Clean up sphinx warnings.

- Fix minor formatting issues.
- Fix reference the gloassary TLS using ':term:'.
- Make sure nothing is between an anchor and the heading where ':ref:' references
  the anchor. This meant moving all the recently added '.. index::' entries.

Update #3232.
Update #3229.

c-user/initialization.rst

@@ -71,7 +71,7 @@ Initializing RTEMS
 ------------------
 
 The Initialization Manager :c:func:`rtems_initialize_executive()` directives is
-called by the :c:ref:`boot_card()` routine which is invoked by the Board
+called by the :c:func:`boot_card()` routine which is invoked by the Board
 Support Package once a basic C run-time environment is set up.  This consists
 of
 
@@ -305,11 +305,12 @@ sequence, related constants, usage, and status codes.
 
    \clearpage
 
-.. _rtems_initialize_executive:
 .. index:: initialize RTEMS
 .. index:: start multitasking
 .. index:: rtems_initialize_executive
 
+.. _rtems_initialize_executive:
+
 INITIALIZE_EXECUTIVE - Initialize RTEMS
 ---------------------------------------