you know exactly what do this client? at 100%?
it's a long story .. such as this http://forums.dropbox.com/topic.php?id=3107
and often company policy does not allow to put the closed source software on the server ..

and what a strange place if the client has proved over the years Secure Shell.
which is practically everywhere. need ftp? there. called sftp

want to connect to your home machine and edit a few files? no problem with SSH. as you suggest, first connect via iSSH copy Dropbox, open Textastic, download files, edit and upload back, then open iSSH, and burn the files back. Why?

better because: opened Textastic, set the path ssh://username@server.ip:/home/username/project and cache files to ipad. after you edit the clicked Sync and all the updated files uploaded to the server. Simple?
I like Dropbox but it is more convenient.

Dropbox on server == big-big backdoor for hackers ;)

do support SSH. then be able to compile your application as you wish.

this style used in rails, look http://ryandaigle.com/articles/2007/2/26/what-s-new-in-edge-rails-source-code-annotations

your can make group in File Properties, like: notes
and scan file to comment

For Ruby :)
Possible so that the user can add completion.
or maybe TextMate Snippets ;)