You need to enable direnv with a bashrc hook on a clean VM

[cognivore]

# enable programmable completion features (you don't need to enable
# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
# sources /etc/bash.bashrc).
if ! shopt -oq posix; then
  if [ -f /usr/share/bash-completion/bash_completion ]; then
    . /usr/share/bash-completion/bash_completion
  elif [ -f /etc/bash_completion ]; then
    . /etc/bash_completion
  fi
fi

eval "$(direnv hook bash)"

Installer doesn't seem to be appending the hooks. Here are hooks: https://github.com/direnv/direnv/blob/master/docs/hook.md

BASH

Add the following line at the end of the ~/.bashrc file:

eval "$(direnv hook bash)"

Make sure it appears even after rvm, git-prompt and other shell extensions
that manipulate the prompt.

ZSH

Add the following line at the end of the ~/.zshrc file:

eval "$(direnv hook zsh)"

Oh my zsh

Oh my zsh has a core plugin with direnv support.

Add direnv to the plugins array in your zshrc file:

plugins=(... direnv)

FISH

Add the following line at the end of the ~/.config/fish/config.fish file:

direnv hook fish | source

Fish supports 3 modes you can set with the global environment variable direnv_fish_mode:

set -g direnv_fish_mode eval_on_arrow    # trigger direnv at prompt, and on every arrow-based directory change (default)
set -g direnv_fish_mode eval_after_arrow # trigger direnv at prompt, and only after arrow-based directory changes before executing command
set -g direnv_fish_mode disable_arrow    # trigger direnv at prompt only, this is similar functionality to the original behavior