Eclipse manages to bring my development workstation to a crawl by wanting to constantly re-index a large PHP project mounted on sshfs (secure network mount)
Obviously 99.9% of the project is not changing so I don't want it re-indexed.
Here is how to flush out the existing DLTK database:
cd <workspace>/.metadata/.plugins/org.eclipse.dltk.core.index.sql.h2
rm *
Now you can disable DLTK for any PHP projects where you don't want it by configuring the build path (Project->Properties->PHP Build Path) and removing all of the entries.