varying location of skeinforge profile files.

I'm fairly sure this is more a repetier problem than skeinforge/SFACT... putting config files under whatever the current STL folder is.

e.g. if I have loaded into Repetier host "W:\MySTLs\Part_one\part_one.stl"
and then from "Slicer / Skeinforge configuration", I alter the default skeinforge profile e.g. change the default layer height from 0.4 to 0.3,
it stores all the files (skeinforge_craft etc) under the current STL folder...
W:\MySTLs\Part_one\sfact_profiles\profiles\extrusion\Default
Same if I add my own skeinforge profile.

If I then go to work on Part_two, in its own folder, skeinforge does not have the modified default profile values, nor can it find any new profiles I added.
(because it must be using a relative path to the sfact_profiles folder rather than an absolute path)

Does repetier host pass or fail to pass some switch to the skeinforge/SFACT configuration that would control where the profile files should be?

The Repetier/skeinforge setup does not appear to have anything configurable to have set this relative profiles path.

The setup values for skeinforge application and craft are:
C:\apps\3d\ahmetcemturan-SFACT-1bc51b0\skeinforge_application\skeinforge.py
C:\apps\3d\ahmetcemturan-SFACT-1bc51b0\skeinforge_application\skeinforge_utilities\skeinforge_craft.py

The host doesn't add any parameter to the skeinforge call except the stl file location. It looks like SFACT (never used it) uses local file pathes from your description.
I will add add a working directory parameter for the next version. So skeinforge will always be called with a fixed starting directory.

You can add your parameter after the application/craft name.

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