Start fleshing out the docs more - rearrange, separate out modules section, move files over to md (from rst)

docs/source/conf.py

@@ -17,6 +17,7 @@ extensions = [
     'sphinxcontrib.mermaid',        # Mermaid diagrams
     "sphinx.ext.viewcode",          # Source code links
     "sphinx.ext.napoleon",          # Google-style and NumPy-style docstrings
+    "sphinx.ext.autosectionlabel",
     # "sphinx.ext.autodoc",           # Include custom docstrings
     # 'sphinx.ext.autosummary',       # Summarize module/class/function docs
 ]
@@ -27,12 +28,13 @@ exclude_patterns = []
 
 # -- AutoAPI Configuration ---------------------------------------------------
 autoapi_type = 'python'
-autoapi_dirs = ["../../src"]
+autoapi_dirs = ["../../src/auto_archiver/core/", "../../src/auto_archiver/utils/", "../../src/auto_archiver/modules/"]
 autodoc_typehints = "signature"     # Include type hints in the signature
-autoapi_ignore = []                 # Ignore specific modules
-autoapi_keep_files = True          # Option to retain intermediate JSON files for debugging
+autoapi_ignore = ["*/version.py", ]                 # Ignore specific modules
+autoapi_keep_files = False          # Option to retain intermediate JSON files for debugging
 autoapi_add_toctree_entry = True    # Include API docs in the TOC
-autoapi_template_dir = None         # Use default templates
+autoapi_python_use_implicit_namespaces = True
+autoapi_template_dir = "../_templates/autoapi"
 autoapi_options = [
     "members",
     "undoc-members",
@@ -53,6 +55,8 @@ myst_enable_extensions = [
     "linkify",              # Auto-detect links
     "substitution",         # Text substitutions
 ]
+myst_heading_anchors = 2
+
 source_suffix = {
     ".rst": "restructuredtext",
     ".md": "markdown",