update a few links in the programmer guide

doc/src/pg_developer.rst

@@ -10,11 +10,14 @@ of time and requests from the LAMMPS user community.
 LAMMPS source files
 ===================
 
-The source files of the LAMMPS code are distributed across two
+The source files of the LAMMPS code are found in two
-directories of the distribution.  The core of the code is located in the
+directories of the distribution: ``src`` and ``lib``.
-``src`` folder and its sub-directories. Almost all of those are C++ files
+Most of the code is C++ but there are small numbers of files
-(implementation files have a ``.cpp`` extension and and headers a
+in several other languages.
-``.h``).  A sizable number of these files are in the ``src`` directory
+
+The core of the code is located in the
+``src`` folder and its sub-directories.
+A sizable number of these files are in the ``src`` directory
 itself, but there are plenty of :doc:`packages <Packages>`, which can be
 included or excluded when LAMMPS is built.  See the :doc:`Include
 packages in build <Build_package>` section of the manual for more
@@ -25,7 +28,7 @@ enabled or disabled for a LAMMPS binary.  The source files for each
 package are in all-uppercase sub-directories of the ``src`` folder, for
 example ``src/MOLECULE`` or ``src/USER-MISC``.  The ``src/STUBS``
 sub-directory is not a package but contains a dummy MPI library, that is
-used when building a serial version of the code. the ``src/MAKE``
+used when building a serial version of the code. The ``src/MAKE``
 directory contains makefiles with settings and flags for a variety of
 configuration and machines for the build process with traditional
 makefiles.
@@ -39,7 +42,8 @@ or CUDA. These libraries are linked to during a LAMMPS build, if the
 corresponding package is installed.
 
 LAMMPS C++ source files almost always come in pairs, such as
-``src/run.cpp`` and ``src/run.h``.  The pair of files defines a C++
+``src/run.cpp`` (implementation file) and ``src/run.h`` (header file).
+Each pair of files defines a C++
 class, for example the :cpp:class:`LAMMPS_NS::Run` class which contains
 the code invoked by the :doc:`run <run>` command in a LAMMPS input script.
 As this example illustrates, source file and class names often have a
@@ -48,6 +52,9 @@ Some source files and classes do not have a corresponding input script
 command, e.g. ``src/force.cpp`` and the :cpp:class:`LAMMPS_NS::Force`
 class.  They are discussed in the next section.
 
+A small number of C++ classes and utility functions are implemented with
+only a ``.h`` file. Examples are the Pointer class and the mergesort function.
+
 LAMMPS class topology
 =====================
 

doc/src/pg_lib_add.rst

@@ -12,7 +12,7 @@ there are now a few requirements for inclusion of changes.
     implement functionality that can already be achieved with the
     existing APIs.
   - All changes and additions should be documented with
-    `Doxygen <https://doxgygen.org>`_ style comments and references
+    `Doxygen <https://doxygen.nl>`_ style comments and references
     to those functions added to the corresponding files in the
     ``doc/src`` folder.
   - If possible, new unit tests to test those new features should

doc/src/pg_python.rst

@@ -14,7 +14,7 @@ There are multiple Python interface classes in the :py:mod:`lammps` module:
 
 - the :py:class:`lammps <lammps.lammps>` class. This is a wrapper around
   the C-library interface and its member functions try to replicate the
-  :doc:`C-library API <pg_library>` closely.  This is the most
+  :ref:`C-library API <lammps_c_api>` closely.  This is the most
   feature-complete Python API.
 - the :py:class:`PyLammps <lammps.PyLammps>` class. This is a more high-level
   and more Python style class implemented on top of the
@@ -63,7 +63,7 @@ MPI ranks after splitting the communicator. Here is a simple example:
    # explicitly close and delete LAMMPS instance (optional)
    lmp.close()
 
-Same as with the :doc:`C library API <pg_lib_create>` this will use the
+Same as with the :ref:`C library API <lammps_c_api>` this will use the
 ``MPI_COMM_WORLD`` communicator for the MPI library that LAMMPS was
 compiled with.  The :py:func:`lmp.close() <lammps.lammps.close>` call is
 optional since the LAMMPS class instance will also be deleted
@@ -113,8 +113,8 @@ The ``lammps`` class API
 ************************
 
 The :py:class:`lammps <lammps.lammps>` class is the core of the LAMMPS
-Python interfaces.  It is a wrapper around the :doc:`LAMMPS C library
+Python interfaces.  It is a wrapper around the :ref:`LAMMPS C library
-API <pg_library>` using the `Python ctypes module
+API <lammps_c_api>` using the `Python ctypes module
 <https://docs.python.org/3/library/ctypes.html>`_ and a shared library
 compiled from the LAMMPS sources code.  The individual methods in this
 class try to closely follow the corresponding C functions.  The handle