Improved handling of keep_outputs_dir for tool testing.

[jmchilton]

• Code quality things - typing and test cases.
• Fix so that it only copies for sim_size and diff - for file comparisons using regular expressions or contains do not replace the output.

The test cases and small fix in the last commit is the most relevant/interesting change. Ping @mvdbeek - is this problem with contains that you mentioned at the meeting?

How to test the changes?

(Select all options that apply)

• [x] I've included appropriate automated tests.
• [x] This is a refactoring of components with existing test coverage.

License

• [x] I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.