Eclipse can't find the tests in TestCLIParsing.scala, TestCLIDebugger.scala and the like due to the package statement at the top not matching the package folder structure.

Example: In TestCLIParsing.scala
package edu.illinois.ncsa.daffodil.CLI.parsing <-- tests can't be found or run
changing it to:
package edu.illinois.ncsa.daffodil.parsing <-- test can be found and run.

After making this change, another issue presents itself. Apparently Eclipse seems to think that its current working directory is wherever the project file is located.

Also, I just did a pull today (06-12-2013) and the daffodil-cli-unittest project in Eclipse can't find the LogFactory class. I right-clicked the project select Properties -> Java Build Path. Select the Libraries tab and add commons-logging-1.1.1.jar and this resolves the exception.

For me this was DFDL_GIT_ROOT\eclipse-projects\cli-test. As a result of this, the calls to Util.getExpectedString could not find the appropriate 'output' files and thus fail the tests with FileNotFound exceptions.