copy from ground up

Doxyfile

@@ -1,5 +1,5 @@
 PROJECT_NAME = reactor-uc
-PROJECT_BRIEF = "A Lingua Franca Runtime for Embedded Systems"
+#PROJECT_BRIEF = "A Lingua Franca Runtime for Embedded Systems"
 PROJECT_NUMBER = 0.1
 PROJECT_LOGO = doc/assets/lf-logo.svg
 
@@ -8,14 +8,237 @@ INPUT = ./README.md ./include/reactor-uc/environment.h ./include/reactor-uc/logg
 USE_MDFILE_AS_MAINPAGE = README.md
 FILE_PATTERNS = *.h *.md
 RECURSIVE = NO
-EXTRACT_ALL = YES
 
 HTML_EXTRA_STYLESHEET  = ./doc/assets/doxygen-awesome.css \
                          ./doc/assets/doxygen-awesome-sidebar-only.css \
                          ./doc/assets/doxygen-awesome-sidebar-only-darkmode-toggle.css \
-                         ./doc/assets/doxygen-awesome-zephyr.css
 
 HTML_EXTRA_FILES       = ./doc/assets/doxygen-awesome-darkmode-toggle.js \
-                         ./doc/assets/doxygen-awesome-zephyr.js
-
+                         ./doc/assets/doxygen-awesome-tabs.js \
+                         ./doc/assets/doxygen-awesome-interactive-toc.js \
+                         ./doc/assets/doxygen-awesome-paragraph-link.js \
+                         ./doc/assets/doxygen-awesome-fragment-copy-button.js 
 
