--- manual/manual_todo.txt	2006/06/29 17:45:14	1.45
+++ manual/manual_todo.txt	2008/01/15 14:47:57	1.48
@@ -26,6 +26,7 @@
 
  Biblio        - EH3
 
+
 Rebuild and set to do cron build - DONE on hugo
 
 To do
@@ -42,31 +43,40 @@
 
 o HTML, scripts and front content
 
-  - pick a URL
-    TBD
+  - pick a URL:  mitgcm.org/r2  <-- EH3's preferred base URL
 
   - mitgcm.org/r2_web_testing/latest
-    o add another short-cut for quick download
+    
+    o --DONE--  add another short-cut for quick download
+
+    o --DONE--  add another short-cut
+                  About
+                  Installation
+                  Contents
+                  Overview
+                  Tutorials (broken)
+                  Browse Code
+
+    o --DONE--  words on http://mitgcm.org/r2_web_testing/latest change to 
+
+    o --DONE--  finite-volume doesn't leap to FV figure
+
+    o -- DONE ??? --  have another go at pnmcrop et al.
 
-    o add another short-cut
-      About
-      Installation
-      Contents
-      Overview
-      Tutorials (broken)
-      Browse Code
-
-    o words on http://mitgcm.org/r2_web_testing/latest
-      change to 
-       "access on-line Auser manual/A and Atable of contents/A
-        and browse the Aoverview section/A"
+         I've tried making a small change in latex2html which fixes
+         the oddball-lower-alignment issue that we were seeing with
+         most in-line expressions (that is, math embedded in text).
+         The fix results in some things being slightly raised but I
+         thin this is more asthetically pleasing than being somewhat
+         lowered as before. --EH3
 
-    o finite-volume doesn't leap to FV figure
+	 To view the altered alignment, see:
 
-    o have another go at pnmcrop et al.
+            http://eddy.csail.mit.edu/r2/latest/
 
     o Need an empty package as part of distribution. Check out atm_common
 
+
 o Latex   
 
     Chapter 1                 - CNH
@@ -255,6 +265,9 @@
 >> evaluated explicitly in time
 <- Leave it general.
 
+ o Time-stepping outline
+   - what gets called when
+
 
 2.2 rigid-lid:
 
@@ -404,6 +417,18 @@
 3.14.5.4 -- ALL of the bold links to variable names are broken
             line 34: link to equation is broken
 
+ o Update basic intro with one and four layer gyres
+   - include advection options
+   - conservation analysis
+   - diagnostics
+
+ o Four degree adjoint
+   - both TAF and OpenAD based.
+
+ o Coupled with biogeo setup
+   - based on CCGS setup
+
+
 >>>> From Ed
 
 Here are the remaining bits for Chap 4 :
@@ -455,6 +480,8 @@
 exch2/                - 6.2.2
 exf/                  - 6.3.4
 fizhi/                - 6.4.3
+ o Including FIZHI doc
+   - get things up to date
 flt/                  - (PH check)
 gchem/                - 6.7.1
 generic_advdiff/      - in chapter 2 (JM check)
@@ -500,6 +527,10 @@
 timeave/              - retiring......
 zonal_filt/           - chapter 2 (JM to check)
 
+ o Cost function packages
+   - floats, weights, profiles etc...
+
+
 list an expeiment which uses package? CNH
 
 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 
@@ -508,19 +539,22 @@
 
 =====  Chapter 7  =====  [EH3 editing] :
 
-7.1.x - JMC: please add description of:
+ + JMC: please add description of:
 	- diagstat
 	- new temporal averaging feature
 
-7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
+ + add Graphix to the list of stuff in utils/matlab (Daniel)
 
-7.5.2 - get bathymetry pre-processing stuff from Patrick
-        and then describe it
+ + get bathymetry pre-processing stuff from Patrick and then describe it
 
-add something on spgrid mesh generator (maybe)?
+ + add something on spgrid mesh generator
+ o Grid generation
+   - more explanation and some step-by-step examples
+   - plotting grid examples
 
-add in gmaze PV calculation scripts plus write up on how it is calculated
-http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/
+
+ + add in gmaze PV calculation scripts plus write up on how it is calculated
+     http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/
 
 
 andrea
@@ -533,8 +567,22 @@
 10. Under development
 
 Constantinos LCML
+ o Legend/LCML examples and explanation
+   - examples and explanation!
+
 
 
 Bibliography
 
  tidy up from misc - .tex
+
+Also
+
+a link to the new manual
+should appear on the front page (even if it's under construction).
+
+updating:
+http://mitgcm.org/r2_web_testing/latest/code_reference/callTree.html
+which points to a 1.5 years old code. Would be good to generate a
+new one, and even better, to try to keep it up-to-date.
+