Fixing a wrong call in the script

[hunterhector]

This PR fixes #860.

Description of changes

1. Correct the function call, with named parameters
2. Correct the corresponding tutorial/readme files
3. Update some warning messages since we find that namespace_depth probably won't work when the target directory exists.

Possible influences of this PR.

This change should be quite local.

Test Conducted

We have test cases in the OntologyGenerator class, but no tests for the command line scripts now.

[codecov]

Codecov Report

Merging #861 (44dc157) into master (62b081a) will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #861      +/-   ##
==========================================
+ Coverage   80.74%   80.75%   +0.01%     
==========================================
  Files         254      254              
  Lines       19364    19364              
==========================================
+ Hits        15635    15637       +2     
+ Misses       3729     3727       -2     

Impacted Files	Coverage Δ
forte/data/ontology/ontology_code_generator.py	90.09% <ø> (ø)
...orte/data/ontology/ontology_code_generator_test.py	100.00% <ø> (ø)
forte/command_line/generate_ontology/__main__.py	23.61% <100.00%> (+2.77%)	⬆️

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