I installed Dreamweaver and when I was downloading the dependent files from my website, it asked me if I always wanted to do this. I said yes, and now, a couple weeks later, I don't want that anymore because it takes 30 seconds to download one little PHP file due to the dependent files.
I cannot find anywhere in the settings where I would be able to disable this again. Any ideas?
If it's not showing the dialog box that allows you to select whether dependant files will be sent, then you need to click the Put button with your actual mouse while holding down Alt. Then you'll be able to change your previous choice.
Edit (Dreamweaver on Mac) -> Preferences -> Site category, check the prompt on GET/PUT checkboxes. The next time you GET/PUT file a dialog will display asking you how you want to handle dependent files. There's a do not show again checkbox on that dialog check/uncheck as appropriate for your usage, and then click OK.
Dreamwveaver CS6
Its late but i'll add.
Edit > Preference > General => Enable Related Files (Uncheck this option)