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JAL-3223 - update swingjs to 3.2.9-j11

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JAL-3577 Removed default JALVIEW_VERSION from gradle.properties. Now being set by build.gradle

JAL-3577 Quick fix adding quotation marks for findProperty("JALVIEW_VERSION")==null...

JAL-3679 Added externally specified plugins dir to J2sPlugin check

JAL-3446 unused imports removed

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JAL-3493 fix patch for 2.11.1_js (nb - these changes should not be merged to 2.11.2!)

JAL-3675 release notes

JAL-3493 clear search highlights when escape/deselect all Conflicts: src/jalview/gui/AlignFrame.java patch migrated to src/jalview/gui/AligmentPanel.java

JAL-3493 failing test - creates a highlight and column selection and then called the deselect all alignfjame action and checks if highlight and selection are still present. Conflicts: test/jalview/gui/SeqCanvasTest.java

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JAL-3659 unnecessary duplication -- test is made in previous block

JAL-3446 unintentially left training message in code.

JAL-3648 resize annotation panel after dragging to resize graph height

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JAL-3662 JAL-3660 JAL-3561 source formatting

Merge branch 'cherrypicks/JAL-3660_JAL-3561_JAL-3662_cli_outputformat' into Jalview-JS/develop

JAL-3659 proper headless check; skips setProperty for JS

JAL-3662 simple fix for CLI not using right format for output of alignment.

JAL-3660 JAL-3561 output alignment as requested file format as validated by FileFormats - report if format cannot be resolved or FileFormatI does not support export. Merged jbp patch for to rhanson's Jalview-JS/develop reworking of args parsing

JAL-3561 JAL-3660 check resolved FileFormatI instances are equivalent to verify format is as expected in test

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Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

JAL-3446 -- YEIKS! two checkURLLinks calls!

Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

JAL-3583 better handling of null or empty tooltip on annotation

JAL-3446 defer size calculations until panel added to window

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JAL-3446 proper call for headless state

JAL-3446 CommandLineOperation test

- cleaner headless check when adding JInternalFrame to Desktop


JAL-3446 CommandLineOperation test

- headless check must be before Desktop.getInstance(), as you can't

make an instance of JFrame() when headless.

JAL-3446 CTRL-DOWN check for headless operation

Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

JAL-3657 SwingJS HashMap.putEntries() coding mistake.

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JAL-3658 Now only making cores from utils/jalviewjs/classlists/*.txt

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