The daffodil/daffodil-extra directory is an empty module intended to contain links to other git/svn repos where there are other projects that fit into the regular daffodil sub-module structure, but which for whatever reason, aren't part of its source tree.
There are several DFDL schemas now maintained at github: https://github.com/DFDLSchemas.
Each has its own git repository.
You clone that repository e.g., for NACHA (which runs on Daffodil) take these steps:
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Then these sorts of things will work:
EDIFACT -> ../../DFDLSchemas/EDIFACT
HL7 -> ../../DFDLSchemas/HL7-v2.7
IBM4690-TLOG -> ../../DFDLSchemas/IBM4690-TLOG
ISO8583 -> ../../DFDLSchemas/ISO8583
.keep
NACHA -> ../../DFDLSchemas/NACHA/2013
vCard -> ../../DFDLSchemas/vCard/2.1cwiki.apache.org/confluence/display/DAFFODIL/For+Contributors