Is there a way to have both desktop entries and binaries in the options list?

[tremby]

It looks like I can run one binary for desktop entries or another for binaries, but how can I have both sets of options together in one search box?

[torusJKL]

I don't think this is supported out of the box.
You could create a wrapper script that curates the applications and feeds the list to tofi.

Here is a proof of concept.
(It is slow and shows duplicates so isn't a drop in solution, ask your local AI to improve it)

#!/bin/bash

XDG_DATA_HOME="${XDG_DATA_HOME:-$HOME/.local/share}"

DESKTOP_FILE=$(mktemp)
trap 'rm -f $DESKTOP_FILE' EXIT

# Build desktop apps list, filtering out CLI/Terminal apps
for dir in "$XDG_DATA_HOME/applications" /usr/share/applications ~/.local/share/applications; do
    [ -d "$dir" ] && find "$dir" -name "*.desktop" 2>/dev/null
done | while read -r f; do
    # Skip if NoDisplay=true
    grep -q "^NoDisplay=true" "$f" 2>/dev/null && continue
    
    # Skip if Terminal=true (CLI apps)
    grep -q "^Terminal=true" "$f" 2>/dev/null && continue
    
    name=$(grep -m1 "^Name=" "$f" 2>/dev/null | cut -d= -f2 | tr -d '\r')
    exec=$(grep -m1 "^Exec=" "$f" 2>/dev/null | cut -d= -f2- | tr -d '\r')
    
    [ -n "$name" ] && [ -n "$exec" ] && printf '%s\t%s\n' "$name" "$exec"
done > "$DESKTOP_FILE"

# Show in tofi: desktop apps first (with suffix), then executables
selection=$(
    {
        cut -f1 "$DESKTOP_FILE" | sed 's/$/ (d)/'
        compgen -c | sed 's/$/ (e)/'
    } | /usr/bin/tofi
)

[ -z "$selection" ] && exit 0

# Strip suffix
selected_name=${selection% \(e\)}
selected_name=${selected_name% \(d\)}

# Look up using line-by-line
app_exec=""
while IFS=$'\t' read -r name cmd; do
    if [ "$name" = "$selected_name" ]; then
        app_exec="$cmd"
        break
    fi
done < "$DESKTOP_FILE"

if [ -n "$app_exec" ]; then
    /usr/bin/swaymsg exec -- "$app_exec"
else
    /usr/bin/swaymsg exec -- "$selected_name"
f