Did you try TextExpander? I bought it for use with Textastic but now use it with other apps. It will do what you need.

It's the possibility of overwriting local changes that causes me pain.

When working on a web site, I find it too cumbersome to download, edit and upload single files. As well, I'm not always online. And I actually DO want to download the whole directory structure. But of course, that's no good to me if there is no way to two-way sync changes between systems.

About other apps, I see your point. There are none, at least that I have, that do FSTP and webdav like I would expect to see on a destop. I don't have any knowledge of how iPad apps actually work or what Apple's rules are, so I'm completely ignorant of what the constraints are. Perhaps if the unison package were ported to the iPad OS, apps could hook into it.

Absolutely. I find the unjailbroken iPad to be too restrictive. My apps like Goodreader, QuickOffice, etc. all point to my /User/Documents directory. This directory is synchronized with all my other machines,(unix & windows) so I can sit at my iPad or any PC anywhere and edit my stuff. I know that within 15 minutes, all my other machines will have the same data. The tricky part is setting up exclusions so that host-specific parts don't get synced.