\begin{tikzpicture}[
  line width=1.5pt,
  black!50,
  text=black,
]

  %% Use small fonts
  \footnotesize

  %% project
  \node [at={(0,4cm)}, anchor=north,
         rectangle,
         very thick,
         text centered,
         font=\ttfamily,
         minimum width=15cm,
         minimum height=7.5cm,
         draw=green!50!black!50,
         fill=black!10!green!2!white,
         label={[shift={(0,-5mm)}]\texttt{top-project-directory/}}] {};
  %% Its files
  \node [node-nonterminal-thin, at={(-6.0cm,-3cm)}] {COPYING};
  \node [node-nonterminal-thin, at={(-3.5cm,-3cm)}] {paper.tex};
  \node [node-nonterminal-thin, at={(-1.0cm,-3cm)}] {project};
  \node [node-nonterminal-thin, at={(+1.5cm,-3cm)}] {README.md};
  \node [node-nonterminal-thin, at={(+4.25cm,-3cm)},
         text width=2.5cm, text depth=-3pt] {README-hacking.md};

  %% reproduce
  \node [at={(-1.4cm,3.5cm)}, anchor=north,
         rectangle,
         very thick,
         text centered,
         font=\ttfamily,
         minimum height=6cm,
         minimum width=11.9cm,
         draw=green!50!black!50,
         fill=black!10!green!2!white,
         label={[shift={(0,-5mm)}]\texttt{reproduce/}}] {};

  %% reproduce/software
  \node [at={(-4.35cm,3cm)}, anchor=north,
         rectangle,
         very thick,
         text centered,
         font=\ttfamily,
         minimum height=5.3cm,
         minimum width=5.7cm,
         draw=green!50!black!50,
         fill=black!10!green!2!white,
         label={[shift={(0,-5mm)}]\texttt{software/}}] {};

  %% reproduce/analysis
  \node [at={(1.55cm,3cm)}, anchor=north,
         rectangle,
         very thick,
         text centered,
         font=\ttfamily,
         minimum height=5.3cm,
         minimum width=5.7cm,
         draw=green!50!black!50,
         fill=black!10!green!2!white,
         label={[shift={(0,-5mm)}]\texttt{analysis/}}] {};

  %% reproduce/software/config
  \node [at={(-5.75cm,2.5cm)}, anchor=north,
         rectangle,
         very thick,
         text centered,
         font=\ttfamily,
         minimum height=2.1cm,
         minimum width=2.6cm,
         draw=green!50!black!50,
         fill=black!10!green!2!white,
         label={[shift={(0,-5mm)}]\texttt{config/}}] {};
  %% Its files
  \node [node-nonterminal-thin, at={(-5.75cm,1.8cm)}] {LOCAL.conf.in};
  \node [node-nonterminal-thin, at={(-5.75cm,1.3cm)}] {versions.conf};
  \node [node-nonterminal-thin, at={(-5.75cm,0.8cm)}] {checksums.conf};


  %% reproduce/software/make
  \node [at={(-2.95cm,2.5cm)}, anchor=north,
         rectangle,
         very thick,
         text centered,
         font=\ttfamily,
         minimum height=2.1cm,
         minimum width=2.6cm,
         draw=green!50!black!50,
         fill=black!10!green!2!white,
         label={[shift={(0,-5mm)}]\texttt{make/}}] {};
  %% Its files
  \node [node-nonterminal-thin, at={(-2.95cm,1.8cm)}] {basic.mk};
  \node [node-nonterminal-thin, at={(-2.95cm,1.3cm)}] {high-level.mk};
  \node [node-nonterminal-thin, at={(-2.95cm,0.8cm)}] {python.mk};

  %% reproduce/software/bash
  \node [at={(-5.75cm,0.2cm)}, anchor=north,
         rectangle,
         very thick,
         text centered,
         font=\ttfamily,
         minimum height=2.1cm,
         minimum width=2.6cm,
         draw=green!50!black!50,
         fill=black!10!green!2!white,
         label={[shift={(0,-5mm)}]\texttt{bash/}}] {};
  %% Its files
  \node [node-nonterminal-thin, at={(-5.75cm,-0.5cm)}] {bashrc.sh};
  \node [node-nonterminal-thin, at={(-5.75cm,-1.0cm)}] {configure.sh};
  \node [node-nonterminal-thin, at={(-5.75cm,-1.5cm)}] {git-pre-comit};

