jalview

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JAL-3384 Added -out to showUsage and clarguments help text

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    /help/help/html/features/clarguments.html
JAL-3384 -out can now be used without getdown launch. -out cannot use '../' in pathname

JAL-3384 Added -out option to specify stdout/stderr file. Can start with File.separator for absolute path, otherwise assumed to be file in getdownappdir

JAL-3384 Redirect stdout and stderr to output.log file

JAL-3384 catch non-float version number of java

JAL-1544 fixed a html encoding of '<' (%lt; -> &lt;) in commandline.html

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    /help/help/html/features/commandline.html
JAL-3111 correct JVL appbase for 2.10.5 via getdown

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    /help/help/html/features/jvlfiles.html
Merge branch 'task/JAL-3337-rm-lib-update-sourceDist' into develop

Merge branch 'develop' of http://source.jalview.org/git/jalview into develop

JAL-3337 round-and-round the process source files again

JAL-3337 more includes and excludes

JAL-3337 remove the old lib directory !

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    /lib/Jmol-14.6.4_2016.10.26-no_netscape.jar
  1. … 35 more files in changeset.
JAL-3337 rejig the source distribution generation to process and replace tokens in source files

JAL-3111 replace year in header for help pages and put processed help in build/distributions

JAL-3225 try/catch for non-deprecated/deprecated property in sourceDist which is not available on older eclipses

JAL-3353 Change to build.gradle to use the file:// enabled getdown-launcher-local.jar for LOCAL and ARCHIVELOCAL builds only. Otherwise the getdown-launcher.jar (with no local file enabled) will be used

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    /getdown/lib/getdown-launcher-local.jar
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

JAL-3111 help pages minor corrections

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    /help/help/html/features/featureschemes.html
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    /help/help/html/features/featuresettings.html
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    /help/help/html/features/importvcf.html
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    /help/help/html/menus/alignmentMenu.html
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    /help/help/html/menus/alwcalculate.html
JAL-3348 fixed an internal href in help to allow building

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    /help/help/html/features/jvlfiles.html
JAL-3337 adjusted building doc as sourceDist uses gradle 5.2 or above properties

Merge branch 'task/JAL-3348_document_cli_memory_settings_when_launching_jalview' into develop

JAL-3111 JAL-3348 JVL file documentation

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    /help/help/html/features/clarguments.html
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    /help/help/html/features/jvlfiles.html
JAL-3348 revised bsoares memory settings documentation and updated docs for launching jalview from command line

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    /help/help/html/features/commandline.html
Merge branch 'develop' into task/JAL-3348_document_cli_memory_settings_when_launching_jalview

merging in develop

JAL-3348 memory.html documentation finished for 2.11.0

JAL-3348 jvmmempc in jvl file now works in linux

JAL-3348 jvmmempc multiple values shouldn't be merged

JAL-3111 tidy up lists/indentation for release notes

JAL-3111 Java 11 only and 'onwards'

JAL-3111 more whatsNew tweaks