Manifest | 2 1 + 1 - 0 !
build.xml | 6 3 + 3 - 0 !
2 files changed, 4 insertions(+), 4 deletions(-)

 use debian packaged jars

build.xml | 1 0 + 1 - 0 !
1 file changed, 1 deletion(-)

 build.xml should simply not touch all files in /usr/bin

src/main/resources/conf/jmodeltest.conf | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 set path to debian packaged phyml

manual/manual.tex | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 natbib.bst as inside the download has a non-free license
 so simply remove it from the tarball (see Files-Excluded) and use plainnat
 instead.

src/main/java/es/uvigo/darwin/jmodeltest/gui/FrameMain.java | 11 0 + 11 - 0 !
1 file changed, 11 deletions(-)

 remove browserlauncher references.

They were just a fallback if java.awt.Desktop.getDesktop() is not available.

manual/sec-theory.tex | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fix ftbfs with tex live 2018

src/main/java/es/uvigo/darwin/jmodeltest/ModelTestService.java | 8 4 + 4 - 0 !
1 file changed, 4 insertions(+), 4 deletions(-)

 the use of alter-lib.jar needs to modify the package name
 on parser and converter call