Minor changes on documentation

docs/index.rst

@@ -17,10 +17,3 @@ Welcome to PSOT - protein sequence observation tool's documentation!
    profiles
    repositories
 
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

docs/repositories.rst

@@ -5,6 +5,7 @@ A repository contains one or multiple modules and profiles. It defines a
 directory structure. 
 
 A repository has the following structure::
+
     ./repository/
                  config.yaml
                  profiles/

docs/usage.rst

-PSOT usage
-==========
+Usage
+=====
 
 PSOT comes along as the commandline tool `psot`. It has two subcommands::