Usually this occurs when doing lots of redeploys. I am surprised you have it using something like indexing. Use virtualvm or jconsole to monitor the Perm gen space and check it levels off after warming up the indexing.
Maybe you should consider changing to another JVM like the IBM JVM. It does not have a Permanent Generation and is immune to this issue.
You can also increase it via the VM arguments in your IDE. In my case, I am using Tomcat v7.0 which is running on Eclipse. To do this, double click on your server (Tomcat v7.0). Click the 'Open launch configuration' link. Go to the 'Arguments' tab. Add -XX:MaxPermSize=512m to the VM arguments list. Click 'Apply' and then 'OK'. Restart your server.
if you found out that the memory settings were not being used and in order to change the memory settings, I used the tomcat7w or tomcat8w in the \bin folder.Then the following should pop up:
Click the Java tab and add the arguments.restart tomcat