that use seeds.
SeedDB is checked in order of:

--seeddb argument (if set)
SEEDDB_PATH environment variable (if set)
%APPDATA%\3ds\seeddb.bin (Windows-specific)
~/Library/Application Support/3ds/seeddb.bin (macOS-specific)
~/.3ds/seeddb.bin
~/3ds/seeddb.bin

Building finalize

Finalize is required for newer games that use seeds. Without finalize, the game may not show up on your 3ds, while it being on your sd card.

In order to build finalize so you can put it in your SD:/3ds/ directory (or whatever directory you prefer for homebrew software), you will need devkitARM, or preferrably, using devkitPro's pacman installer:

If you tell everyone you use Arch (btw), your current pacman package manager will work, you just need the dependencies, skip the step below and see here.

Installation instructions for devkitPro Pacman

macOS/Linux: sudo pacman -S 3ds-dev

You may need to add dpk- to the devkitPro pacman build, tab completion might help

Now head to the directory finalize/ where you see the Makefile, and run:

macOS/Linux: make

Usage

Use -h to view arguments.

Examples:

py -3 custominstall.py -b boot9.bin -m movable.sed --sd E:\ file.cia file2.cia
python3 custominstall.py -b boot9.bin -m movable.sed --sd /Volumes/GM9SD file.cia file2.cia
python3 custominstall.py -b boot9.bin -m movable.sed --sd /media/GM9SD file.cia file2.cia

License/Credits

pyctr/ is from ninfs 795373d.

save3ds by wwylele is used to interact with the Title Database (details in bin/README).

Thanks to @BpyH64 for researching how to generate the cmacs.