Fix setuptools build and add other small fixes

[davcri]

Please check if the PR fulfills these requirements:

• The commit message follows our guidelines.
• For bug fixes and features:
  • You tested the changes. (couldn't test PyPi package upload)
  • You updated the docs or changelog.

Related issue (if applicable): #63, #76

What kind of change does this PR introduce?

• Fixed Add __init__.py to modules folder. #77 (I committed the file in the build path) + created .gitignore to avoid such errors in the future
• Updated ReferenceCollectorCLI.gd directories path: integrated workaround suggested in Can't get it to work without modifying ReferenceCollectorCLI.gd #63
• Refactored gdscript_docs_maker/modules → src/gdscript_docs_maker following setuptools recommended src layout.
  Now this workflow works as expected:

make build
python3 -m pip install dist/gdscript_docs_maker-1.5.1-py3-none-any.whl # this build now contains all the necessary python files
python3 -m gdscript_docs_maker # this now runs correctly

Does this PR introduce a breaking change?

Only if ReferenceCollectorCLI.gd needs var directories := ["res://src"].

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Disclaimer: I don't have previous experience with Python setuptools or packaging, I just spent some hours reading the doc and tinkering with this repo in order to fix the main workflows of make build and ./generate_reference.

[NathanLovato]

Just tested it, looking good, thanks. Having a src/ directory wasn't necessary but if it's common and people understand it, that's fine. Merging!

[davcri]

Thanks for taking time to review this, have a great January! 🎉 💒