Move test entities and input and output files to sub-directories

[jesper-friis]

Description

Moved entities, input and output files to respectively sub-directories in the Python tests.

Closes #689
Addresses also issue #609

While updating the tests to use the new sub-directories, a few other path-related issues were discovered and fixed:

• two potential segfaults in dlite-storage.i and dlite.rdf.c if an invalid path is provided were fixed
• raise DLiteParseError instead of DLiteOtherError for invalid json input
• allow to hide DLiteOtherError by using DLiteUnknownError.

Type of change

• Bug fix & code cleanup
• New feature
• Documentation update
• Test update

Checklist for the reviewer

This checklist should be used as a help for the reviewer.

• Is the change limited to one issue?
• Does this PR close the issue?
• Is the code easy to read and understand?
• Do all new feature have an accompanying new test?
• Has the documentation been updated as necessary?