begin{document}
input{contents}
end{document}

% compile with pdflatex -shell-escape

documentclass[preview,border=12pt]{standalone}
usepackage{filecontents}

begin{filecontents*}{template.tex}
documentclass[preview,border=12pt]{standalone}
newififsecret
begin{document}
common 1

ifsecret
I have a top secret message here.
fi

common 2
end{document}
end{filecontents*}

usepackage{graphicx}

begin{document}
immediatewrite18{unexpanded{pdflatex -jobname=secret-included "AtBeginDocument{secrettrue} input{template}"}}
immediatewrite18{unexpanded{pdflatex -jobname=secret-excluded "AtBeginDocument{secretfalse} input{template}"}}
Done, secret-included.pdf and secret-excluded.pdf have been generated!

fbox{includegraphics[width=.5linewidth]{secret-included}}%
fbox{includegraphics[width=.5linewidth]{secret-excluded}}
end{document}

documentclass[final]{article}
makeatletter
newififfinal
@ifclasswith{article}{final}{
  typeout{FINAL}finaltrue}{
  typeout{DRAFT}finalfalse}
makeatother

begin{document}
iffinal
  textbf{fbox{This is the author's manuscript.}}
fi

blabla
end{document}

newtoggle{<section>}
settoggle{<section>}{true}

iftoggle{<section>}{input{section.tex}}{}