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JAL-3521 'Debian-safe' version of minimal build.gradle and patch. Using existing doc/*.html and build_properties from source tarball.

JAL-3521 Created a patch file to transform build.gradle into debian_build.gradle

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    ./build_gradle.patch
JAL-3521 working minimal build.gradle for debian and 2.11.2. Flexmark plugin might be a problem

JAL-3521 not quite working minimal build.gradle for debian and 2.11.2

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    ./debian_build.gradle
JAL-3521 High quality file icons for jalview associated files, and associated mime-type icon references

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    ./debian/icons/128x128/apps/jalview-icon.png
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    ./debian/icons/16x16/apps/jalview-icon.png
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    ./debian/icons/16x16/mimetypes/x-jalview-file.png
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    ./debian/icons/22x22/mimetypes/x-jalview-file.png
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    ./debian/icons/24x24/mimetypes/x-jalview-file.png
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    ./debian/icons/256x256/apps/jalview-icon.png
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    ./debian/icons/32x32/apps/jalview-icon.png
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    ./debian/icons/32x32/mimetypes/x-jalview-file.png
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    ./debian/icons/48x48/apps/jalview-icon.png
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    ./debian/icons/48x48/mimetypes/x-jalview-file.png
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    ./debian/icons/512x512/apps/jalview-icon.png
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    ./debian/icons/512x512/mimetypes/x-jalview-file.png
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    ./debian/icons/64x64/apps/jalview-icon.png
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    ./file_associations_template-shared-mime-info.xml
JAL-3521 High quality file icons for jalview associated files, and associated mime-type icon references

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    ./debian/icons/128x128/apps/jalview-icon.png
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    ./debian/icons/16x16/apps/jalview-icon.png
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    ./debian/icons/16x16/mimetypes/x-jalview-file.png
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    ./debian/icons/22x22/mimetypes/x-jalview-file.png
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    ./debian/icons/24x24/mimetypes/x-jalview-file.png
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    ./debian/icons/256x256/apps/jalview-icon.png
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    ./debian/icons/32x32/apps/jalview-icon.png
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    ./debian/icons/32x32/mimetypes/x-jalview-file.png
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    ./debian/icons/48x48/apps/jalview-icon.png
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    ./debian/icons/48x48/mimetypes/x-jalview-file.png
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    ./debian/icons/512x512/apps/jalview-icon.png
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    ./debian/icons/512x512/mimetypes/x-jalview-file.png
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    ./debian/icons/64x64/apps/jalview-icon.png
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    ./file_associations_template-shared-mime-info.xml
JAL-3521 Adjusted wrapper shell script and .desktop file to cater for opening a file with or without -open arg

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    ./debian/wrappers/jalview
JAL-3521 Adjusted wrapper shell script and .desktop file to cater for opening a file with or without -open arg

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    ./debian/wrappers/jalview
JAL-3815 default /etc/jalview_properties under utils/debian

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    ./etc/jalview_properties
JAL-3815 default /etc/jalview_properties under utils/debian

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    ./etc/jalview_properties
JAL-3251 debian build using maven, simplified build.gradle not needed

JAL-3521 Moved the debian build.gradle to utils/debian/build.gradle.debian

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    ./build.gradle.debian
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JAL-3521 Updating file opening marker to %u

JAL-3521 Updating file opening marker to %u

JAL-3521 Debian mime-type and desktop helper files, and script to create them

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    ./debian/jalview-file.png
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    ./debian/jalview-icon.png
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    ./debian/jalview-mailcap
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    ./debian/jalview-mime.xml
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    ./debian/jalview.desktop
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    ./file_associations_template-mailcap.txt
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    ./file_associations_template-shared-mime-info.xml
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    ./mime_types_for_debian.pl
JAL-3521 Debian mime-type and desktop helper files, and script to create them

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    ./debian/jalview-file.png
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    ./debian/jalview-icon.png
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    ./debian/jalview-mailcap
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    ./debian/jalview-mime.xml
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    ./debian/jalview.desktop
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    ./file_associations_template-mailcap.txt
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    ./file_associations_template-shared-mime-info.xml
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    ./mime_types_for_debian.pl