When using the daffodil CLI, if you specify a relative path to the schema file, the parse works without issues. If you try to give an absolute path, you get an error, even though the path tab-completes and exists.
$ echo "0,1,2"| daffodil-cli/target/universal/stage/bin/daffodil parse -s daffodil-test/src/test/resources/edu/illinois/ncsa/daffodil/section06/entities/charClassEntities.dfdl.xsd
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<tns:matrix
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xmlns:fn="http://www.w3.org/2005/xpath-functions" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:dfdl="http://www.ogf.org/dfdl/dfdl-1.0/" xmlns:tns="http://www.example.org/example1/" xmlns="http://www.w3.org/2001/XMLSchema">
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<tns:row>
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<tns:cell>0</tns:cell>
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<tns:cell>1</tns:cell>
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<tns:cell>2</tns:cell>
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</tns:row>
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</tns:matrix>
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jchab@WIN-EEA4S63ULQH ~/daffodil
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$ echo "0,1,2"| daffodil-cli/target/universal/stage/bin/daffodil parse -s /home/jchab/daffodil/daffodil-test/src/test/resources/edu/illinois/ncsa/daffodil/section06/entities/charClassEntities.dfdl.xsd
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[error] Bad arguments for option 'schema': '/home/jchab/daffodil/daffodil-test/src/test/resources/edu/illinois/ncsa/daffodil/section06/entities/charClassEntities.dfdl.xsd' - wrong arguments format
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