build.gradle | 2540 22 + 2518 - 0 !
1 file changed, 22 insertions(+), 2518 deletions(-)

 removing parts of build.gradle that are useless for a debian build
 Also "destinationDirectory" is "destinationDir" in the jar task for gradle 4,
 and "archiveFileName" is "archiveName".

src/jalview/ws/io/mime/JalviewMimeContentHandler.java | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 patch to use the latest version of apache mime4j

src/jalview/gui/SequenceRenderer.java | 2 1 + 1 - 0 !
src/jalview/io/HtmlSvgOutput.java | 4 2 + 2 - 0 !
src/jalview/renderer/AnnotationRenderer.java | 2 1 + 1 - 0 !
src/jalview/util/ImageMaker.java | 4 2 + 2 - 0 !
4 files changed, 6 insertions(+), 6 deletions(-)

 change the package for org.jfree, which is not the correct one

src/jalview/bin/Jalview.java | 11 1 + 10 - 0 !
1 file changed, 1 insertion(+), 10 deletions(-)

 get rid of quaqua look and feel, only licensed for mac

src/jalview/io/JSONFile.java | 2 1 + 1 - 0 !
src/jalview/util/JSONUtils.java | 4 2 + 2 - 0 !
2 files changed, 3 insertions(+), 3 deletions(-)

 jsonobject was wrongly invoked
 It was called with a wrong package name, "simple" being forgotten.
 Moreover it is called on an AlignmentPojo object, I added the getAppSettings
 method in the call to get a HashMap<String, Object>.

build.gradle | 1 1 + 0 - 0 !
src/jalview/bin/Cache.java | 144 0 + 144 - 0 !
src/jalview/bin/Jalview.java | 16 0 + 16 - 0 !
3 files changed, 1 insertion(+), 160 deletions(-)

 not using getdown inside jalview

test/jalview/bin/CommandLineOperations.java | 36 1 + 35 - 0 !
test/jalview/bin/HiDPISettingTest2.java | 30 1 + 29 - 0 !
test/jalview/util/Log4jTest.java | 29 1 + 28 - 0 !
3 files changed, 3 insertions(+), 92 deletions(-)

 avoid using classgraph, not needed to find the debian jar

src/jalview/bin/Jalview.java | 15 0 + 15 - 0 !
src/jalview/jbgui/GPreferences.java | 2 2 + 0 - 0 !
2 files changed, 2 insertions(+), 15 deletions(-)

 turn off google analytics call, relies on non-packaged software

build.gradle | 63 62 + 1 - 0 !
test/jalview/ext/htsjdk/VCFReaderTest.java | 2 1 + 1 - 0 !
2 files changed, 63 insertions(+), 2 deletions(-)

 removing tests that use the network, the gui, unpackaged classes
 or non-existing files

build.gradle | 14 3 + 11 - 0 !
1 file changed, 3 insertions(+), 11 deletions(-)

 modifying the .build_properties file to account for debian repackaging
 Also ensuring build reproductibility as timestamps are used.

build.gradle | 8 8 + 0 - 0 !
1 file changed, 8 insertions(+)

 omitting to build jalviewlite (because it needs applets, that are
 not supported anymore from openjdk-17) and the classes that need it.

build.gradle | 22 21 + 1 - 0 !
1 file changed, 21 insertions(+), 1 deletion(-)

 putting the timestamp of the latest debian/changelog entry instead
 of the one of compile time, in order to enhance build reproducibility

src/jalview/gui/AlignFrame.java | 2 1 + 1 - 0 !
src/jalview/gui/Desktop.java | 6 3 + 3 - 0 !
2 files changed, 4 insertions(+), 4 deletions(-)

 changing a package name to comply with debian-packaged groovy

src/jalview/bin/Jalview.java | 122 1 + 121 - 0 !
src/jalview/gui/APQHandlers.java | 22 0 + 22 - 0 !
src/jalview/gui/QuitHandler.java | 15 0 + 15 - 0 !
3 files changed, 1 insertion(+), 158 deletions(-)

 classes from com.formdev.flatlab are not packaged in debian

src/jalview/bin/Jalview.java | 8 4 + 4 - 0 !
src/jalview/bin/Launcher.java | 4 2 + 2 - 0 !
2 files changed, 6 insertions(+), 6 deletions(-)

 disabling java version checks, which cause trouble with our 
 home-made build_properties file.

src/jalview/bin/Launcher.java | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 wiaint a bit for the launcher to start instead of failing at
 startup. This seems to be problematic only with the Debian packaging.