--- manual/manual_todo.txt	2006/07/02 18:12:45	1.46
+++ manual/manual_todo.txt	2008/01/17 17:35:59	1.50
@@ -265,6 +265,9 @@
 >> evaluated explicitly in time
 <- Leave it general.
 
+ o Time-stepping outline
+   - what gets called when
+
 
 2.2 rigid-lid:
 
@@ -414,6 +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 :
@@ -436,9 +451,12 @@
 
 Chapter 6
 
-   the master package diagram does not appear in the document
+   update organigramme
+    - include rbcs
+    (<- needs an update: e.g. atm2d, salt_plume, shelfice ...)
 
 Master list of packages (add this to beginning of chap 6)
+ (<- needs an update: e.g. atm2d, salt_plume, shelfice ...)
 
 admtlm/               - autodiff (chapter 5)
 aim/                  - retired
@@ -465,6 +483,8 @@
 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)
@@ -510,6 +530,10 @@
 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 
@@ -522,11 +546,19 @@
 	- diagstat
 	- new temporal averaging feature
 
+ + update the RW / MDSIO description 
+   -> new meta file
+   -> list all RW S/R that one should use instead of calling directly MDSIO
+
  + add Graphix to the list of stuff in utils/matlab (Daniel)
 
  + get bathymetry pre-processing stuff from Patrick and then describe it
 
  + 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/
@@ -542,8 +574,22 @@
 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.
+