Edits part of review of PR#54

[FLomb]

These edits fix some of the issues we identified in our review of PR #54. More precisely:

• the example input files are cleaned from outdated parameters that were leading to errors
• outdated paths are updated based on the latest code structure
• a bug in the setup.py file is corrected
• the test_run.py is updated and some previously unnoticed issues are fixed
• the ramp_run.py is updated to run example files in .xlsx format by default, resorting to the .py files only in case .xlsx are not found