Eclipse modifies server.xml each time run the project (Run-->Run on Server)
In {workspace}/Servers you will find a folder for every Tomcat configuration, containing several configuration files, including the server.xml. There you then can edit the file directly.
To get changes taken into account restart Eclipse. That is imho better than removing and adding the configuration back all the time. Tested using Eclipse Mars and Tomcat 7.
(the solution is from: Eclipse with tomcat - eclipse modifies server.xml)
I found an applicable solution but not a perfect one.
What I have done is;
1.Changed server.xml file in installation location (In my case C:\apache-tomcat-7.0.35\conf)
2.Remove tomcat server from eclipse server panel (please see the image below)
3.Create a new server in eclipse server panel.
4.Then Server project will be generated new server.xml with my customized changes.
5.The trick is, initially eclipse picks server.xml from installation location when create a new server in panel.
Thanks
Make sure you are editing the files right beneath the tomcat server folder, not the ones beneath the config folder. Check the attached screenshot for the files I'm referring to.