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I am looking for a graphical FTP client that allows me to enter FTP commands manually.

The reason I ask is because we have an old real-time system on the job with an odd file structure without tree structure. For example, to go to a "directory" I have to write:

CD ~TNA=AMP,VNA=VOL03,FNA=U-EQ-Y-SLM
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Maybe Filezilla can do what you want. You probably have to test it yourself:

http://www.ehow.com/how_2272127_create-custom-commands-filezilla.html

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I have test, but if I try to give command CWD ~TNA=AMP,VNA=VOL03,FNA=U-ED-TEST-USL it dosn't list any files –  magol Jan 2 '13 at 11:41
    
Try turning on Filezilla's debug logging level to 2 or higher; it will display what it receives over the control connection even if it doesn't know how to handle it (I think). –  Andrew Lambert Jan 3 '13 at 7:25
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