+CREATE_SUBDIRS         = NO
+CREATE_SUBDIRS_LEVEL   = 8
+ALLOW_UNICODE_NAMES    = NO
+OUTPUT_LANGUAGE        = English
+BRIEF_MEMBER_DESC      = YES
+REPEAT_BRIEF           = YES
+ABBREVIATE_BRIEF       = YES
+ALWAYS_DETAILED_SEC    = YES
+INLINE_INHERITED_MEMB  = YES
+FULL_PATH_NAMES        = YES
+STRIP_FROM_PATH        = ./include
+STRIP_FROM_INC_PATH    =
+SHORT_NAMES            = NO
+JAVADOC_AUTOBRIEF      = YES
+JAVADOC_BANNER         = NO
+QT_AUTOBRIEF           = YES
+MULTILINE_CPP_IS_BRIEF = NO
+PYTHON_DOCSTRING       = YES
+INHERIT_DOCS           = YES
+SEPARATE_MEMBER_PAGES  = NO
+TAB_SIZE               = 8
+OPTIMIZE_OUTPUT_FOR_C  = YES
+OPTIMIZE_OUTPUT_SLICE  = NO
+EXTENSION_MAPPING      =
+MARKDOWN_SUPPORT       = YES
+TOC_INCLUDE_HEADINGS   = 5
+MARKDOWN_ID_STYLE      = DOXYGEN
+AUTOLINK_SUPPORT       = YES
+BUILTIN_STL_SUPPORT    = NO
+CPP_CLI_SUPPORT        = YES
+SIP_SUPPORT            = NO
+IDL_PROPERTY_SUPPORT   = YES
+DISTRIBUTE_GROUP_DOC   = NO
+GROUP_NESTED_COMPOUNDS = NO
+SUBGROUPING            = YES
+INLINE_GROUPED_CLASSES = NO
+INLINE_SIMPLE_STRUCTS  = NO
+TYPEDEF_HIDES_STRUCT   = NO
+LOOKUP_CACHE_SIZE      = 9
+NUM_PROC_THREADS       = 1
+TIMESTAMP              = YES
+EXTRACT_ALL            = YES
+EXTRACT_PRIVATE        = NO
+EXTRACT_PRIV_VIRTUAL   = NO
+EXTRACT_PACKAGE        = YES
+EXTRACT_STATIC         = YES
+EXTRACT_LOCAL_CLASSES  = YES
+EXTRACT_LOCAL_METHODS  = YES
+EXTRACT_ANON_NSPACES   = NO
+RESOLVE_UNNAMED_PARAMS = YES
+HIDE_UNDOC_MEMBERS     = NO
+HIDE_UNDOC_CLASSES     = NO
+HIDE_FRIEND_COMPOUNDS  = NO
+HIDE_IN_BODY_DOCS      = NO
+INTERNAL_DOCS          = NO
+CASE_SENSE_NAMES       = YES
+HIDE_SCOPE_NAMES       = NO
+HIDE_COMPOUND_REFERENCE= NO
+SHOW_HEADERFILE        = YES
+SHOW_INCLUDE_FILES     = YES
+SHOW_GROUPED_MEMB_INC  = YES
+FORCE_LOCAL_INCLUDES   = NO
+INLINE_INFO            = YES
+SORT_MEMBER_DOCS       = YES
+SORT_BRIEF_DOCS        = NO
+SORT_MEMBERS_CTORS_1ST = NO
+SORT_GROUP_NAMES       = YES
+SORT_BY_SCOPE_NAME     = YES
+STRICT_PROTO_MATCHING  = YES
+GENERATE_TODOLIST      = NO
+GENERATE_TESTLIST      = NO
+GENERATE_BUGLIST       = NO
+GENERATE_DEPRECATEDLIST= YES
+ENABLED_SECTIONS       =
+MAX_INITIALIZER_LINES  = 300
+SHOW_USED_FILES        = YES
+SHOW_FILES             = YES
+SHOW_NAMESPACES        = YES
+FILE_VERSION_FILTER    =
+LAYOUT_FILE            =
+QUIET                  = YES
+WARNINGS               = YES
+WARN_IF_UNDOCUMENTED   = YES
+WARN_IF_DOC_ERROR      = YES
+WARN_IF_INCOMPLETE_DOC = YES
+WARN_NO_PARAMDOC       = NO
+WARN_IF_UNDOC_ENUM_VAL = NO
+WARN_AS_ERROR          = NO
+WARN_FORMAT            = "$file:$line: $text"
+WARN_LINE_FORMAT       = "at line $line of file $file"
+WARN_LOGFILE           =
+INPUT_ENCODING         = UTF-8
+INPUT_FILE_ENCODING    =
+EXAMPLE_PATH           =
+EXAMPLE_PATTERNS       =
+EXAMPLE_RECURSIVE      = YES
+IMAGE_PATH             =
+INPUT_FILTER           =
+FILTER_PATTERNS        =
+FILTER_SOURCE_FILES    = NO
+FILTER_SOURCE_PATTERNS =
+SOURCE_BROWSER         = NO
+INLINE_SOURCES         = NO
+STRIP_CODE_COMMENTS    = YES
+REFERENCED_BY_RELATION = NO
+REFERENCES_RELATION    = NO
+REFERENCES_LINK_SOURCE = YES
+SOURCE_TOOLTIPS        = YES
+USE_HTAGS              = NO
+VERBATIM_HEADERS       = YES
+ALPHABETICAL_INDEX     = YES
+IGNORE_PREFIX          =
+GENERATE_HTML          = YES
+HTML_OUTPUT            = html
