Feat/Dev tools and centralising model name in YAML files

[LaansDole]

• Update README.md with make commands from Makefile
• Implement dev tools, include a tool to read all YAML files and uploads them to the VueGraph database.
• Update ${MODEL_NAME} in YAML Files to centralised model name from .env
• Replace .env with .env.example and hide .env in .gitignore, which is a better practice because why not

[NA-Wen]

Hi LaansDole,

Thank you so much for this wonderful contribution! I really appreciate the time and effort you've put into improving the developer experience with the new Makefile, dev tools, and documentation updates.

I've reviewed the PR and most of the changes look great. However, I'd like to kindly suggest a few adjustments:

1. Changes to check/check.py
Would it be possible to revert the modifications to check/check.py? It seems these changes might not be directly related to the main goals of this PR.

2. Modifications to yaml_instance/ files
I'd like to respectfully ask if we could revert the changes to the YAML files in the yaml_instance/ directory. The reason is that we intentionally designed the system to allow users the flexibility to specify different model names for different agents directly in their YAML configurations. By using a centralized .env variable, we might limit this flexibility. We believe giving users more control over individual agent configurations is important for the project's use cases.

Would you be able to update the PR to address these points? I'm really excited about merging the core improvements you've made. Thank you again for your contribution and understanding! 😊