DOCS: use manual toctree with implicit namespace option

Author: Puerling

core/docs/python-api/API_Reference.rst

@@ -4,4 +4,18 @@ Full API reference
 .. toctree::
    :maxdepth: 5
 
-   apidoc/modules
+   apidoc/spirit.chain
+   apidoc/spirit.configuration
+   apidoc/spirit.constants
+   apidoc/spirit.geometry
+   apidoc/spirit.hamiltonian
+   apidoc/spirit.htst
+   apidoc/spirit.io
+   apidoc/spirit.log
+   apidoc/spirit.parameters
+   apidoc/spirit.quantities
+   apidoc/spirit.simulation
+   apidoc/spirit.state
+   apidoc/spirit.system
+   apidoc/spirit.transition
+   apidoc/spirit.legacy