remove outdated and duplicate mention of specific arkode files

doc/arkode/guide/source/Organization.rst

@@ -25,26 +25,29 @@ Code Organization
 
 .. _ARKODE.Organization.ARKODE:
 
-ARKODE organization
+ARKODE Organization
 ===================
 
-The ARKODE package is written in the ANSI C language.  The
-following summarizes the basic structure of the package, although
+The following summarizes the basic structure of the ARKODE package, although
 knowledge of this structure is not necessary for its use.
 
+.. TODO(CJB): we should really update the organization figure to include
+   the steppers, root-finding, Butcher table "modules" etc. 
+   Also, unless we talk about the file structure here, we should avoid
+   mentioning specific files so it does not go stale.
+
 The overall organization of the ARKODE package is shown in
-:numref:`ARKODE.Organization.ARKODE.Figure`.  The central integration modules,
-implemented in the files ``arkode.h``, ``arkode_impl.h``, ``arkode_butcher.h``,
-``arkode.c``, ``arkode_arkstep.c`` , ``arkode_erkstep.c``, ``arkode_mristep.h``,
-and ``arkode_butcher.c``, deal with the evaluation of integration stages, the
-nonlinear solvers, estimation of the local truncation error, selection of step
-size, and interpolation to user output points, among other issues.  ARKODE
+:numref:`ARKODE.Organization.ARKODE.Figure`.  
+
+The central integration modules, deal with the evaluation of integration stages,
+the nonlinear solvers, estimation of the local truncation error, selection of
+step size, and interpolation to user output points, among other issues.  ARKODE
 supports SUNNonlinearSolver modules in either root-finding or fixed-point form
 (see section :numref:`SUNNonlinSol`) for any nonlinearly implicit problems that
 arise in computing each internal stage. When using Newton-based nonlinear
 solvers, or when using a non-identity mass matrix :math:`M\ne I`, ARKODE has
 flexibility in the choice of method used to solve the linear sub-systems that
-arise.  Therefore, for any user problem invoking the Newton solvers, or any user
+arise. Therefore, for any user problem invoking the Newton solvers, or any user
 problem with :math:`M\ne I`, one (or more) of the linear system solver modules
 should be specified by the user; this/these are then invoked as needed during
 the integration process.
@@ -56,7 +59,7 @@ the integration process.
    *ARKODE organization*: Overall structure of the ARKODE package.
    Modules specific to ARKODE are the timesteppers (ARKODE), linear solver
    interfaces (ARKLS), nonlinear solver interfaces (ARKNLS), and preconditioners
-   (ARKBANDPRE and ARKBBDPRE); all other items correspond to generic SUNDIALS
+   (ARKBANDPRE and ARKBBDPRE); all other items correspond to the SUNDIALS core
    vector, matrix, and solver modules.
 
 For solving these linear systems, ARKODE's linear solver interface