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I'll leave the original question to @jelovirt, but we should probably take this opportunity to review parameter descriptions w/r/t their support for absolute vs. relative paths and provide guidance on the preferred method(s) for specifying absolute paths for parameters like args.[ftr|hdf|hdr] that require them.
IIRC, when you pass args.filter as an Ant property, it's assumed it's an absolute file and if it happens to be relative, it's resolved against DITA-OT base directory (for backwards compatibility). If you pass --filter to CLI, relative paths are resolved against the current directory.
I think this should be explicitly explained in the dita command arguments page.
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