diff --git a/core/docs/README.md b/core/docs/README.md
index a2fc8cc23..84961862d 100644
--- a/core/docs/README.md
+++ b/core/docs/README.md
@@ -25,9 +25,5 @@ The `State` is the object that holds every information needed for the simulation
 
 ### Further information
 * [Input File Reference](Input.md)
-* [How to: Energy minimisation](Use_Minimisation.md)
-* [How to: LLG dynamics](Use_LLG.md)
-* [How to: GNEB](Use_GNEB.md)
-* [How to: HTST](Use_HTST.md)
-* [How to: MMF](Use_MMF.md)
-* [Input File Reference](Input.md)
\ No newline at end of file
+* [C API Examples](C_API.md)
+* [Python API Examples](Python_API.md)
\ No newline at end of file
diff --git a/core/docs/c-api/API_Reference.rst b/core/docs/c-api/API_Reference.rst
index c9a115d00..4a51cfe2b 100644
--- a/core/docs/c-api/API_Reference.rst
+++ b/core/docs/c-api/API_Reference.rst
@@ -21,4 +21,4 @@ Full API reference
     Spirit/Simulation.h         <Simulation>
     Spirit/State.h              <State>
     Spirit/System.h             <System>
-    Spirit/Transition.h         <Transition>
\ No newline at end of file
+    Spirit/Transitions.h        <Transitions>
\ No newline at end of file
diff --git a/conf.py b/docs/conf.py
similarity index 94%
rename from conf.py
rename to docs/conf.py
index 609298081..a78b537ca 100644
--- a/conf.py
+++ b/docs/conf.py
@@ -80,7 +80,7 @@
 
 
 # The master toctree document.
-master_doc = 'docs/index'
+master_doc = 'index'
 
 
 # man_pages = [ master_doc, ("docs/BUILD", "build", "building", "authors", "sectionbuild") ]
@@ -222,7 +222,7 @@ def run_apidoc(_):
     build on readthedocs.
     See also https://github.com/rtfd/readthedocs.org/issues/1139
     """
-    source_dir = os.path.abspath(os.path.dirname(__file__))
+    source_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), '..')
     apidoc_dir = os.path.join(source_dir, 'core', 'docs', 'python-api')
     package_dir = os.path.join(source_dir, 'core', 'python', 'spirit')
 
@@ -242,20 +242,20 @@ def run_apidoc(_):
         '--maxdepth', '4',
     ]
 
-    builddir = os.path.join(source_dir, 'build')
-    if not os.path.exists(builddir):
-        os.mkdir(builddir)
-    subprocess.check_call(['cmake', '..', '-DSPIRIT_BUILD_FOR_CXX=OFF', '-DSPIRIT_SKIP_HTST=ON'], cwd=builddir)
-    subprocess.check_call(['make'], cwd=builddir)
+    build_dir = os.path.join(source_dir, 'build')
+    if not os.path.exists(build_dir):
+        os.mkdir(build_dir)
+    subprocess.check_call(['cmake', '..', '-DSPIRIT_BUILD_FOR_CXX=OFF', '-DSPIRIT_SKIP_HTST=ON'], cwd=build_dir)
+    subprocess.check_call(['make'], cwd=build_dir)
 
     # See https://stackoverflow.com/a/30144019
     env = os.environ.copy()
     env["SPHINX_APIDOC_OPTIONS"] = 'members,special-members,private-members,undoc-members,show-inheritance'
-    subprocess.check_call([cmd_path] + options, env=env)
+    subprocess.check_call([cmd_path] + options, env=env, cwd=source_dir)
 
     #####################
     with open(os.path.join(apidoc_dir, 'parameters.rst'), "w") as parameters_file:
-        parameters_file.write("Parameters\n==================================\n\n")
+        parameters_file.write("spirit.parameters\n==================================\n\n")
         with open(os.path.join(apidoc_dir, 'spirit.parameters.mc.rst'), 'r') as generated_file:
             parameters_file.write(generated_file.read())
         with open(os.path.join(apidoc_dir, 'spirit.parameters.llg.rst'), 'r') as generated_file: