Formatting updates to "Input for KPP" and "Output from KPP" chapters

Made several formatting updates to the "Input for KPP" and "Output from
KPP" chapters, mostly involving tables and references.  Also added some
extra information in the form of "information" or "tip" boxes.

Also added references to bibtex.json, which will list in the References
page.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

docs/source/bibtex.json

@@ -3,6 +3,9 @@
         "using_kpp/04_input_for_kpp": [
             "1996:Sandu_Potra_Damian_and_Carmichael",
         ],
+        "using_kpp/05_output_from_kpp": [
+            "1996:Sandu_Potra_Damian_and_Carmichael",
+        ],
         "citations/09_acknowledgments": [
             "1996:Damian-Iordache",
         ],

docs/source/using_kpp/04_input_for_kpp.rst

@@ -51,7 +51,7 @@ mechanism.
 KPP sections
 ============
 
-A sign at the beginning of a line followed by a section name starts a
+A :code:`#` sign at the beginning of a line followed by a section name starts a
 new KPP section. Then a list of items separated by semicolons follows. A
 section ends when another KPP section or command occurs, i.e. when
 another sign occurs at the beginning of a line. The syntax of an item
@@ -173,10 +173,7 @@ parameterize organic reactions that branch into several side reactions:
 .. code-block:: console
 
    CH4 + O1D = .75 CH3O2 + .75 OH + .25 HCHO
-               + .4 H + .05 H2 : k_CH4_O1D;
-
-**((TODO: CHECK IF THE FOLLOWING DESCRIPTION OF PROD AND HV IS
-CORRECT))**
+               + 0.4 H + .05 H2 : k_CH4_O1D;
 
 KPP provides two pre-defined dummy species: and . Using dummy species
 does not affect the numerics of the integrators. It only serves to
@@ -333,7 +330,7 @@ included in the transport calculations.
 KPP commands
 ============
 
-A command begins on a new line with a sign, followed by a command name
+A command begins on a new line with a :code:`#` sign, followed by a command name
 and one or more parameters.  Details about each command are given in
 the following subsections.
 
@@ -656,10 +653,9 @@ more lines of code follow, written in the target language (Fortran90,
 Fortran77, C, or Matlab) as specified by the *inline_type*. The
 inlined code ends with :command:`#ENDINLINE`. The code is inserted
 into the KPP output at a position which is also
-determined by *inline_type* as explained in the table
-:ref:`list-of-inlined-types` below.  If two inline commands with the
-same inline type are declared, then the contents of the second is
-appended to the first one.
+determined by *inline_type* as explained in :ref:`table-inl-type`. If two
+inline commands with the same inline type are declared, then the
+contents of the second is appended to the first one.
 
 .. _list-of-inlined-types:
 
@@ -668,9 +664,12 @@ List of inlined types
 
 In this manual, we show the inline types for Fortran90. The inline
 types for the other languages are produced by replacing :code:`F90_`
-by :code:`F77`, :code:`C`, or :code:`matlab`, respectively.
+by :code:`F77`, :code:`C`, or :code:`matlab`, respectively, as shown
+in Table 1:
+
+.. _table-inl-type:
 
-.. table:: KPP inlined types
+.. table:: Table 1: KPP inlined types
    :align: center
 
    +---------------------+------+---------------------+---------------------+
@@ -838,9 +837,12 @@ in the generated Fortran90 output file.
 List of auxiliary files for Fortran 90
 ---------------------------------------
 
-KPP inline codes or other instructions contained in the following files:
+KPP inline codes or other instructions contained in the following
+files, as shown in :ref:`table-aux-files`.
 
-.. table:: Auxiliary files for Fortran90
+.. _table-aux-files:
+
+.. table:: Table 2: Auxiliary files for Fortran90
    :align: center
 
    +-----------------------------+--------------------------------------------+
@@ -878,9 +880,11 @@ List of symbols replaced by the substitution preprocessor
 ----------------------------------------------------------
 
 The following symbols in KPP-generated source code will be replaced
-with corresponding values, as highlighted in the table below.
+with corresponding values, as highlighted in :ref:`table-sym-repl`.
+
+.. _table-sym-repl:
 
-.. table:: Symbols and their replacements
+.. table:: Table 3: Symbols and their replacements
    :align: center
 
    +--------------------+-------------------------------+---------------------+