I suspect you are running tomcat using an own user - it's a common practice in unix systems - and that that user does not have read privilege to your home directory /Users/adamatan
.
Then you could try to add the tomcat user to you the group your user belongs to.
Better yet try to change the server location as described in this so question to a location where eclipse has write access and the tomcat user has read access.
EDIT
Actually its a setting in the Dynamic Web Project
wizard, If you choose Dynamic web module version 3.0
(which is default) or higher on the first page then on the last page the checkbox for Generate web.xml deployment descriptor
is disabled by default. If you choose 2.5 or lower it is then enabled by default. It has nothing to do with which tomcat you are actually using. If you want to use annotations though, then you have to have tomcat 7 with servlet specs 3.0