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In a custom level
Edwards did this first (and maybe others have too), but he didn't document the process so I thought I'd do that for ya'll.
The custom level save is a file, and is stored alongside the "normal" save files. If you want to stop playing and still be able to resume later, you can make a copy of this file. It's located in ~/Library/Application Support/SketchFighter and named "Game 999".
In order to resume your save, you have to trick the game into loading it. Here's what you do:
Load the map, find a save point, and save.
Switch out of SF and replace the Game 999 file just created with your backed-up copy, giving it the appropriate name of course.
Switch back to the game and commit suicide. Hit "Try Again" (return) and the game will happily load your previous save.
While this process may be something of a pain, the fact that it's possible gives me hope that custom levels may one day be blessed with a proper save system. My uninformed guess is that it was simply too large a feature for 1.0.1, because a new interface would have been necessary and this release was mostly about fixing bugs.
Warning: Because of how the game handles time cumulative time for a level, any time you have accumulated in the previous save will be lost when you resume it using this technique. Basically, although the game saves the cumulative time in the saved game file, when the game is loaded, the time that is used is whatever was on the clock when you died. This allows the game to tally up the total time spent playing under normal conditions, rather than just the time spent on the segments that lead to success, but it really messes up the time when you resume a save after quitting- I had to manually add several hours to my Temple of the Pen score after dong this.
Edwards