  %% reproduce/software/bibtex
  \node [at={(-2.95cm,0.2cm)}, anchor=north,
         rectangle,
         very thick,
         text centered,
         font=\ttfamily,
         minimum height=2.1cm,
         minimum width=2.6cm,
         draw=green!50!black!50,
         fill=black!10!green!2!white,
         label={[shift={(0,-5mm)}]\texttt{bibtex/}}] {};
  %% Its files
  \node [node-nonterminal-thin, at={(-2.95cm,-0.5cm)}] {fftw.tex};
  \node [node-nonterminal-thin, at={(-2.95cm,-1.0cm)}] {numpy.tex};
  \node [node-nonterminal-thin, at={(-2.95cm,-1.5cm)}] {gnuastro.tex};

  %% reproduce/analysis/config
  \node [at={(0.15cm,2.5cm)}, anchor=north,
         rectangle,
         very thick,
         text centered,
         font=\ttfamily,
         minimum height=2.1cm,
         minimum width=2.6cm,
         draw=green!50!black!50,
         fill=black!10!green!2!white,
         label={[shift={(0,-5mm)}]\texttt{config/}}] {};
  %% Its files
  \node [node-nonterminal-thin, at={(0.15cm,1.8cm)}] {INPUTS.conf};
  \node [node-nonterminal-thin, at={(0.15cm,1.3cm)}] {param-1.conf};
  \node [node-nonterminal-thin, at={(0.15cm,0.8cm)}] {param-2.conf};

  %% reproduce/analysis/make
  \node [at={(2.95cm,2.5cm)}, anchor=north,
         rectangle,
         very thick,
         text centered,
         font=\ttfamily,
         minimum height=2.1cm,
         minimum width=2.6cm,
         draw=green!50!black!50,
         fill=black!10!green!2!white,
         label={[shift={(0,-5mm)}]\texttt{make/}}] {};
  %% Its files
  \node [node-nonterminal-thin, at={(2.95cm,1.8cm)}] {initialize.mk};
  \node [node-nonterminal-thin, at={(2.95cm,1.3cm)}] {download.mk};
  \node [node-nonterminal-thin, at={(2.95cm,0.8cm)}] {analysis-1.mk};

  %% reproduce/analysis/bash
  \node [at={(0.15cm,0.2cm)}, anchor=north,
         rectangle,
         very thick,
         text centered,
         font=\ttfamily,
         minimum height=2.1cm,
         minimum width=2.6cm,
         draw=green!50!black!50,
         fill=black!10!green!2!white,
         label={[shift={(0,-5mm)}]\texttt{bash/}}] {};
  %% Its files
  \node [node-nonterminal-thin, at={(0.15cm,-0.5cm)}] {process-1.sh};
  \node [node-nonterminal-thin, at={(0.15cm,-1.0cm)}] {process-2.sh};
  \node [node-nonterminal-thin, at={(0.15cm,-1.5cm)}] {process-3.sh};

  %% reproduce/analysis/python
  \node [at={(2.95cm,0.2cm)}, anchor=north,
         rectangle,
         very thick,
         text centered,
         font=\ttfamily,
         minimum height=2.1cm,
         minimum width=2.6cm,
         draw=green!50!black!50,
         fill=black!10!green!2!white,
         label={[shift={(0,-5mm)}]\texttt{python/}}] {};
  %% Its files
  \node [node-nonterminal-thin, at={(2.95cm,-0.5cm)}] {operation-1.py};
  \node [node-nonterminal-thin, at={(2.95cm,-1.0cm)}] {operation-2.py};
  \node [node-nonterminal-thin, at={(2.95cm,-1.5cm)}] {fitting-plot.py};

  %% tex
  \node [at={(6cm,3.5cm)}, anchor=north,
         rectangle,
         very thick,
         text centered,
         font=\ttfamily,
         minimum height=6cm,
         minimum width=2.7cm,
         draw=green!50!black!50,
         fill=black!10!green!2!white,
         label={[shift={(0,-5mm)}]\texttt{tex/}}] {};

  %% tex/src
  \node [at={(6cm,3cm)}, anchor=north,
         rectangle,
         very thick,
         text centered,
         font=\ttfamily,
         minimum width=2.5cm,
         minimum height=5.3cm,
         draw=green!50!black!50,
         fill=black!10!green!2!white,
         label={[shift={(0,-5mm)}]\texttt{src/}}] {};
  %% Its files
  \node [node-nonterminal-thin, at={(6cm,2.2cm)}] {preamble-1.tex};
  \node [node-nonterminal-thin, at={(6cm,1.7cm)}] {preamble-2.tex};
  \node [node-nonterminal-thin, at={(6cm,1.2cm)}] {figure-1.tex};
  \node [node-nonterminal-thin, at={(6cm,0.7cm)}] {figure-2.tex};

\end{tikzpicture}