Fix autoapi configuration

- Disable autoapi_add_toctree_entry to prevent warnings about
  non-existent chipflow-lib/autoapi/index document
- Add post-copy processing to include autoapi-generated indices
  (chipflow/index and chipflow_lib/index) in the chipflow-lib toctree
- This properly integrates the auto-generated API documentation into
  the navigation while avoiding the toctree reference errors

Remaining warnings (18) are from docstring formatting issues in
chipflow-lib source code that would need to be fixed upstream.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: robtaylor

docs/source/conf.py

@@ -115,6 +115,22 @@
 if platform_api_path.exists():
     platform_api_path.write_text(platform_api_content)
 
+# Add autoapi toctree to chipflow-lib index
+chipflow_lib_index_path = Path('chipflow-lib/index.rst')
+if chipflow_lib_index_path.exists():
+    content = chipflow_lib_index_path.read_text()
+    if 'autoapi/chipflow/index' not in content:
+        # Add API Reference section pointing directly to autoapi-generated indices
+        content += """
+.. toctree::
+   :maxdepth: 2
+   :caption: API Reference
+
+   autoapi/chipflow/index
+   autoapi/chipflow_lib/index
+"""
+        chipflow_lib_index_path.write_text(content)
+
 # -- Project information
 
 project = 'ChipFlow'
@@ -192,6 +208,7 @@
     'imported-members',
 ]
 autoapi_root = "chipflow-lib/autoapi"
+autoapi_add_toctree_entry = False  # Don't auto-add to toctree (we link manually)
 
 # Exclude autoapi templates and in-progress stuff
 exclude_patterns = [