When using watchfolders in AME, it automatically moves the source files into a "source" directory. I don't want that as it screws up my file structure. Is there any way to turn it off?
Not really. AME is moving the source file so that it wouldn't be re-encoded every time AME restarts.
There is a hacky workaround if you really need this functionality - after adding your watch folder, set it as read only and change the output to go into a different folder which has read+write permissions. Of course this means you have to change folder permissions every time you want to add media to it.
Moving all the source files to a single folder would not work when you two files by the same name are passed through the watch folder. Either the first one processesd would be overwritten by the second, or the second one would fail to be moved out of the watched folder (in which case, AME would reprocess it repeatedly.)
This could be resolved by the following:
gets added and processed.
If a 2nd MovieFile.mov gets added, and a MovieFile.mov is already in the single "Processed" folder, the 2nd MovieFile.mov should automatically get renamed to MovieFile(2).mov.
This behavior is standard in Windows Explorer, Mac Finder, and other file management applications.
I agree that this is an important feature to add. Moving the source files breaks associations in other applications. I think the best solution would be to have AME keep track of which files have been processed internally, and only process new ones. You could do this by tracking file name, size, modification date, etc. Even better - give us a preference option to choose which attributes to track.
Or, an alternative would be to watch for when new items are added to the folder, rather than constantly watching the contents of the folder.
Another option you could add, for power users, is the ability to add new jobs via shell or AppleScript. Then I would not have to use watch folders at all.
Is the option to disable the "source" folder move available in CS6?
Also, it is not possible to edit head/tail of of watched media (useful if the "automotic" feature is unchecked). Is this feature available in CS6, or do I need to request it?
If you're on a Mac, you can use Automator to collect the files back into one folder.
After transcoding is complete, and you’ve removed your folder from the watch folder panel within AME, run this Automator workflow. Be sure to select the “Source” folder in the “Find Finder Items” step, and select folder you want as the destination for the original files in the “Move Finder Items” step.