/usr/share/lilypond/2.16.2/ly/generate-documentation.ly is in lilypond-data 2.16.2-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 | \version "2.16.0"
%
% Running LilyPond on this file generates the documentation
%
#(ly:set-option 'protected-scheme-parsing #f)
#(load-from-path "documentation-generate.scm")
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