Generate common doxygen.config for all projects

[TzuChieh]

There are too many common doxygen settings for the projects. We should add a config file generating stage in the setup script.

• [x] Ignore Generated folders (must check if any tracked folder will be affected)
• [x] Add script for generating a base_doxygen.config in the Generated folder for each project
• [x] doxygen.config for each project can (optionally) include the ./Generated/base_doxygen.config