The DLTK indexing is a feature of Eclipse that indexes information about dynamic languages like PHP or Perl. For PHP, this includes class definitions including their properties and methods, function prototypes, resolves code that is included or required in other files as well as many other things.
Without it, you would lose things like autocompletion for classes and functions defined by your project. It also helps with refactoring so if you rename a function, it can update all the other files that reference that function.
It's generally a good thing but I feel your pain and have ran into the same issue a number of times.
You can prevent certain directories from being indexed by right-clicking on the folder you would like to exclude from indexing in your project and selecting Build Path
and then clicking Exclude
. This should prevent it from getting indexed by this process.
Alternatively, you can pull up the project properties and manage the excluded paths from there: