If you want the long explanation, I think you can search this forum and find one. Ever so often I go on a long-winded rant about why
you should never try and write into any part of a web application. Short answer: because it doesn't always work. Treat the app as something read-only that isn't necessarily a real directory with real files in it.
Eclipse isn't a web server, so if your webapp is attempting to write to itself, Eclipse doesn't get involved - all it's doing is running a copy of Tomcat in embedded mode. Technically, Tomcat's not doing it either. You're doing it to yourself in your webapp code.
But as I said, you'll have a happier life if you don't do it at all.