jalview

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JAL-3937 enable AIA download of intermediate certificates when needed

JAL-3806 JAL-3725 propagate relaxed criteria for stop codon truncation from EMBLXmlSource to EMBLFlatFile parser

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    /test/jalview/io/EmblFlatFileTest.java
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3746 update release history for 2.11.1.5 and 2.11.1.6 patch releases

JAL-3934 update whats new

Merge branch 'critical/JAL-3933_log4j_update_for_develop_branch' into develop

Merge branch 'task/JAL-3934_update_log4j_again' into releases/Release_2_11_1_Branch

JAL-3934 trigger patch release for log4j version bump

Merge branch 'JAL-3927_ws_preferences_dialog_fix' into alpha/JAL-3066_Jalview_212_slivka-integration

Merge branch 'update/JAL-3066_updated_testng' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3878 Use AlignViewport interface instead of concrete implementation in AlignmentWorker

Merge branch 'develop' into critical/JAL-3933_log4j_update_for_develop_branch

JAL-3934 updated log4j from 2.16.0 to 2.17.0

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    /j11lib/log4j-1.2-api-2.17.0.jar
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    /j11lib/log4j-api-2.17.0.jar
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    /j11lib/log4j-core-2.17.0.jar
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    /j11lib/log4j-slf4j18-impl-2.16.0.jar
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    /j11lib/log4j-slf4j18-impl-2.17.0.jar
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    /j8lib/log4j-1.2-api-2.17.0.jar
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    /j8lib/log4j-api-2.17.0.jar
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    /j8lib/log4j-core-2.17.0.jar
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    /j8lib/log4j-slf4j18-impl-2.16.0.jar
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    /j8lib/log4j-slf4j18-impl-2.17.0.jar
JAL-3934 updated log4j from 2.16.0 to 2.17.0

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    /j11lib/log4j-1.2-api-2.17.0.jar
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    /j11lib/log4j-api-2.17.0.jar
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    /j11lib/log4j-core-2.17.0.jar
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    /j11lib/log4j-slf4j18-impl-2.16.0.jar
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    /j11lib/log4j-slf4j18-impl-2.17.0.jar
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    /j8lib/log4j-1.2-api-2.17.0.jar
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    /j8lib/log4j-api-2.17.0.jar
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    /j8lib/log4j-core-2.17.0.jar
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    /j8lib/log4j-slf4j18-impl-2.16.0.jar
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    /j8lib/log4j-slf4j18-impl-2.17.0.jar
Merge branch 'releases/Release_2_11_1_Branch'

JAL-3842 remove replacement tokens in html text - not properly resolved in this release branch

JAL-3753 avoid appending unreplaced html content in help pages

JAL-3842 patch what’s new text

JAL-3842 release 2.11.1.5 release notes

Merge branch 'critical/JAL-3933_log4shell_mitigation' into releases/Release_2_11_1_Branch

JAL-3933 updated THIRDPARTYLIBS

JAL-3933 updated THIRDPARTYLIBS

JAL-3933 updated THIRDPARTYLIBS

JAL-3933 updated THIRDPARTYLIBS

JAL-3933 remove obsolete Castor logging configuration

JAL-3933 remove obsolete Castor logging configuration

JAL-3933 configure root logger console appender to stderr (2.11.2 version)

JAL-3933 configure root logger console appender to stderr

JAL-3933 updated log4j and slf4j jars with log4j1.2 compatibility API jar. Removed log4j from jabaws-min-client and Jmol jars

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    /j11lib/Jmol-NO_LOG4J-14.31.53.jar
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    /j11lib/jabaws-min-client-2.2.0.jar
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    /j11lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
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    /j11lib/log4j-1.2-api-2.16.0.jar
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    /j11lib/log4j-api-2.16.0.jar
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    /j11lib/log4j-core-2.16.0.jar
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    /j11lib/log4j-slf4j18-impl-2.16.0.jar
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    /j11lib/slf4j-api-1.7.32.jar
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    /j11lib/slf4j-log4j12-1.7.32.jar
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    /j8lib/Jmol-NO_LOG4J-14.31.53.jar
  1. … 13 more files in changeset.
JAL-3933 updated slf4j to 1.7.32

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    /j11lib/slf4j-api-1.7.32.jar
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    /j11lib/slf4j-log4j12-1.7.32.jar
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    /j8lib/slf4j-api-1.7.32.jar
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    /j8lib/slf4j-log4j12-1.7.32.jar