added doxygen links

Author: timdmacdo

_posts/2000-01-04-mission_solver.md

@@ -40,7 +40,7 @@ Most of the missions in SUAVE, including this one, are broken into several point
 
 <img src="http://suave.stanford.edu/images/drag_components_2.png" width="800" height="234" />
 
-At each of these points the aerodynamic analysis is queried to find CL and CD, which are then converted to lift and drag. These values will be dependent on the body angle unknown and other aerodynamic parameters. Thrust is found from the vehicle's energy network, which is dependent on the throttle unknown. A weight is determined by looking at the initial weight and subsequent mass rate (typically corresponding with fuel burn). In this cruise segment, these forces are summed in 2D and the results are put in the residuals. The functions needed to arrive these forces are found in the Update Conditions section of the [Analysis file](dox_link). This section is also shown below in one of the steps to create a new mission.  
+At each of these points the aerodynamic analysis is queried to find CL and CD, which are then converted to lift and drag. These values will be dependent on the body angle unknown and other aerodynamic parameters. Thrust is found from the vehicle's energy network, which is dependent on the throttle unknown. A weight is determined by looking at the initial weight and subsequent mass rate (typically corresponding with fuel burn). In this cruise segment, these forces are summed in 2D and the results are put in the residuals. The functions needed to arrive these forces are found in the Update Conditions section of the Analysis file. This section is also shown below in one of the steps to create a new mission.  
 
 Once the evaluation process has been performed at all points, the unknowns and residuals are fed back to the solve routine, which in this case is scipy's fsolve. The file that performs this process is [here](https://github.com/suavecode/SUAVE/blob/develop/trunk/SUAVE/Methods/Missions/Segments/converge_root.py). This routine continues evaluating the points until convergence is reached. Once this happens, post processing is done to put the data in the results output.
 

_posts/2000-01-06-optimization.md

@@ -14,7 +14,7 @@ This is an overview of how optimization is done in SUAVE. A specific tutorial ca
 
 ### Nexus Class
 
-The Nexus class is the underlying data structure that is used for optimization. It is created to hold all data and functionality needed to link together optimizers and the various analysis modules in SUAVE. Detailed information on each of the functions can be found in our [doxygen site](dox_link).
+The Nexus class is the underlying data structure that is used for optimization. It is created to hold all data and functionality needed to link together optimizers and the various analysis modules in SUAVE. Detailed information on each of the functions can be found on our [doxygen page](/doxygen).
 
 ### Standard Optimization File Structure
 

_posts/2015-06-14-doc_instructions.md

@@ -10,7 +10,7 @@ permalink: /guides/docs.html
 
 ### How to Read (and Write) the Documentation
 
-This is an explanation of how documentation is built in SUAVE so that the user can know what to look for and how to write it if they wish to add their own code.
+This is an explanation of how documentation is built in SUAVE so that the user can know what to look for and how to write it if they wish to add their own code. The doxygen page is available [here](/doxygen).
 
 ### Docstrings
 

guides/index.html

@@ -15,7 +15,8 @@ <h1 class="title">Guides</h1>
 
 
 	<section class="content">
-	<p>These are code structure/style guides and tutorials for SUAVE. The first set give general information on how SUAVE operated and how our code is formatted. The tutorials will then help you get started with SUAVE.   We recommend starting with the Boeing 737-800 tutorial and then moving to the Transport Optimization or the Turbofan Network tutorial.  These will allow you to explore the capabilities of SUAVE.</p>
+	<p>These are code structure/style guides and tutorials for SUAVE. The first set gives general information on how SUAVE is operated and how our code is formatted. The tutorials will then help you get started with SUAVE.   We recommend starting with the Boeing 737-800 tutorial and then moving to the Transport Optimization or the Turbofan Network tutorial.  These will allow you to explore the capabilities of SUAVE. A direct link 
+	to the documentation for individual functions is <a href="http://suave.stanford.edu/doxygen">here</a></p>
 
 	<ul class="posts">
 		{% for post in site.posts %}

index.html

@@ -16,7 +16,7 @@ <h1 class="title">SUAVE</h1>
 
                 <p><img src="../images/bwb_inside.png" alt="Blended Wing Body" /></p>
 
-                <p>SUAVE is an open source suite constructed as a modular set of analysis tools written in Python. Additional capabilities can be incorporated using extensible interfaces and prototyped with a top-level script. The flexibility of the environment allows the creation of arbitrary mission profiles, unconventional propulsion networks, and right-fidelity at right-time discipline analyses. SUAVE is currently being developed in the <a href="http://adl.stanford.edu">Aerospace Design Lab at Stanford University</a>. </p>
+                <p>SUAVE is an open source suite constructed as a modular set of analysis tools written in Python. Additional capabilities can be incorporated using extensible interfaces and prototyped with a top-level script. The flexibility of the environment allows the creation of arbitrary mission profiles, unconventional propulsion networks, and right-fidelity at right-time discipline analyses. SUAVE is currently being developed in the <a href="http://adl.stanford.edu">Aerospace Design Lab</a> at Stanford University. </p>
 
                 <h3> Capabilities Available </h3>