| 391 |  |  | 
| 392 | Almost all of the 'math mode' text is dropped down as subscripts | Almost all of the 'math mode' text is dropped down as subscripts | 
| 393 |  |  | 
|  | 3.1 - don't need a link to the outside of the document (remove it) |  | 
|  | - link to htdig is broken |  | 
|  |  |  | 
|  | 3.2.1 - link at bottom to source code points to section 3.2.1 |  | 
|  | (ie, to itself) - link should point to cvs code archive |  | 
|  |  |  | 
|  | 3.2.2.1  - ('upgrading from an earlier version') belongs under |  | 
|  | the cvs part, ie, should be 3.2.1.1 |  | 
|  |  |  | 
|  | 3.3 - remove reference to 'diags' section under MITgcm |  | 
|  | - remove reference to 'exe' and 'bin' sections also |  | 
|  | (remove the .cvsignore file under these directories in cvs) |  | 
|  | - add a 'jobs' section, and a description as examples of run scripts |  | 
|  | - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions |  | 
|  | - under 'tools' add a reference to 'build_options'. refer to the 'optfiles' |  | 
|  | - under 'tools' the adjoint points to section 5 - this is now section 8 |  | 
|  | (but should be a floating reference) |  | 
|  | - under 'utils' add a reference to exch2 - stuff for different resolutions |  | 
|  | - the description of the pkg section refers directly to |  | 
|  | section 3. should be section 6 (actually should be a floating reference) |  | 
|  |  |  | 
|  | 3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10) |  | 
|  | 3.4.1 - links to the following experiments don't exist or are broken: |  | 
|  | exp2 - should link to section 3.9 |  | 
|  | hs94.cs-32x32x5 - link to section 3.12 |  | 
|  | add 'convection' to the list, link to section 3.13 |  | 
|  | add 'plume on slope` to the list, link to section 3.14 |  | 
|  | add '??' link to section 3.15 |  | 
|  | add 'dic_example on slope` to the list, link to section 3.16 |  | 
|  | add '??' link to section 3.17 |  | 
|  | add 'offline' and link to section 3.18 |  | 
|  | clean up others and make links where they are needed |  | 
|  | 3.4.2 - text suggests to see section 2 for details about what is in the 'code' |  | 
|  | and 'input' directories - should refer to the examples in this section |  | 
|  | - add 'build' bullet - this is where the model is compiled and exectuable lives |  | 
|  |  |  | 
|  | 3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options |  | 
|  | as the place where they live (add a link?) |  | 
|  |  |  | 
|  | 3.6.1 - Add some general 'approach' text - ie, output is controlled either by the |  | 
|  | 'data' file in the input directory or by the data.[pkg name] file for any |  | 
|  | package running. And there is some default behavior when the 'state' dumps |  | 
|  | are written. |  | 
|  | 3.6.1.2 - needs to be moved to inside section 3.6.2 |  | 
|  |  |  | 
|  | All the 'overview' sections need some reference to the name of the experiment in |  | 
|  | the verification directory |  | 
|  |  |  | 
| 394 | 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript | 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript | 
| 395 | - is this experiment in the list from section 3.4??? | - is this experiment in the list from section 3.4??? | 
| 396 | 3.10.3.1 - refers to figures and equations, links are broken | 3.10.3.1 - refers to figures and equations, links are broken |