(debian-policy.info)Installation directory issues

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11.8.7 Installation directory issues
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Historically, packages using the X Window System used a separate set of
installation directories from other packages.  This practice has been
discontinued and packages using the X Window System should now generally
be installed in the same directories as any other package.
Specifically, packages must not install files under the ‘/usr/X11R6/’
directory and the ‘/usr/X11R6/’ directory hierarchy should be regarded
as obsolete.

Include files previously installed under ‘/usr/X11R6/include/X11/’
should be installed into ‘/usr/include/X11/’.  For files previously
installed into subdirectories of ‘/usr/X11R6/lib/X11/’, package
maintainers should determine if subdirectories of ‘/usr/lib/’ and
‘/usr/share/’ can be used.  If not, a subdirectory of ‘/usr/lib/X11/’
should be used.

Configuration files for window, display, or session managers or other
applications that are tightly integrated with the X Window System may be
placed in a subdirectory of ‘/etc/X11/’ corresponding to the package
name.  Other X Window System applications should use the ‘/etc/’
directory unless otherwise mandated by policy (such as for Note:
Application defaults files.).