IntelliJ needs to copy tomcat/conf directory to project directory

Try chmod -R 777 /var/lib/tomcat7/conf/, it works to me.

Make sure that files under /var/lib/tomcat7/conf/ directory have read permission for the user IntelliJ IDEA is running from.

chmod -R 644 /var/lib/tomcat7/conf/

should help.

Also check that /home/adonis/.IntelliJIdea12/system/tomcat/ has correct permissions and owner. Could be that it was created from a different user and your current user doesn't have the rights to write into it.

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If it doesn't help, download and unpack a new Tomcat installation from .tar.gz file, configure IDEA to use this installation instead.

Note that Tomcat installed using the package manager on some Linux systems has non-standard layout and permissions, and therefore will not work with IDEA.