Internal/lobster json refactoring tests #189
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The function `LOBSTER_Tool.process_commandline_options` does two things. It processes - the common command line options - and the tool specific command line options. The code has been refactored such that there are dedicated functions for each of these two steps. This increases readability of the code. Type hints have been added to some functions. The implementation of the method `LOBSTER_Per_File_Tool.process` has been replaced by a single `pass`, because it is abstract.
Write a requirement to specify the behavior of `lobster-json` if input files or directories are specified by the user. Add system tests for this requirement.
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