A few doc fixes to BApplication and BHandler.

* Since <em> is used for parameters we can't use it for emphasis.
* Add \a in a few places it was missing to indicate a parameter.
* Change \a to a \c in one instance, param -> constant.
* Lots of whitespace fixes, most just deleting leading tabs.
* Don't indent code blocks, they should be flush to left since any
  indentation is preserved in the output.

docs/user/app/Application.dox

@@ -387,10 +387,10 @@ main()
 
 /*!
 	\fn BWindow* BApplication::WindowAt(int32 index) const
-	\brief Returns the BWindow object at the specified index in the
+	\brief Returns the BWindow object at the specified \a index in the
 		application's window list.
-		
-	If index is out of range, this function returns \c NULL.
+
+	If \a index is out of range, this function returns \c NULL.
 
 	\warning Locking the BApplication object doesn't lock the window list.
 
@@ -520,7 +520,8 @@ main()
 	If the \a rate is set to 0 then the \c B_PULSE messages are not sent.
 	The pulse rate can be no faster than once per 100,000 microseconds or so.
 
-	\param rate The rate \a B_PULSE messages are sent to the application.
+	\param rate The rate at which \c B_PULSE messages are sent to the
+		application.
 */