Add an :orphan: tag to documents that are not in the toctree so that sphinx…

doc/cifarSC2011/index.txt

+:orphan:
 
 .. _index:
 

doc/citation.txt

+:orphan:
 
 .. _citation:
 

doc/core_development_guide.txt

+:orphan:
 
 Core Development Guide
 =======================

doc/crei2013/index.txt

+:orphan:
 
 .. _crei2013_index:
 

doc/developer/index.txt

+:orphan:
 
 .. _developer:
 

doc/faq.txt

+:orphan:
 
 .. _faq:
 

doc/index.txt

@@ -245,7 +245,6 @@ StackOverflow, follow their guidance for `answering questions <http://stackoverf
    glossary
    links
    internal/index
-   proposals/index
    acknowledgement
    LICENSE
 

doc/install_centos6.txt

+:orphan:
 
 .. _install_centos6:
 

doc/install_ubuntu.txt

+:orphan:
+
 .. _install_ubuntu:
 
 Easy Installation of an Optimized Theano on Current Ubuntu

doc/install_windows.txt

+:orphan:
 
 .. _install_windows:
 

doc/library/compile/opfromgraph.txt

+:orphan:
+
 .. _opfromgraph:
 
 ===========

doc/nice_quotes.txt

-
+:orphan:
 
 "Thank YOU for correcting it so quickly. I wish all packages I worked
 with would have such an active maintenance - this is as good as it

doc/proposals/index.txt

+:orphan:
 
 .. _proposals:
 
@@ -7,9 +8,7 @@ Proposals for new/revised features
 
 .. toctree::
     :maxdepth: 1
+    :glob:
+
+    *
 
-    pfunc
-    noupdates
-    opt_patterns2
-    graphical_models
-    complex_gradient

doc/sandbox/index.txt

+:orphan:
+
 =========================================================
 Sandbox, this documentation may or may not be out-of-date
 =========================================================