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Been having this problem continuously with version 3 of MonoDevelop. I'll add a new iPhone ViewController which gives me a .cs, a designer.cs & a .xib - so far so good. Sometimes when I double-click the .xib & go to Xcode, it's all fine & the .m & .h files are there & let me add outlets & actions. Invariably though, if I add another ViewController, and double-click the .xib, when I get to Xcode the new .m file is missing (it's in red) and so is the AppDelegate.m. On further investigation of the actual Xcode files in the Finder, I find a new folder for each change, and when I open these folders I find the required AppDelegate.m and the new ViewController's .m - if I drag them into the newest build folder, the files are found by Xcode. However, it gets weirder, the xib's class claims to be the right one, but when you click on the list of available classes, the right one isn't there, which means you get an error if you attempt to make an outlet or an action. This can be solved by adding a new VC in Xcode (use any name), which somehow makes it register the existing ones, then you can begin to add outlets & actions. Obviously, this is far from ideal and causes a tremendous waste of time throughout the day. I'm wondering if it's new with version 3, as we've only been experiencing it this week. Many thanks for taking this on board!
Like you've noticed, we *do* generate a new output directory every time you change something in MonoDevelop, but we also tell Xcode to close the old project and open the freshly generated one.
(Note: we can't re-use the same directory because Xcode blows up if we rewrite the project.pbxproj out from under it).
What version of Xcode are you using?
The only thing I can think of is that I added some applescript timeouts between 2.8 and 3.0 (those are the only changes I made) and maybe the close/open applescript calls are timing out? They are set to 30 seconds, though. Is this happening on a large project? Or is your machine "slow"? I don't know how to quantify "slow", but I guess if you are on a mac-mini or something, that could explain it.
I've bumped up the timeouts to 60 seconds instead of 30
this should be fixed in the 188.8.131.52 beta
Found the actual bug regarding the missing AppDelegate.m, the migration code from 1 location to another was broken.
Fix didn't make it into 184.108.40.206 (obviously, since it's been out a week or so) but I'm going to backport the fix to the 3.0.3 branch so that the next beta build will have it.