Optimize/improve packaging to make it lintian free and ideally uploadable to stock Debian

[mih]

The present Debian packaging is functional, but also suboptimal. Here is what lintian the Debian package checker thinks:

% lintian -iv afni_16.2.07\~dfsg.1-1_amd64.changes
N: Using profile debian/main.
N: Setting up lab in /tmp/temp-lintian-lab-up_VqNV8nS ...
N: Unpacking packages in group afni/16.2.07~dfsg.1-1
N: ----
N: Processing changes file afni (version 16.2.07~dfsg.1-1, arch source all amd64) ...
N: ----
N: Processing source package afni (version 16.2.07~dfsg.1-1, arch source) ...
E: afni source: build-depends-on-obsolete-package build-depends: hardening-includes => use dpkg-buildflags instead
N: 
N:    The package build-depends on a package that has been superseded. If the
N:    superseded package is part of an ORed group, it should not be the first
N:    package in the group.
N:    
N:    Severity: important, Certainty: possible
N:    
N:    Check: fields, Type: binary, udeb, source
N: 
W: afni source: syntax-error-in-dep5-copyright line 386: Duplicate field copyright.
N: 
N:    The machine-readable copyright file didn't pass Debian control file
N:    syntax check.
N:    
N:    This issue may hide other issues as Lintian skips some checks on the
N:    file in this case.
N:    
N:    Refer to
N:    https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ for
N:    details.
N:    
N:    Severity: normal, Certainty: possible
N:    
N:    Check: source-copyright, Type: source
N: 
N: ----
N: Processing binary package afni-common (version 16.2.07~dfsg.1-1, arch all) ...
W: afni-common: manpage-has-errors-from-man usr/share/man/man1/afni.1.gz 28: warning: macro `Ev' not defined
N: 
N:    This man page provokes warnings or errors from man.
N:    
N:    "cannot adjust" or "can't break" are trouble with paragraph filling,
N:    usually related to long lines. Adjustment can be helped by left
N:    justifying, breaks can be helped with hyphenation, see "Manipulating
N:    Filling and Adjusting" and "Manipulating Hyphenation" in the groff
N:    manual (see info groff).
N:    
N:    "can't find numbered character" usually means latin1 etc in the input,
N:    and this warning indicates characters will be missing from the output.
N:    You can change to escapes like \[:a] described on the groff_char man
N:    page.
N:    
N:    Other warnings are often formatting typos, like missing quotes around a
N:    string argument to .IP. These are likely to result in lost or malformed
N:    output. See the groff_man (or groff_mdoc if using mdoc) man page for
N:    information on macros.
N:    
N:    This test uses man's --warnings option to enable groff warnings that
N:    catch common mistakes, such as putting . or ' characters at the start of
N:    a line when they are intended as literal text rather than groff
N:    commands. This can be fixed either by reformatting the paragraph so that
N:    these characters are not at the start of a line, or by adding a
N:    zero-width space (\&) immediately before them.
N:    
N:    At worst, warning messages can be disabled with the .warn directive, see
N:    "Debugging" in the groff manual.
N:    
N:    Lintian also stricter in regards to declaring manpage preprocessors.
N:    
N:    To test this for yourself you can use the following command:
N:     LC_ALL=en_US.UTF-8 MANROFFSEQ='' MANWIDTH=80 \
N:            man --warnings -E UTF-8 -l -Tutf8 -Z <file> >/dev/null
N:    
N:    Refer to the groff_man(7) manual page and the groff_mdoc(7) manual page
N:    for details.
N:    
N:    Severity: normal, Certainty: certain
N:    
N:    Check: manpages, Type: binary
N: 
W: afni-common: csh-considered-harmful usr/lib/afni/bin/1dRplot
N: 
N:    The Debian policy for scripts explicitly warns against using csh and
N:    tcsh as scripting languages.
N:    
N:    Refer to Debian Policy Manual section 10.4 (Scripts) for details.
N:    
N:    Severity: normal, Certainty: certain
N:    
N:    Check: scripts, Type: binary
N: 
W: afni-common: unusual-interpreter usr/lib/afni/bin/1dRplot.R #!AFNI_Batch_R
N: 
N:    This package contains a script for an interpreter that is not shipped in
N:    the package and is not known to Lintian. It is possible that there is a
N:    typo or the interpreter is not executable. If not, please file a
N:    wishlist bug against lintian, so it can be added to the list of known
N:    interpreters.
N:    
N:    Severity: normal, Certainty: possible
N:    
N:    Check: scripts, Type: binary
N: 
W: afni-common: unusual-interpreter usr/lib/afni/bin/3dAOV.R #!afni_run_R
W: afni-common: unusual-interpreter usr/lib/afni/bin/3dGC.R #!AFNI_Batch_R
W: afni-common: unusual-interpreter ... use --no-tag-display-limit to see all (or pipe to a file/program)
W: afni-common: csh-considered-harmful usr/lib/afni/bin/3dLME
W: afni-common: csh-considered-harmful usr/lib/afni/bin/3dMEMA
W: afni-common: csh-considered-harmful ... use --no-tag-display-limit to see all (or pipe to a file/program)
W: afni-common: executable-not-elf-or-script usr/lib/afni/bin/demo.mobile.niml.do
N: 
N:    This executable file is not an ELF format binary, and does not start
N:    with the #! sequence that marks interpreted scripts. It might be a sh
N:    script that fails to name /bin/sh as its shell, or it may be incorrectly
N:    marked as executable. Sometimes upstream files developed on Windows are
N:    marked unnecessarily as executable on other systems.
N:    
N:    If you are using debhelper to build your package, running dh_fixperms
N:    will often correct this problem for you.
N:    
N:    Refer to Debian Policy Manual section 10.4 (Scripts) for details.
N:    
N:    Severity: normal, Certainty: certain
N:    
N:    Check: scripts, Type: binary
N: 
W: afni-common: executable-not-elf-or-script usr/lib/afni/bin/demo.fixed.niml.do
N: ----
N: Processing binary package afni-dev (version 16.2.07~dfsg.1-1, arch amd64) ...
N: ----
N: Processing binary package afni-dbg (version 16.2.07~dfsg.1-1, arch amd64) ...
N: ----
N: Processing binary package afni (version 16.2.07~dfsg.1-1, arch amd64) ...
N: 5 tags overridden (2 errors, 3 warnings)