+HTML_FILE_EXTENSION    = .html
+HTML_FOOTER            =
+HTML_STYLESHEET        =
+HTML_COLORSTYLE        = LIGHT
+HTML_COLORSTYLE_HUE    = 220
+HTML_COLORSTYLE_SAT    = 100
+HTML_COLORSTYLE_GAMMA  = 80
+HTML_DYNAMIC_MENUS     = YES
+HTML_DYNAMIC_SECTIONS  = YES
+HTML_CODE_FOLDING      = YES
+HTML_COPY_CLIPBOARD    = YES
+HTML_PROJECT_COOKIE    =
+HTML_INDEX_NUM_ENTRIES = 100
+GENERATE_DOCSET        = YES
+DOCSET_FEEDNAME        = "Doxygen generated docs"
+DOCSET_FEEDURL         =
+DOCSET_BUNDLE_ID       = org.doxygen.Project
+DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
+DOCSET_PUBLISHER_NAME  = Publisher
+GENERATE_HTMLHELP      = NO
+CHM_FILE               = NO
+HHC_LOCATION           =
+GENERATE_CHI           = NO
+CHM_INDEX_ENCODING     =
+BINARY_TOC             = YES
+TOC_EXPAND             = NO
+SITEMAP_URL            =
+GENERATE_QHP           = NO
+QCH_FILE               =
+QHP_NAMESPACE          = org.doxygen.Project
+QHP_VIRTUAL_FOLDER     = doc
+QHP_CUST_FILTER_NAME   =
+QHP_CUST_FILTER_ATTRS  =
+QHP_SECT_FILTER_ATTRS  =
+QHG_LOCATION           =
+GENERATE_ECLIPSEHELP   = NO
+ECLIPSE_DOC_ID         = org.doxygen.Project
+DISABLE_INDEX          = NO
+GENERATE_TREEVIEW      = YES
+FULL_SIDEBAR           = NO
+ENUM_VALUES_PER_LINE   = 4
+TREEVIEW_WIDTH         = 300
+EXT_LINKS_IN_WINDOW    = NO
+OBFUSCATE_EMAILS       = NO
+HTML_FORMULA_FORMAT    = png
+FORMULA_FONTSIZE       = 10
+FORMULA_MACROFILE      =
+USE_MATHJAX            = NO
+MATHJAX_VERSION        = MathJax_2
+MATHJAX_FORMAT         = HTML-CSS
+MATHJAX_RELPATH        = http://cdn.mathjax.org/mathjax/latest
+MATHJAX_EXTENSIONS     =
+MATHJAX_CODEFILE       =
+SEARCHENGINE           = YES
+SERVER_BASED_SEARCH    = NO
+EXTERNAL_SEARCH        = NO
+SEARCHENGINE_URL       =
+SEARCHDATA_FILE        = searchdata.xml
+EXTERNAL_SEARCH_ID     =
+EXTRA_SEARCH_MAPPINGS  =
+ENABLE_PREPROCESSING   = YES
+MACRO_EXPANSION        = YES
+EXPAND_ONLY_PREDEF     = NO
+SEARCH_INCLUDES        = YES
+INCLUDE_PATH           =
+INCLUDE_FILE_PATTERNS  =
+EXPAND_AS_DEFINED      =
+SKIP_FUNCTION_MACROS   = NO
+TAGFILES               =
+GENERATE_TAGFILE       = ./doc/html/reactor-uc.tag
+ALLEXTERNALS           = NO
+EXTERNAL_GROUPS        = YES
+EXTERNAL_PAGES         = YES
+HIDE_UNDOC_RELATIONS   = YES
+HAVE_DOT               = NO
+DOT_NUM_THREADS        = 0
+DOT_COMMON_ATTR        = "fontname=Helvetica,fontsize=10"
+DOT_EDGE_ATTR          = "labelfontname=Helvetica,labelfontsize=10"
+DOT_NODE_ATTR          = "shape=box,height=0.2,width=0.4"
+DOT_FONTPATH           =
+CLASS_GRAPH            = TEXT
+COLLABORATION_GRAPH    = YES
+GROUP_GRAPHS           = YES
+UML_LOOK               = NO
+UML_LIMIT_NUM_FIELDS   = 10
+DOT_UML_DETAILS        = NO
+DOT_WRAP_THRESHOLD     = 17
+TEMPLATE_RELATIONS     = NO
+INCLUDE_GRAPH          = YES
+INCLUDED_BY_GRAPH      = YES
+CALL_GRAPH             = NO
+CALLER_GRAPH           = NO
+GRAPHICAL_HIERARCHY    = YES
+DIRECTORY_GRAPH        = YES
+DIR_GRAPH_MAX_DEPTH    = 1
+DOT_IMAGE_FORMAT       = png
+INTERACTIVE_SVG        = NO
+DOT_PATH               =
+DOTFILE_DIRS           =
+DIA_PATH               =
+DIAFILE_DIRS           =
+PLANTUML_JAR_PATH      =
+PLANTUML_CFG_FILE      =
+PLANTUML_INCLUDE_PATH  =
+DOT_GRAPH_MAX_NODES    = 50
+MAX_DOT_GRAPH_DEPTH    = 0
+DOT_MULTI_TARGETS      = NO
+GENERATE_LEGEND        = YES
+DOT_CLEANUP            = YES