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I am configuring custom commands in Texmaker, I can use % as a token for the name of the file (minus the extension) but I cannot find an equivalent for the full path.

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I'm afraid such a token might not exist. The Texmaker manual, section 1.2 Configuring the latex related commands only mentions these tokens:

The % character represents the name of the file without the extension (the master document in the "master" mode) and the @ character will be replaced by the current line number. Additional parameter : # will be replaced by the current file name without extension (even in the "master" mode)

But you can see if there's a similar feature request on the Texmaker issue tracker already, and if not, file one.

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I've added a feature request: code.google.com/p/texmaker/issues/detail?id=496 – Ben Feb 1 '12 at 17:12
@Ben Your feature request seems to have been deleted -- did you get any feedback why? – doncherry Oct 14 '12 at 21:48
I don't remember - I haven't kept any of the emails so I couldn't say. I seem to recall that people misunderstood the subtle problem and said I was mistaken for adding it. – Ben Oct 15 '12 at 9:24
...I seem to recall that people misunderstood the subtle problem (Opening the PDF in Foxit Reader if FR was already open), or thought that I was mistaken and that such a token would never be necessary under any circumstance. Presumably the working directory of the reader is set to the directory containing the PDF, so that a full path is not necessary - except if the reader is already open in which case it fails. – Ben Oct 15 '12 at 9:31

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