Heya Flow. There is really only one choice for a site script at this point in time and that's nxTools. As far as zipscripts go, you do have a few choices but ioNinja seems like the popular choice as it has a eggdrop bot that works with it and nxTools. There are problems with both but no show stoppers.
As far as ioYil goes, I haven't really touched it in a months as I've been mainly playing with this release. There are a number of tricky elements with site scripts like ioYil because they are tied to the FTP pretty closely and can be rather fragile. For instance, the recent change to preserve symbolic links in the path is actually a rather important change because it affects resolving all relative paths that a site script needs to process when deleting/moving/renaming directories or files. Luckily normal usage isn't relative so everything sorta works if you just ignore the problem, but that isn't a good solution. There are perhaps 2-3 "big" items like the disk spanning / free space logic that I need to support in the server before I think it makes sense to switch back to the script writing so it will probably be a while...
I'm also going to have to seriously consider switching over to openSSL just to ditch the MS encryption libraries in the hope that doing so reduces or eliminates the lockup bug. Unfortunately I don't think I can't use the easy high level interfaces that most people use because of the way ioFTPD is setup so it will be harder to do...
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