This assumes you are in the dokuwiki install directory. You should see bin and data under your current directory. This is for the rare occassions when the dokuwiki index is not showing the correct structure, or if you can not find and article and suspect your indexing is corrupt. Also removes the cache.

# manually remove all meta information, indicies and cache. Probably not needed
rm -fR data/meta/* data/index/*  data/cache/*
# rebuild index and clear beforehand 
sudo -u www-data php bin/indexer.php --clear