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JAL-3449 More whitespace in installer. Tidying

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    ./install4j/auto_file_associations.pl
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    ./install4j/bs_install4j_template.install4j
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    ./install4j/file_associations_auto-install4j.xml
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    ./install4j/file_associations_template-install4j.xml
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    ./install4j/install4j8_template.install4j
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    ./install4j/install4j_template.install4j
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JAL-3449 Fixed Info.plist file insertion. Simplified install4j conf filename

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    ./install4j/install4j8_template.install4j
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JAL-3449 Work in progress improving XML replacements by gradle

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    ./install4j/install4j8_template.install4j
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JAL-3394 Changed most of the token replacement for adding compiler variables

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    ./install4j/install4j8_template.install4j
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JAL-3420 multiple file extensions for the same mime-type now work in unix installer

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    ./install4j/auto_file_associations-i4j8.pl
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    ./install4j/file_associations_auto-install4j8.xml
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    ./install4j/file_associations_template-install4j8.xml
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    ./install4j/install4j8_template.install4j
JAL-3449 install4j version, install4j template version, getdown version now all being reported in Javliew console

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JAL-3393 Improved background image for DMG finder window, and associated files for creating it

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    ./getdown/jalview_logo_background_fade-640x480.xcf
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    ./install4j/install4j8_template.install4j
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    ./install4j/jalview_dmg_background-old.png
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    ./install4j/jalview_dmg_background.png
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    ./install4j/jalview_dmg_background_large.png
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    ./install4j/jalview_dmg_background_layers.pdf
JAL-3449 adding an installer template version. Really an md5 and a commit hash

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    ./install4j/DMG_creation_README.md
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JAL-3449 added an install4j compiler var

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    ./install4j/install4j8_template.install4j
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JAL-3210 Added in the build*xml files for helper tasks

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    ./jalviewjs/buildxml/build-libjs.xml
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    ./jalviewjs/buildxml/build-site.xml
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    ./jalviewjs/buildxml/build.Bob-Windows.xml
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    ./jalviewjs/buildxml/build.xml
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    ./jalviewjs/buildxml/buildcore.xml
JAL-3477 New sensible default decisions on memory, and new jvmmemmax setting for setting absolute memory level

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    ./testnglibs/classgraph-4.1.6.jar
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JAL-3210 multiple core templates. work in progress

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    ./jalviewjs/classlists/all.txt
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    ./jalviewjs/coretemplate.html
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JAL-3210 Test with coreall.z.js

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    ./jalviewjs/classlists/all.txt
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Revert "JAL-3210 merging in Jalview-JS/develop"

This reverts commit 9499aed89323b8f53689d6428ffc9b32250eae6c, reversing

changes made to fb616bbaa70ca0f8bbae7e076f3c403a737205a9.

Still not working right in Eclipse

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    ./jalviewjs/_j2sclasslist.txt
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    ./jalviewjs/_j2sclasslist_jmol.txt
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    ./jalviewjs/classlists/jalview.txt
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    ./jalviewjs/classlists/jvexamplefile.txt
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JAL-3210 BuildAllCores dependencies carefully implemented so Eclipse does not call headless task

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    ./jalviewjs/_j2sclasslist.txt
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    ./jalviewjs/_j2sclasslist_jmol.txt
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Revert "JAL-3210 work in progress on closures"

This reverts commit 581fcc0aab400bcdd52f5c0ec64f34a8fd5e786a.

Seems to have broken development in Eclipse IDE. Reverting.

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    ./jalviewjs/classlists/jalview.txt
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    ./jalviewjs/classlists/jvexamplefile.txt
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JAL-3210 work in progress on closures

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    ./jalviewjs/classlists/jalview.txt
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    ./jalviewjs/classlists/jvexamplefile.txt
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JAL-3474 removed all .cvsignore files stored in the repo

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JAL-3210 Some tidying and now using swingjs/*

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    ./jalviewjs/Java2ScriptCompilationParticipant.java
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    ./jalviewjs/Java2ScriptCompiler.java
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JAL-3210 tidying j2s and swingjs

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    ./jalviewjs/eclipse/cleanEclipseOptions
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    ./jalviewjs/eclipse/dropins/com.seeq.eclipse.importprojects.jar
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JAL-3210 Tidied more build.gradle. Different j2s versions for different eclipse versions -- temporary. Only 2019-06 working.

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    ./jalviewjs/SwingJS-site.zip_4.12
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    ./jalviewjs/SwingJS-site.zip_4.13
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JAL-3210 Using j2s plugins that work for 4.12. net.sf.j2s.core-3.2.4.08.jar not working yet

JAL-3210 Trying out new 3.2.4.08 j2s

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    ./jalviewjs/_j2sclasslist.txt
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JAL-3120 consistent paths/property interpolation in build.gradle. Test classes. Clean task corrections.

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    ./jalviewjs/test/src/jalview/bin/Jalview.java
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    ./jalviewjs/test/test/jalview/bin/Test.java
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JAL-3210 changed .classpath in eclipse_files.zip

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    ./jalviewjs/eclipse/eclipse_files.zip
JAL-3210 renamed jar for consistency

JAL-3120 Emergency eclipse files in case you don't have gradle CLI

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    ./jalviewjs/eclipse/eclipse_files.zip
JAL-3210 Different j2s plugin for different versions of eclipse. Not great, but good for now

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    ./jalviewjs/eclipse/dropins_4.12/com.seeq.eclipse.importprojects-1.4.0.jar
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    ./jalviewjs/eclipse/dropins_4.13/com.seeq.eclipse.importprojects-1.4.0.jar
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JAL-3210 Changed eclipse workspace dir to be a system temp dir [held in build/jalviewjs/eclipse_workspace_location] that persists until a gradle clean

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    ./jalviewjs/eclipse/dropins/net.sf.j2s.core_3.2.4-FOR_4.13.jar
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JAL-3210 changed classes for net.sf.j2s.core

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    ./jalviewjs/Java2ScriptCompilationParticipant.java
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    ./jalviewjs/Java2ScriptCompiler.java