If you control the sending side, make it right a 'filename.tmp.done' empty file next to the processed file. Then in Mule you could extend the File receiver to check for this marker file, and proceed only if it is there. If not - the file is still being worked on. There are some edge cases where this scenario may need manual intervention (e.g. in some crash scenarios), but otherwise very robust. I have never come around implementing it as an OOTB functionality in Mule, but know that many have done this in their custom deployments (e.g. with ftp too).
HTH,
Andrew
