gradle.properties

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JAL-4004 locations for markdown to go into whatsnew.html, releases.html and Version-VERSION/_index.md

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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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JAL-3989 slight refactor of build.gradle, add more metadata to JSON file. Added some commented out path changes to gradle.properties for future gathering of built files into more sensible places

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JAL-3978 Using getdowninstanceappdir and getdowninstanceappbase to avoid conflict with getAppbaseBuildProperties(). Added an if around fetching build_properties to avoid failing to fetch local file appbase.

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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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Merge branch 'develop' into improvement/JAL-3830_install4j9_macos_setup_application

Merge branch 'develop' into improvement/JAL-3594_BG_and_UoD_logos_added

JAL-3949 Complete new abstracted logging framework in jalview.log. Updated log calls for this. Removal of jalview.javascript.log4j. Improvements to the Java Console (controllable autoscrolling).

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New jalview.log.JLogger logging framework. Remove jalview.javascript.log4j as no longer needed

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Merge branch 'develop' into improvement/JAL-3830_install4j9_macos_setup_application

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Merge branch 'bug/JAL-3633_read_proxy_settings_from_jalview_properties_in_getdown' into develop

Conflicts:

src/jalview/bin/MemorySetting.java

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JAL-3746 update Jalview 2.12 branch from build.gradle for 2.11.2

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JAL-3746 update Jalview 2.12 branch from build.gradle for 2.11.2

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JAL-3907 changed two commented out lines to reflect location of future upgraded JRE zipfiles.

JAL-3830 Added steps for install4j9 to create macOS symbolic link to wrapper script (link) at /Applications/Jalview.app/Contents/MacOS/jalview and to add icon to Dock

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JAL-3594 added BG and UoD logo and banner to splashscreens, and adjusted status text box

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JAL-3874 attempt to add source jars to eclipse through buildship

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JAL-3830 BAT file wrapper around powershell, so jalview works in command prompt. Added install4j option for installer to add Jalview's bin dir to Path in Windows. Added install4j option to create symlink to bash script to user's local bin (first of ~/bin, ~/.local/bin, ~/local/bin, ~/opt/bin that exists. First two of these usually automatically in PATH).

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JAL-3830 Moved wrappers to bin/jalview.* and make a symlink bin/jalview. Install4j script now jalviewg

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JAL-3503 Added a Startup tab in Preferences, with gui for JVMMEMMAX and JVMMEMPC settings. Allowed jalview.bin.Launcher and getdown to read/use these memory settings at launch. Added channel.props to getdown appdir, used to determing correct .jalview_properties file. Refactored MemorySetting a bit, with more helper methods for the Preferences tab.

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JAL-3830 Now using a single universal bash script (jalviewc) for bash in linux, macos, cygwin and WSL. It keeps things together.

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JAL-3830 add the windows bash script to getdown files and install4j installers

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JAL-3830 improved bash scripts. Added powershell script. Needs testing

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JAL-3830 unix and macos wrappers. Symbolic link to jalviewc-macos in Contents/MacOS/jalviewc.

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JAL-3830 install4j adds script to Jalview.app/Contents/MacOS/jalview but we need install4j9 to make it executable

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Merge branch 'develop' into task/JAL-3796_notarization_no_uninstaller

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Merge branch 'develop' into task/JAL-3796_notarization

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JAL-3796 update to Install4j 8.0.10 and add config for code notarization

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JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalviewjs/config/j2s settings file when running a headless build in gradle

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