Unit test to check invalid inputs are failure and other handling of the input file

• Add a couple of more common files to the clean test list

• Make runcommand_expect_fail also capture error stream

• Add a few tests of our input file handling

Some of these are currently failing either because of bugs in our handling (invalid_input_name_indexed) or because of differences between my assumptions and the actual handling in the code (circular dependencies, missing inputs)

See Issue #102 for some discussion of the invalid_input_name_indexed failure.

The other two failures may warrant some discussion – do we actually expect these cases to fail or do we consider these as valid situations to proceed with?