I think I misspoke by referring to the 'working directory'. I am a pea-green newbie when it comes to J2EE. I am just transitioning from application programming and hopefully will learn something. I have been following along with the HeadFirst JSP book and it does show a pretty basic directory structure using Tomcat 5. I was just noting that I did get my single page to work by putting it all by itself in my (only) app directory. I haven't gotten to the creating a WAR parts yet but I do have mine set up with the structure described in the book. There is just nothing in any of the other folders yet.
In Eclipse there is a server setting titled Deploy Path which is what I think I meant to refer to. I assume you can use that to tell Tomcat where to look for your webapps if you don't use the default directory. I noticed that Eclipse created a much more complex directory structure when using Tomcat 7. Antigioni originally had his page in what I assume is the Java src file, which I am pretty sure is not where anything but java source files should go and is what I assume you meant...
J2EE - meaning webapps - does not have a "working directory". Using the stock Java working directory is done at your peril, since you never know what may be changing it externally and asynchronously.