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Merge branch 'develop' into JAL-3416_different_look_and_feel_on_linux

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-3937 enable AIA download of intermediate certificates when needed

JAL-3937 enable AIA download of intermediate certificates when needed

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 jars with log4j-2.16.0 and compatibility API log4j-1.2-api-2.16.0. Stripped...
JAL-3933 Updated log4j jars with log4j-2.16.0 and compatibility API log4j-1.2-api-2.16.0. Stripped...
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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JAL-3933 Updated log4j jars with log4j-2.16.0 and compatibility API log4j-1.2-api-2.16.0. Stripped log4j classes from jabaws-min-client jar. Updated sl4j jars in j8lib

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JAL-3911 HiDPISetting update. jalview.bin.* update. Attempt to detect SHIFT key -- Order of app config and window appearance wrong. must create a window to click instead.

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JAL-3416 make flat default laf for linux

JAL-3416 updated FlatLaf to 1.6 and added some tabbed pane properties

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Merge branch 'develop' into JAL-3416_different_look_and_feel_on_linux

JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately

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JAL-3741 http to https (and jar to jvp for exampleFile defaults!) Conflicts: src/jalview/bin/Jalview.java src/jalview/gui/Desktop.java

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JAL-2422 More helpful highlighting/user guidance of missing structure viewer path

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JAL-3851 fix caching and tidy up old methods

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JAL-3851 API handling of rest calls

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JAL-3851 convenience methods for logging exceptions

JAL-3851 throwaway code

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JAL-3851 start a listener with -testlistener and suggest a port with -testlistener_port. wget -S -O...
JAL-3851 start a listener with -testlistener and suggest a port with -testlistener_port. wget -S -O...
JAL-3851 start a listener with -testlistener and suggest a port with -testlistener_port. wget -S -O - http://localhost:20212/jalview/TEST/viewgene/ENSG00000139618

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JAL-3848 add compbio and jalview to direct connection list for J2S