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JAL-4064 JAL-4054 Combined install4j10 template with new architectures. Added scheme associations for macOS.

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    ./install4j/install4j10_template.install4j
JAL-4054 Altered file association templates and generated install4j xml and Info.plist snippets.

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    ./install4j/auto_file_associations-i4j10.pl
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    ./install4j/file_associations_auto-Info_plist.xml
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    ./install4j/file_associations_auto-install4j10.xml
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    ./install4j/file_associations_template-Info_plist.xml
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    ./install4j/file_associations_template-install4j10.xml
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    ./install4j/install4j10_template.install4j
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JAL-4054 Altered file association templates and generated install4j xml and Info.plist snippets.

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    ./install4j/auto_file_associations-i4j10.pl
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    ./install4j/file_associations_auto-Info_plist.xml
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    ./install4j/file_associations_auto-install4j10.xml
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    ./install4j/file_associations_template-Info_plist.xml
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    ./install4j/file_associations_template-install4j10.xml
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    ./install4j/install4j10_template.install4j
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JAL-4064 re-added bundled macOS JREs as Filesets, which is the only way to get them in the DMG where we want them

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    ./install4j/install4j9_template.install4j
JAL-4064 Cleaned up file sets in install4j template. New media installers for AARCH64 JVMs for macOS and Linux in install4j template. New variables passed to install4j by gradle.

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    ./install4j/install4j9_template.install4j
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JAL-4064 Download JRE/JDKs from Azul if not os/arch combination not available from Adoptium

Now fallback to Azul when downloading JREs or JDKs. Gets macos aarch64 Java 8 JRE

JAL-4064 First attempt at building an M1 native Jalview DMG

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    ./install4j/install4j9_template.install4j
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JAL-4059 update Jmol and JSmol to 15.2.69 - revised Jalview classes interating with Jmol API to handle double precision structure data

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JAL-3059 upgrade Jmol from 14.31.53 to 15.2.69 (double precision) - required patches to structure data related classes and Jmol API implementors for float->double

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Merge branch 'kjvdh/features/PhylogenyViewer_tabbedsupport' into merge/2_11_2/kjvdh/features/PhylogenyViewer_tabbedsupport Update from Release 2.11.2 develop branch JAL-1953 Conflicts: .classpath .project resources/lang/Messages.properties src/jalview/bin/Jalview.java src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java src/jalview/fts/core/GFTSPanel.java src/jalview/fts/service/pdb/PDBFTSPanel.java src/jalview/gui/AlignFrame.java src/jalview/gui/CalculationChooser.java src/jalview/gui/DasSourceBrowser.java src/jalview/gui/Desktop.java src/jalview/gui/PopupMenu.java src/jalview/gui/SplashScreen.java src/jalview/gui/StructureViewerBase.java src/jalview/gui/TreePanel.java src/jalview/gui/WebserviceInfo.java src/jalview/io/BioJsHTMLOutput.java src/jalview/io/FileLoader.java src/jalview/io/HtmlSvgOutput.java src/jalview/io/NewickFile.java src/jalview/math/Matrix.java src/jalview/math/MatrixI.java src/jalview/util/MappingUtils.java src/jalview/ws/DBRefFetcher.java src/jalview/ws/DasSequenceFeatureFetcher.java src/jalview/ws/jws2/Jws2Discoverer.java utils/eclipse/org.eclipse.jdt.core.jalview.prefs utils/eclipse/org.eclipse.jdt.ui.prefs

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    ./eclipse/org.eclipse.jdt.core.jalview.prefs
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JAL-3066 update classlist for jalviewjs

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    ./jalviewjs/classlists/jalview.txt
JAL-4004 Temporary mechanism to add JalviewJS link for selected versions to hugo website

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JAL-3989 Code tidying, added JVL_HEADER for older versions of Jalview, allow time in release date header

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JAL-4004 Now generating hugo files from help/markdown/...

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    ./hugo/old_task_to_extract_markdown_from_old_releases_html.txt
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JAL-3989 improved parsing and formatting now using flex CSS layout for columns

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JAL-3989 Populate template files for hugo build: archive version files including changes from releases.html, and installers data file

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JAL-3989 moved getdown build dirs to build/website/docroot/getdown/CHANNEL, build/website/docroot/old/VERSION and build/getdown/files, and files for hugo into build/website/hugo/... This is better in multiple ways including collating files needed for the hugo website and website docroot.

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    ./install4j/install4j9_template.install4j
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Merge branch 'task/JAL-3553_improved_install4j_output_txt' into merge/JAL-3978+JAL-3553+develop

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    ./install4j/install4j8_template.install4j
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JAL-3851 merged to develop 2022-03-22

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    ./eclipse/eclipse_run.sh
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JAL-3978 New tasks to build archive 'old' dir with appropriate getdown resources, JVL file and digest

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    ./channels/archive/jalview_archive_getdown_background.png
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    ./channels/archive/jalview_archive_getdown_background.xcf
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    ./channels/archive/jalview_archive_getdown_background_error.png
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    ./channels/archive/jalview_archive_getdown_background_initialising.png
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    ./channels/archive/jalview_archive_getdown_progress_bar.png
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    ./channels/default/resources/channel.props
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    ./channels/develop/resources/channel.props
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    ./channels/old/images/jalview_archive_getdown_background.png
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    ./channels/old/images/jalview_archive_getdown_background.xcf
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    ./channels/old/images/jalview_archive_getdown_background_error.png
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    ./channels/old/images/jalview_archive_getdown_background_initialising.png
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    ./channels/old/images/jalview_archive_getdown_progress_bar.png
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    ./channels/old/images/jalview_logo.png
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    ./channels/release/resources/channel.props
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JAL-3978 task stub and getdown splash screens

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    ./channels/archive/jalview_archive_getdown_background.png
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    ./channels/archive/jalview_archive_getdown_background.xcf
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    ./channels/archive/jalview_archive_getdown_background_error.png
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    ./channels/archive/jalview_archive_getdown_background_initialising.png
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    ./channels/archive/jalview_archive_getdown_progress_bar.png
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JAL-3393 Updated DS_Store files, script and doc

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    ./channels/release/images/jalview_dmg_DS_Store
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JAL-3393 updated DMG DS_Store files

JAL-3393 updated Jalview Test DMG background image

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    ./channels/test-release/images/jalview_test-release_dmg_background.svg
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JAL-3393 improved flexibility of script and updated doc

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JAL-3393 Made an all-in-one script to create the DS_Store from scratch (has to be run on a mac desktop, it incorporates the AppleScript Finder adjustments). Updated docs. Updated the release DMG background image with the script. Changed install4j9 to put the background image as .background/background.png.

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    ./channels/release/images/jalview_dmg_DS_Store
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    ./install4j/install4j9_template.install4j
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    ./install4j/mk_ds_store.sh
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    ./install4j/set_relative_dmg_background_image.applescript
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JAL-3393 Added version number to DMG Volume name. New jalview_dmg_DS_Store and documentation about it

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    ./channels/release/images/jalview_dmg_DS_Store
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    ./install4j/set_relative_dmg_background_image.applescript
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JAL-3796 include entitlements when codesigning for macOS - doesn't actually help :(

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    ./install4j/install4j9_template.install4j
JAL-3962 Added jre/bin and dist folders to the native library path to try and fix the awt.dll problem

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    ./install4j/install4j9_template.install4j