Move scripts directory into doc/scripts

doc/install.txt

@@ -175,8 +175,8 @@ This should give you the gist of it:
 
 .. code-block:: bash
 
-   $ python scripts/docgen.py --help
-   Usage: scripts/docgen.py [OPTIONS]
+   $ python doc/scripts/docgen.py --help
+   Usage: doc/scripts/docgen.py [OPTIONS]
      -o <dir>: output the html files in the specified dir
      --rst: only compile the doc (requires sphinx)
      --epydoc: only compile the api documentation (requires epydoc)

doc/internal/metadocumentation.txt

@@ -25,7 +25,7 @@ If you are lazy, you can try::
 However, if the link target is ambiguous, Sphinx will generate errors.
 
 NB the ``:api:`` reference is special magic by Olivier, in
-./scripts/docgen.py.
+./doc/scripts/docgen.py.
 
 How to add TODO comments in Sphinx documentation
 -------------------------------------------------
@@ -61,12 +61,12 @@ the `epydoc <http://epydoc.sourceforge.net/>`__ and `sphinx
 The following technique uses Olivier's code to insert :api: links::
 
     cd Theano/
-    python ./scripts/docgen.py
+    python ./doc/scripts/docgen.py
 
 If you don't want to rerun epydoc, do the following::
 
     cd Theano/
-    python ./scripts/docgen.py --rst
+    python ./doc/scripts/docgen.py --rst
 
 
 
@@ -105,5 +105,5 @@ TO WRITE
  * where the documentation is getting built, and epy.
  * How epydoc and sphinx are integrated
  * The nightly build process.
- * Explain the special magic in ./scripts/docgen.py
+ * Explain the special magic in ./doc/scripts/docgen.py
  * We also want examples of good documentation, to show people how to write sphinx,