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It should really ask where to save the file. Even saving to the same location as the file being worked on would make more sense than the current behaviour, which saves to the current working directory (CWD).
It should probably name the output files based on the name of the file being worked on.
If the CWD is read-only then it fails, but doesn't explain why. see comment below
EDIT:
It should ask whether or not to overwrite, at least if item 2 isn't fixed. Silently overwriting things is not good, especially users might not even know where it is going to save. Other things that we write without confirmation are noise.dat [EDIT: we no longer write it at all] and cdrdao.toc (using the secret functionality to append the selection to it, when pressing a) [EDIT: as the whole point of this is to append to a file, this is intended]