--- manual/s_phys_pkgs/text/packages.tex	2005/07/18 20:45:27	1.6
+++ manual/s_phys_pkgs/text/packages.tex	2010/08/30 23:09:21	1.8
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_phys_pkgs/text/packages.tex,v 1.6 2005/07/18 20:45:27 molod Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_phys_pkgs/text/packages.tex,v 1.8 2010/08/30 23:09:21 jmc Exp $
 % $Name:  $
 
 \section{Using MITgcm Packages}
@@ -20,7 +20,7 @@
 There are numerous ways that one can specify compile--time package
 inclusion or exclusion and they are all implemented by the
 \texttt{genmake2} program which was previously described in Section
-\ref{sect:buildingCode}.  The options are as follows:
+\ref{sec:buildingCode}.  The options are as follows:
 \begin{enumerate}
 \item Setting the \texttt{genamake2} options \texttt{--enable PKG}
   and/or \texttt{--disable PKG} specifies inclusion or exclusion.
@@ -41,8 +41,9 @@
   automatically obtains all packages in that group.
 
 \item By default (that is, if a \texttt{packages.conf} file is not
-  found), the \texttt{genmake2} program will use the contents of the
-  \texttt{pkg/pkg\_default} file to obtain a list of packages.
+  found), the \texttt{genmake2} program will use the
+  package group default ``\texttt{default\_pkg\_list}'' as defined 
+  in \texttt{pkg/pkg\_groups} file.
 
 \item To help prevent users from creating unusable package groups, the
   \texttt{genmake2} program will parse the contents of the
@@ -228,7 +229,7 @@
 
         #ifdef ALLOW_${PKG}
           if ( use${Pkg} )
-     &       CALL ${PKG}_DIAGS( )
+     &       CALL ${PKG}_OUTPUT( )
         #endif
 
      7. S/R PACKAGES_WRITE_PICKUP()
@@ -243,7 +244,7 @@
 \subsubsection{Adding a package to PARAMS.h and  packages\_boot()}
 
 An MITgcm package directory contains all the code needed for that package apart
-from one variable for each package. This variable is the {\tt use\$\{Pkg\} } 
+from one variable for each package. This variable is the {\it use\$\{Pkg\} } 
 flag. This flag, which is of type logical, {\bf must} be declared in the 
 shared header file {\it PARAMS.h} in the {\it PARM\_PACKAGES} block. This 
 convention is used to support a single runtime control file {\it data.pkg} 
@@ -251,8 +252,8 @@
 flag controlling the runtime use of a package. This routine needs to be able to 
 read the flags for packages that were not built at compile time. Therefore
 when adding a new package, in addition to creating the per-package directory
-in the {\it pkg/} subdirectory a developer should add a {\tt use\$\{Pkg\} }
-flag to {\it PARAMS.h} and a {\tt use\$\{Pkg\} } entry to the 
+in the {\it pkg/} subdirectory a developer should add a {\it use\$\{Pkg\} }
+flag to {\it PARAMS.h} and a {\it use\$\{Pkg\} } entry to the 
 {\it packages\_boot()} {\it PACKAGES} namelist.
 The only other package specific code that should appear outside the individual 
 package directory are calls to the specific package API.
