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JAL-3394 A little streamlining and fixing of helper script

JAL-3394 remove no longer used files

JAL-3532 TODO comment

fix for JAL-3529

JAL-3531 failing test

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JAL-3529 more detailed asserts to detect whitespace in DBRefs imported from Stockholm

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JAL-3529 preferentially output source dbrefs or principle db for sequence type before others.

JAL-3529 failing test for bug

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JAL-3187 alternative solution - gather feature settings for CDS/Protein as tabs in a window managed by SplitFrame

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JAL-1354 JAL-3528 fix bug from b594d516dac69eebcccdc743933880b00fb6d44c only try to look up message via formatMessage once.

JAL-3449 getdown resilience change to launcher classpath, includes the backup getdown-launcher.jar

JAL-3227 helper shell scripts for setting up a build environment

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JAL-3449 fix a getdownAppDir error introduced in previous commit 55f545014

JAL-3449 More tidying of build.gradle for CHANNEL selection

JAL-3187 applet alignFrame needs new api method

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JAL-3187 first stab at ‘show CDS/Protein Settings’ for convenient switching between complementary feature settings

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JAL-3187 view controller UI api method to show feature settings UI

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JAL-3187 convenience method on SplitContainerI to retrieve a complement’s alignFrame

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JAL-1354 JAL-3528 report missing keys for MessageManager.format calls

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JAL-3407 release notes for JAL-3121

JAL-3289 Updated doc/building.md to explain possible values of the CHANNEL property during building

JAL-3289 Updated doc/building.md to explain possible values of the CHANNEL property during building

JAL-3523 No longer change CWD of getdown when invoked by install4j launcher

JAL-3407 release notes for JAL-3375

JAL-3376 highlighted in what’s new

JAL-3407 - JAL-3376 JAL-3377 release notes

JAL-3407 start of whats new for

JAL-3376 documentation for standard attributes for variants from VCF

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JAL-3407 release notes (JAL-3386 signoff, new-knowns JAL-3523 JAL-3525)

JAL-3407 JAL-3508 move to point release versioning and signed off JAL-3510 JAL-3513 JAL-3388 JAL-3389 JAL-3441 JAL-3473 JAL-3406

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