I have an issue with Eclipse (version: 2022-06 [4.24.0]). For some reason when publishing to Tomcat server (version 9) some class files and XMLs with beans are not being pushed. Missing in pushed Jar files. It does not affect all the class files and it is happening only with project Jars which I have in Deployment Assembly.
Even stranger is that it does not happen with the first attempt. When I first create and build the full project. It seems to start when I refresh/update my workspace.
To better explain I normally add my project war file into the Tomcat and then publish it by using clean and/or publish. But also, in Deployment Assembly of this project I have linked other projects I need.
And I used this approach many times before without troubles but now I am on a different Eclipse version and project and I simply don't know what I am missing.
I was thinking that it might be an issue with Eclipse version (2022-06) but I tried different versions and the issue is still there. I also tried different version of Tomcat (9 and 8,5) but that also did not help. Now I am thinking that it might be somehow related to used JRE / JDK but so far, no conclusion.
Please, can anyone help? Give some suggestion?

