\documentclass{article}

% Use the input encoding UTF-8 and the font encoding T1.
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}

% Support for Agda code.
\usepackage{agda}

% Customised setup for certain characters.
\usepackage{newunicodechar}
\newunicodechar{∀}{\ensuremath{\mathnormal{\forall}}}
\newunicodechar{→}{\ensuremath{\mathnormal{\to}}}
\newunicodechar{₁}{\ensuremath{{}_1}}

% Support for Greek letters.
\usepackage{alphabeta}

% Disable ligatures that start with '-'. Note that this affects the
% entire document!
\usepackage{microtype}
\DisableLigatures[-]{encoding=T1}

\begin{document}

Some code:
\begin{code}
{-# OPTIONS --without-K --count-clusters #-}

open import Agda.Builtin.String

-- A comment with some TeX ligatures:
-- --, ---, ?`, !`, `, ``, ', '', <<, >>.

Θ₁ : Set → Set
Θ₁ = λ A → A

a-name-with--hyphens : ∀ {A : Set} → A → A
a-name-with--hyphens ff--fl = ff--fl

ffi : String
ffi = "--"
\end{code}
Note that the code is indented.

\end{document}