Small improvements internal documentation

Some small improvements and completions of the doxygen internal documentation

Author: albert-github

doc_internal/doxygen.md

@@ -111,7 +111,7 @@ Within doxygen there are a number of ways to obtain debug output. Besides the
 invasive method of putting print statements in the code there are a number of
 easier ways to get debug information.
 
-For a debug build (build option `-DCMAKE_BUILD_TYPE=Debug`)
+For a debug build (build option `-DCMAKE_BUILD_TYPE=%Debug`)
 these options are always available, but for a release build some debug capabilities have to be enabled explicitly
 (see build options `-Denable_tracing=YES` and `-Denable_lex_debug=YES`).
 
@@ -123,61 +123,67 @@ which can be used (by experts) to diagnose problems.
 During a run of doxygen it is possible to specify the `-d` command line option with one of the
 following values (each option has to be preceded by `-d`):
 
-  - preprocessor<br>
+  - `preprocessor`<br>
     Shows the results of the preprocessing phase, i.e. results from include files,
     <tt>\#define</tt> statements etc., definitions in the doxygen configuration file like:
     `EXPAND_ONLY_PREDEF`, `PREDEFINED` and `MACRO_EXPANSION`.
-  - nolineno<br>
+  - `nolineno`<br>
     In case the line numbers in the results of the preprocessing phase are not wanted they
     can be removed by means of this option (without `-d preprocessor` this option has no effect.
-  - commentcnv<br>
+  - `commentcnv`<br>
     Shows the results of the comment conversion, the comment conversion does the
     following:
      - It converts multi-line C++ style comment blocks (that are aligned)
        to C style comment blocks (if `MULTILINE_CPP_IS_BRIEF` is set to `NO`).
      - It replaces aliases with their definition (see `ALIASES`)
      - It handles conditional sections (<tt>\\cond ... \\endcond</tt> blocks)
-  - commentscan<br>
+  - `commentscan`<br>
     Will print each comment block before and after the comment is interpreted by
     the comment scanner.
-  - printtree<br>
+  - `printtree`<br>
     Give the results in pretty print way, i.e. in an XML like way with each
     level indented by a `"."` (dot).
-  - time<br>
+  - `time`<br>
     Provides information of the different stages of the doxygen process.
-  - extcmd<br>
+  - `extcmd`<br>
     Shows which external commands are executed and which pipes are opened.
-  - markdown<br>
+  - `markdown`<br>
     Will print each comment block before and after Markdown processing.
-  - filteroutput<br>
+  - `filteroutput`<br>
     Gives the output of the output as result of the filter command (when a filter
     command is specified)
-  - validate<br>
-    Currently not used
-  - cite<br>
+  - `cite`<br>
     Retains the temporary files as created and used for the non LaTeX output results of the 
     generation of the bibliographical references.
-  - fortranfixed2free<br>
+  - `fortranfixed2free`<br>
     Shows the result of the conversion of Fortran fixed formatted files to Fortran free formatted 
     files as done by doxygen.
-  - plantuml<br>
+  - `plantuml`<br>
     Shows information about the plantuml process run and the used input / output filenames, the content of the
     input file.
-  - rtf<br>
+  - `rtf`<br>
     - Shows the original names and the anchors names (called bookmarks in RTF) where they are mapped to.
     - At the end of the generation of the RTF files these files are merged into one large RTF file, with
       this option the original files are retained.
-  - qhp<br>
+  - `qhp`<br>
     - The qhp file is created with indentation for better readability (normally no indentation so the file is smaller).
     - When the setting `QHG_LOCATION` is pointing to the `qhelpgenerator` besides generating the `qch` file 
       also some extra checks are done by means of the `-c` flag of the `qhelpgenerator`.
-  - tag<br>
+  - `tag`<br>
     Shows the results of reading the tag files.
-  - lex<br>
+  - `alias`<br>
+    Show the results of the `ALIASES` resolving process
+  - `entries`<br>
+    Dump the tree of Entries as found by doxygen
+  - `formula`<br>
+    Don't remove the intermedate files generated by the creation of the images with the formulas.
+  - `sections`<br>
+    Show the sections as found by doxygen
+  - `lex`<br>
     Provide output of the `lex` files used. When a lexer is started and when a lexer
     ends the name of the `lex` file is given so it is possible to see in which lexer the
     problem occurs. This makes it easier to select the file to be compiled in `lex` debug mode.
-  - lex:lexer<br>
+  - `lex:lexer`<br>
     Enables output for a specific lexer only, where `lexer` should be replaced by the name of the specific lexer.
 
 Producing output
@@ -212,7 +218,7 @@ Documentation Topics TODO
   - via Graphviz dot
   - via mscgen
   - PNG generation
-- Output formats: OutputGen, OutputList, and DocVisitor
+- Output formats: OutputGenerator, OutputList, and DocVisitor
   - Html:  HtmlGenerator and HtmlDocVisitor
   - Latex: LatexGenerator and LatexDocVisitor
   - RTF:   RTFGenerator and RTFDocVisitor