Open Source Document Management System | OpenKM

Not sure if this issue goes here, but wasn't sure where to post this. We have been running OpenKM 6.3 on a RedHat Linux 6.4 machine for sometime now without any issues. Then recently, the OpenKM website became unaccessible. The log file states that _phm.cfs doesn't exist and provides a path, which turns out to be an index for the repository. Sure enough this file doesn't exist. I cannot access the OpenKM website. Is there a way, through commandline to get OpenKM/Lucene to re-index? Can I recover the repository in some way?
I'm not sure how Lucene fits in other than for searching. Is there someway in which I can keep the documents, recover OpenKM and get OpenKM to magically fix itself where it will re-index everything? I don't want to lose the documents/repository, and I need to get OpenKM back up and running. Any help would be much appreciated!

Can you share here the catalina.log file to see the error with more detail.

1- First of all, make a backup.
2- With OpenKM stopped go to $TOMCAT/repository/ and delete the "index" folder ( do not worry the lucene search index can be build again ).
3- Start OpenKM
4- Go to administration and click on "Rebuild indexes" -> Choose "Lucene indexes" option ( will take some time ).

The instructions provided by jllort resolved the issues! Thank you very much for the instructions.