Simplify directory structure

[neopragma]

As of 0.0.4 CobolCheck requires users to place their Cobol sources under subdirectories with the same names as the source programs. That's unnecessary. We should remove that intermediate directory.

The structure mirrors the test suite directory structure, where it makes sense to have the intermediate directory because there can be many test suites for each program under test. But there's no need for this additional layer of directories in the application source tree.