doxygen: Trying to get the Doxygen output looking like I want

Doxyfile

@@ -42,7 +42,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "FrznChessboard MCU Code"
+PROJECT_NAME           = FrznChessboard
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
@@ -54,7 +54,7 @@ PROJECT_NUMBER         =
 # for a project that appears at the top of each page and should give viewers a
 # quick idea about the purpose of the project. Keep the description short.
 
-PROJECT_BRIEF          = "All the code for the MCU inside the chessboard"
+PROJECT_BRIEF          = "PIC32MX code inside the chessboard"
 
 # With the PROJECT_LOGO tag one can specify a logo or an icon that is included
 # in the documentation. The maximum height of the logo should not exceed 55
@@ -67,7 +67,7 @@ PROJECT_LOGO           = /home/amr/Pictures/frznchess_pawn_30.png
 # when the HTML document is shown. Doxygen will copy the logo to the output
 # directory.
 
-PROJECT_ICON           =
+PROJECT_ICON           = ../../Pictures/frznchess_pawn_30.png
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
 # into which the generated documentation will be written. If a relative path is
@@ -534,7 +534,7 @@ TIMESTAMP              = DATETIME
 # normally produced when WARNINGS is set to YES.
 # The default value is: NO.
 
-EXTRACT_ALL            = YES
+EXTRACT_ALL            = NO
 
 # If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
 # be included in the documentation.
@@ -991,7 +991,8 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = /home/amr/MPLABXProjects/chessmcu.X
+INPUT                  = "./README.md ./" \
+                         /home/amr/MPLABXProjects/chessmcu.X
 
 # This tag can be used to specify the character encoding of the source files
 # that Doxygen parses. Internally Doxygen uses the UTF-8 encoding. Doxygen uses
@@ -1456,7 +1457,8 @@ HTML_STYLESHEET        =
 # documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_STYLESHEET  = doxygen-awesome-css/doxygen-awesome.css
+HTML_EXTRA_STYLESHEET  = doxygen-awesome-css/doxygen-awesome.css \
+                         doxygen-awesome-css/doxygen-awesome-sidebar-only.css
 
 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
 # other source files which should be copied to the HTML output directory. Note
@@ -1490,7 +1492,7 @@ HTML_COLORSTYLE        = LIGHT
 # Minimum value: 0, maximum value: 359, default value: 220.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_COLORSTYLE_HUE    = 249
+HTML_COLORSTYLE_HUE    = 208
 
 # The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
 # in the HTML output. For a value of 0 the output will use gray-scales only. A
@@ -1498,7 +1500,7 @@ HTML_COLORSTYLE_HUE    = 249
 # Minimum value: 0, maximum value: 255, default value: 100.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_COLORSTYLE_SAT    = 64
+HTML_COLORSTYLE_SAT    = 158
 
 # The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
 # luminance component of the colors in the HTML output. Values below 100
@@ -1851,7 +1853,7 @@ SHOW_ENUM_VALUES       = NO
 # Minimum value: 0, maximum value: 1500, default value: 250.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-TREEVIEW_WIDTH         = 250
+TREEVIEW_WIDTH         = 600
 
 # If the EXT_LINKS_IN_WINDOW option is set to YES, Doxygen will open links to
 # external symbols imported via tag files in a separate window.
@@ -1902,7 +1904,7 @@ FORMULA_MACROFILE      =
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-USE_MATHJAX            = NO
+USE_MATHJAX            = YES
 
 # With MATHJAX_VERSION it is possible to specify the MathJax version to be used.
 # Note that the different versions of MathJax have different requirements with
@@ -1913,7 +1915,7 @@ USE_MATHJAX            = NO
 # The default value is: MathJax_2.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_VERSION        = MathJax_2
+MATHJAX_VERSION        = MathJax_3
 
 # When MathJax is enabled you can set the default output format to be used for
 # the MathJax output. For more details about the output format see MathJax
@@ -2247,7 +2249,7 @@ LATEX_EMOJI_DIRECTORY  =
 # readers/editors.
 # The default value is: NO.
 
-GENERATE_RTF           = YES
+GENERATE_RTF           = NO
 
 # The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of

inc/Board.hpp

@@ -44,7 +44,9 @@ struct Square;
  */
 class Board {
   private:
-    std::vector<std::vector<std::unique_ptr<Piece>>> boardGrid; /**< This holds the game state. It is a 2D vector of Piece types, or nullptr for empty squares @image html boardGrid.png "Logical diagram of boardGrid vector" */
+    std::vector<std::vector<std::unique_ptr<Piece>>> boardGrid; /**< This holds the game state. 
+                                                                 * It is a 2D vector of Piece types, or nullptr for empty squares 
+                                                                 * @image html boardGrid.svg "Logical diagram of boardGrid vector" */
     Players playerTurn;
     // let's get super object-oriented, baby
     // these help the getters and setters access the boardGrid
@@ -108,15 +110,59 @@ class Board {
         return at(sq) == nullptr;
     }
 
+    /** A function to setup the initial board
+     * 
+     * This initializes the boardGrid with the black and white pieces
+     * in their normal starting positions. All empty squares are set
+     * to nullptr.
+     */
     void setupInitialPosition();
-
+    /** This function sets the entire board to nullptr
+     * 
+     * This should, if I understand correctly, destroy
+     * all the Piece instances that existed because they will no longer
+     * have any owners, and smart pointers should auto destruct.
+     */
     void clearBoard();
+    /** This does the actual moving of a piece from one square to another
+     * 
+     * Beware! This function does \e not validate if the move is legal. It
+     * will simply do whatever it is told to do. So only call this once you
+     * are positive the move is legal.
+     * Moves to an empty square are simple, just move the Piece to that other
+     * square. Captures have to also take note of the piece type captured
+     * and add it to the total captured by that side. This should also destroy
+     * the smart pointer automatically.
+     * @param from The originating square for the Piece that is moving
+     * @param to And of course, where it will end up
+     */
     void movePiece(Square from, Square to);
     void nextTurn();
+    /** This function takes a standard FEN string and sets up the board.
+     * 
+     * FEN is a standard notation that describes only an exact position and
+     * other important things like whose turn it is, whether sides can castle,
+     * but it does \e not include the move history of the game. This makes it
+     * a simpler format for sharing particular interesting positions.
+     * 
+     * @param strFEN A std::string that contains a valid FEN position
+     * @return 0 on success, -1 if the FEN string is invalid
+     */
     int setupFromFEN(std::string strFEN);
     bool isInBounds(Square square) const;
     // serial shift register stuff
     uint64_t serialBoard = 0xFFFF00000000FFFF; // opening position
+    /** This takes an incoming serial stream and detects if anything has moved.
+     * 
+     * The input is one bit per piece, so it can only detect the presence or
+     * absence of pieces on any particular square. This is the crux of our design,
+     * using simpler reed switches for detection instead of RFID or any other two-way
+     * communication with the pieces. This moves a lot of the complexity into software,
+     * though a lot of the complexity is actually quite easy to deal with from a software
+     * point of view.
+     * 
+     * @param incomingBoard A 64-bit value, representing 1 bit per piece.
+     */
     void deserializeBoard(uint64_t incomingBoard);
 };