EDIT

After pushing a specific commit to the server and runing the build pipeline the resulting cdm-server is nor making use of that commit. It seems to be running on the old code.
A comparison of the md5sums of the cdmlib-remote-webapp.war artifacts as used in the jenkins pipeline revealed that the problem occures in the cdm-webapp project.
The correct war file is downloaded by maven but when creating the war overlay an old version of that artifact is used.

Summary of the md5sum comparison:

cdmlib-remote-4.4.0-SNAPSHOT.jar in different steps of the build pipeline:¶

all checksums are md5

as produced by the cdmlib integration job¶

~/tmp/check/cdmlib-remote-webapp-4.4.0-SNAPSHOT/WEB-INF/lib
0a56ced3b5412f44acd6e83204bb833b cdmlib-remote-4.4.0-SNAPSHOT.jar

what has been downloaded by the cdm-webapp job¶

Downloaded: http://wp5.e-taxonomy.eu/mavenrepo/eu/etaxonomy/cdmlib-remote-webapp/4.4.0-SNAPSHOT/cdmlib-remote-webapp-4.4.0-20161125.142844-97.war (72706 KB at 86967.7 KB/sec)
11f44279c56f9e4da5e8d3b05b88223a cdmlib-remote-webapp-4.4.0-20161125.142844-97.war

Downloaded: http://wp5.e-taxonomy.eu/mavenrepo/eu/etaxonomy/cdm-vaadin/4.4.0-SNAPSHOT/cdm-vaadin-4.4.0-20161125.140639-1562.war (90568 KB at 88100.6 KB/sec)

89276735c628bbc48820f3b374d13005 cdmlib-remote-4.4.0-SNAPSHOT.jar

what is contained in the cdm-webapp¶

~/tmp/check/cdm-webapp-4.4.0-20161125.142945-1630/WEB-INF/lib
89276735c628bbc48820f3b374d13005 cdmlib-remote-4.4.0-SNAPSHOT.jar

what is contained in the cdm-servers cdm-webapp¶

~/tmp/check/cdm-server-4.4.0-SNAPSHOT/cdm-webapp-4.4.0-SNAPSHOT/WEB-INF/lib

89276735c628bbc48820f3b374d13005 cdmlib-remote-4.4.0-SNAPSHOT.jar

Conclusion:¶

The problem obviously is the order of the overlays. In the pom vaadin comes first and thus determines the version of the cdmlib-remote-webapp artifact. Swapping the order solves the probelm.

The blog post https://dzone.com/articles/mavens-war-overlays-how-manage has interesting details on skinny overlays an is woirth reading even if it is not directly helpful in understanding the issue here.