Fiddle with formatting to get it looking ok and make links work.

doc/extending/extending_theano_gpu.txt

@@ -191,12 +191,14 @@ Dealing with float16
 To support limited-precision storage in a kernel you have to be
 careful to load values properly, declare working memory in float32 and
 write results properly.  To help with that some functions have been
-declared in `theano.gpuarray.fp16_help`.
+declared in :mod:`theano.gpuarray.fp16_help`.
 
 To load the inputs you should wrap the read with the function returned
-by :function:`load_w`. Similarly writes should be wrapped in the
-function returned by :function:`write_w`.  Finally working data should
-have the type returned by :function:`work_dtype`.
+by :func:`load_w() <theano.gpuarray.fp16_help.load_w>`. Similarly writes
+should be wrapped in the function returned by :func:`write_w()
+<theano.gpuarray.fp16_help.write_w>`.  Finally working data should
+have the type returned by :func:`work_dtype()
+<theano.gpuarray.fp16_help.work_dtype>`.
 
 Here is a +1 kernel that is not ready to deal with float16 input::
 

doc/extending/scan.txt

@@ -91,8 +91,8 @@ designated **inner inputs** and **inner outputs**, respectively.
 Scan variables
 ==============
 
-The following are the different types of variables that Scan has the capacity to
-handle, along with their various caracteristics.
+The following are the different types of variables that Scan has the
+capacity to handle, along with their various caracteristics.
 
 **Sequence** : A sequence is a Theano variable which Scan will iterate
 over and give sub-elements to its inner function as input. A sequence
@@ -103,10 +103,10 @@ of the ``theano.scan()`` function.
 
 **Non-sequences** : A non-sequence is a Theano variable which Scan
 *will provide as-is* to its inner function. Like a sequence, a
-*non-sequence has no associated output. For a non-sequence variable
-*``X``, at timestep ``t``, the inner function will receive as input
-*the variable ``X``. These variables are used through the argument
-*``non_sequences`` of the ``theano.scan()`` function.
+non-sequence has no associated output. For a non-sequence variable
+``X``, at timestep ``t``, the inner function will receive as input
+the variable ``X``. These variables are used through the argument
+``non_sequences`` of the ``theano.scan()`` function.
 
 **Nitsot (no input tap, single output tap)** : A nitsot is an output
 variable of the inner function that is not fed back as an input to the

doc/index.txt

@@ -135,7 +135,6 @@ Roughly in order of what you'll want to check out:
 * :ref:`optimizations` -- Guide to Theano's graph optimizations.
 * :ref:`extending` -- Learn to add a Type, Op, or graph optimization.
 * :ref:`dev_start_guide` -- How to contribute code to Theano.
-* :ref:`developer` -- Primarily of interest to developers of Theano
 * :ref:`internal` -- How to maintain Theano and more...
 * :ref:`release` -- How our release should work.
 * :ref:`acknowledgement` -- What we took from other projects.

doc/library/gpuarray/extra.txt

@@ -15,3 +15,9 @@ Kernel generation
 
 .. automodule:: theano.gpuarray.kernel_codegen
    :members:
+
+float16
+-------
+
+.. automodule:: theano.gpuarray.fp16_help
+   :members:

doc/library/gpuarray/fft.txt

 .. _libdoc_gpuarray_fft:
 
-==============================================
-:mod:`gpuarray.fft` -- Fast Fourier Transforms
-==============================================
+=====================================================
+:mod:`theano.gpuarray.fft` -- Fast Fourier Transforms
+=====================================================
 
 Performs Fast Fourier Transforms (FFT) on the GPU.
 

doc/library/gpuarray/type.txt

 .. _libdoc_gpuarray_type:
 
 ===================================================
-:mod:`gpuarray.type` -- Type classes
+:mod:`theano.gpuarray.type` -- Type classes
 ===================================================
 
 .. automodule:: theano.gpuarray.type