diff --git a/docs/index.rst b/docs/index.rst
index 8e36a24fb1fc749b99ba7658590ed5b96014e5b3..9ba3f9d9d0786209ed6c0831229bad670a7f516a 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -5,6 +5,7 @@
the Multiscale Object-Oriented Simulation Environment
=====================================================
+
What is MOOSE and what is it good for?
--------------------------------------
@@ -15,7 +16,7 @@ MOOSE can operate at many levels of detail, from stochastic chemical
computations, to multicompartment single-neuron models, to spiking neuron
network models.
-.. figure:: ../../images/Gallery_Moose_Multiscale.png
+.. figure:: ./images/Gallery_Moose_Multiscale.png
:alt: **multiple scales in moose**
:scale: 50%
@@ -56,4 +57,3 @@ Indices and tables
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
-
diff --git a/docs/introduction/changes/index.rst b/docs/introduction/changes/index.rst
index 9f43a992de85f97950befeaf71f1072ec8d1bfe2..9a167f14daf7633c581babd2cd82e2b452ad0900 100644
--- a/docs/introduction/changes/index.rst
+++ b/docs/introduction/changes/index.rst
@@ -1,2 +1,4 @@
Changes
=======
+
+.. todo:: collect changes from OBS.
diff --git a/docs/introduction/index.rst b/docs/introduction/index.rst
index 7561ac41fb69d526e8b6972346b6cc5cc2cc1131..88ba2bdae746ec62908fd7cf40a715af3e909b8a 100644
--- a/docs/introduction/index.rst
+++ b/docs/introduction/index.rst
@@ -2,7 +2,6 @@ Introduction
============
.. toctree::
- :maxdepth: 1
install/index
release_notes/index
diff --git a/docs/introduction/known_issues/index.rst b/docs/introduction/known_issues/index.rst
index f8b15cd39bdbb9daedad090e1659d5b35e8ec93b..0ad5cdd653f187c374b75e0d605f748d2e3c8ea9 100644
--- a/docs/introduction/known_issues/index.rst
+++ b/docs/introduction/known_issues/index.rst
@@ -1,5 +1,5 @@
Known issues
-===========
+============
Full report can be found at the following places
diff --git a/docs/introduction/release_notes/index.rst b/docs/introduction/release_notes/index.rst
index 1d58ca6d404e81f6177ce7442fc69b7d56f8bfb4..862216e95c1d42e9c53d4f176e75ffdfe2987165 100644
--- a/docs/introduction/release_notes/index.rst
+++ b/docs/introduction/release_notes/index.rst
@@ -1,2 +1,4 @@
Release Notes
============
+
+.. todo:: Collect release notes from github.
diff --git a/docs/user/py/classes/index.rst b/docs/user/py/classes/index.rst
index c9490cbed134147f8a0b51d0bacc13ca827ad1e4..fa64a75bf241d10d51b49e9ce586a6e9a456f571 100644
--- a/docs/user/py/classes/index.rst
+++ b/docs/user/py/classes/index.rst
@@ -2,7 +2,6 @@
.. As visible in the Python module
.. Auto-generated on October 01, 2014
-=============
MOOSE Classes
=============
diff --git a/docs/user/py/cookbook/index.rst b/docs/user/py/cookbook/index.rst
index de31923895cfefeb9eecc6f415488c2ddfdd7809..193d3eee706a21084b1b8293a949fd0afa329fec 100644
--- a/docs/user/py/cookbook/index.rst
+++ b/docs/user/py/cookbook/index.rst
@@ -25,7 +25,7 @@ The Hodgkin-Huxley demo
This is a self-contained graphical demo implemented by Subhasis Ray,
closely based on the 'Squid' demo by Mark Nelson which ran in GENESIS.
-.. figure:: ../../images/squid_demo.png
+.. figure:: ../../../images/squid_demo.png
:alt: Hodgkin-Huxley's squid giant axon experiment
Simulation of Hodgkin-Huxley's experiment on squid giant axon
@@ -51,7 +51,7 @@ Accessing and tweaking parameters
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. automodule:: tweakingParameters
:members:
-.. figure:: ../../images/tweakingParameters.png
+.. figure:: ../../../images/tweakingParameters.png
:alt: Three oscillation patterns after tweaking model parameters.
Storing simulation output
@@ -73,7 +73,7 @@ Sometimes you want to calculate arbitrary function of the state
variables of one or more elements and feed the result into another
element during a simulation. The Function class is useful for this.
-.. figure:: ../../images/function.png
+.. figure:: ../../../images/function.png
:alt: Outputs of Function object calculating z = c0 * exp(c1 * x) * cos(y)
:scale: 50%
@@ -142,7 +142,7 @@ Finding steady states
Making a dose-response curve
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. figure:: ../../images/chemDoseResponse.png
+.. figure:: ../../../images/chemDoseResponse.png
:alt: Dose-response curve example for a bistable system.
.. automodule:: chemDoseResponse
:members:
@@ -323,7 +323,7 @@ in every compartment of the model neurons, so as to see nice oscillations
and animations. The first example has a particularly striking pseudo-3D
rendition of the neuron and the molecular spatial oscillations within it.
-.. figure:: ../../images/reacDiffBranchingNeuron.png
+.. figure:: ../../../images/reacDiffBranchingNeuron.png
:alt: Pseudo-3-D rendition of branching neuron and the concs in it.
.. automodule:: reacDiffBranchingNeuron
@@ -374,7 +374,7 @@ C\ :sub:`m`\ , as in the figure below.
--------------
-.. figure:: ../../images/neuroncompartment.png
+.. figure:: ../../../images/neuroncompartment.png
:align: center
:alt: **Equivalent circuit of neuronal compartments**
@@ -621,7 +621,7 @@ stimulating the presynaptic cell as part of experimental setup. The
cells are defined as single-compartments with Hodgkin-Huxley type Na+
and K+ channels (see :ref:`hhmodel`)
-.. figure:: ../../images/twoCells.png
+.. figure:: ../../../images/twoCells.png
:scale: 50%
:alt: Two cells connected via synapse
@@ -643,7 +643,7 @@ Providing random input to a cell
.. automodule:: randomspike
:members:
-.. figure:: ../../images/randomSpike.png
+.. figure:: ../../../images/randomSpike.png
:scale: 50%
:alt: Random spike input to a cell
diff --git a/docs/user/py/rdesigneur/index.rst b/docs/user/py/rdesigneur/index.rst
index 9a86e7856e72222d96c53dab95ffa6cf3d601641..796bfddd419fb5fca63e832d64ee33fe6536e06a 100644
--- a/docs/user/py/rdesigneur/index.rst
+++ b/docs/user/py/rdesigneur/index.rst
@@ -755,9 +755,9 @@ predefined chemical model file for Rdesigneur, which resides in the
electrical calculations here as they are not needed. Here we plot out
the number of receptors on every single spine as a function of time.
-(stuff here)
+.. todo:: (stuff here)
Make a full multiscale model with complex spiny morphology and electrical and chemical signaling.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-(stuff here)
+.. todo:: (stuff here)