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/util/ImageMaker.java | 4 2 + 2 - 0 !
3 files changed, 5 insertions(+), 5 deletions(-)

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

src/jalview/bin/Jalview.java | 24 2 + 22 - 0 !
1 file changed, 2 insertions(+), 22 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>.

src/jalview/bin/Cache.java | 136 0 + 136 - 0 !
src/jalview/bin/Jalview.java | 20 0 + 20 - 0 !
2 files changed, 156 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 | 9 0 + 9 - 0 !
src/jalview/jbgui/GPreferences.java | 2 2 + 0 - 0 !
2 files changed, 2 insertions(+), 9 deletions(-)

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

build.gradle | 336 172 + 164 - 0 !
1 file changed, 172 insertions(+), 164 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".

build.gradle | 64 62 + 2 - 0 !
test/jalview/ext/htsjdk/VCFReaderTest.java | 2 1 + 1 - 0 !
2 files changed, 63 insertions(+), 3 deletions(-)

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

build.gradle | 10 6 + 4 - 0 !
1 file changed, 6 insertions(+), 4 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.

src/jalview/bin/Jalview.java | 12 6 + 6 - 0 !
src/jalview/jbgui/APQHandlers.java | 8 4 + 4 - 0 !
2 files changed, 10 insertions(+), 10 deletions(-)

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