[doc] Fix toctree of documentation

[Routhleck]

This pull request includes several changes to the documentation configuration and structure. The most important changes are the addition of new modules and adjustments to the table of contents.

Documentation Configuration Updates:

• docs/conf.py: Added the current directory to the system path and imported the auto_generater module.
• docs/conf.py: Included the matplotlib.sphinxext.plot_directive extension to the list of Sphinx extensions.
• docs/conf.py: Changed the show_toc_level option in html_theme_options from 2 to 1.

Documentation Structure Adjustments:

• docs/index.rst: Modified the table of contents to separate the tutorial and API documentation sections, and updated the included files.