fixed up the doxygen, its good now.

Doxyfile

@@ -1,4 +1,4 @@
-# Doxyfile 1.9.1
+# Doxyfile 1.9.3
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -44,14 +44,14 @@ PROJECT_NUMBER         = v3.0
 # for a project that appears at the top of each page and should give viewer a
 # quick idea about the purpose of the project. Keep the description short.
 
-PROJECT_BRIEF          = "Jit linker, mapper, obfuscator, and mutator"
+PROJECT_BRIEF          = "Jit linker, symbol mapper, and obfuscator"
 
 # 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
 # pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
 # the logo to the output directory.
 
-PROJECT_LOGO           =
+PROJECT_LOGO           = doxygen/icon.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
@@ -93,14 +93,6 @@ ALLOW_UNICODE_NAMES    = NO
 
 OUTPUT_LANGUAGE        = English
 
-# The OUTPUT_TEXT_DIRECTION tag is used to specify the direction in which all
-# documentation generated by doxygen is written. Doxygen will use this
-# information to generate all generated output in the proper direction.
-# Possible values are: None, LTR, RTL and Context.
-# The default value is: None.
-
-OUTPUT_TEXT_DIRECTION  = None
-
 # If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
 # descriptions after the members that are listed in the file and class
 # documentation (similar to Javadoc). Set to NO to disable this.
@@ -258,16 +250,16 @@ TAB_SIZE               = 4
 # the documentation. An alias has the form:
 # name=value
 # For example adding
-# "sideeffect=@par Side Effects:\n"
+# "sideeffect=@par Side Effects:^^"
 # will allow you to put the command \sideeffect (or @sideeffect) in the
 # documentation, which will result in a user-defined paragraph with heading
-# "Side Effects:". You can put \n's in the value part of an alias to insert
-# newlines (in the resulting output). You can put ^^ in the value part of an
-# alias to insert a newline as if a physical newline was in the original file.
-# When you need a literal { or } or , in the value part of an alias you have to
-# escape them by means of a backslash (\), this can lead to conflicts with the
-# commands \{ and \} for these it is advised to use the version @{ and @} or use
-# a double escape (\\{ and \\})
+# "Side Effects:". Note that you cannot put \n's in the value part of an alias
+# to insert newlines (in the resulting output). You can put ^^ in the value part
+# of an alias to insert a newline as if a physical newline was in the original
+# file. When you need a literal { or } or , in the value part of an alias you
+# have to escape them by means of a backslash (\), this can lead to conflicts
+# with the commands \{ and \} for these it is advised to use the version @{ and
+# @} or use a double escape (\\{ and \\})
 
 ALIASES                =
 
@@ -277,7 +269,7 @@ ALIASES                =
 # members will be omitted, etc.
 # The default value is: NO.
 
-OPTIMIZE_OUTPUT_FOR_C  = NO
+OPTIMIZE_OUTPUT_FOR_C  = YES
 
 # Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
 # Python sources only. Doxygen will then generate output that is more tailored
@@ -312,8 +304,8 @@ OPTIMIZE_OUTPUT_SLICE  = NO
 # extension. Doxygen has a built-in mapping, but you can override or extend it
 # using this tag. The format is ext=language, where ext is a file extension, and
 # language is one of the parsers supported by doxygen: IDL, Java, JavaScript,
-# Csharp (C#), C, C++, D, PHP, md (Markdown), Objective-C, Python, Slice, VHDL,
-# Fortran (fixed format Fortran: FortranFixed, free formatted Fortran:
+# Csharp (C#), C, C++, Lex, D, PHP, md (Markdown), Objective-C, Python, Slice,
+# VHDL, Fortran (fixed format Fortran: FortranFixed, free formatted Fortran:
 # FortranFree, unknown formatted Fortran: Fortran. In the later case the parser
 # tries to guess whether the code is fixed or free formatted code, this is the
 # default for Fortran type files). For instance to make doxygen treat .inc files
@@ -466,7 +458,7 @@ LOOKUP_CACHE_SIZE      = 0
 # than 0 to get more control over the balance between CPU load and processing
 # speed. At this moment only the input processing can be done using multiple
 # threads. Since this is still an experimental feature the default is set to 1,
-# which efficively disables parallel processing. Please report any issues you
+# which effectively disables parallel processing. Please report any issues you
 # encounter. Generating dot graphs in parallel is controlled by the
 # DOT_NUM_THREADS setting.
 # Minimum value: 0, maximum value: 32, default value: 1.
@@ -610,6 +602,12 @@ HIDE_SCOPE_NAMES       = NO
 
 HIDE_COMPOUND_REFERENCE= NO
 
+# If the SHOW_HEADERFILE tag is set to YES then the documentation for a class
+# will show which file needs to be included to use the class.
+# The default value is: YES.
+
+SHOW_HEADERFILE        = YES
+
 # If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
 # the files that are included by a file in the documentation of that file.
 # The default value is: YES.
@@ -627,7 +625,7 @@ SHOW_GROUPED_MEMB_INC  = NO
 # files with double quotes in the documentation rather than with sharp brackets.
 # The default value is: NO.
 
-FORCE_LOCAL_INCLUDES   = NO
+FORCE_LOCAL_INCLUDES   = YES
 
 # If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
 # documentation for inline members.
@@ -767,7 +765,8 @@ FILE_VERSION_FILTER    =
 # output files in an output format independent way. To create the layout file
 # that represents doxygen's defaults, run doxygen with the -l option. You can
 # optionally specify a file name after the option, if omitted DoxygenLayout.xml
-# will be used as the name of the layout file.
+# will be used as the name of the layout file. See also section "Changing the
+# layout of pages" for information.
 #
 # Note that if you run doxygen from a directory containing a file called
 # DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
@@ -813,18 +812,26 @@ WARNINGS               = YES
 WARN_IF_UNDOCUMENTED   = YES
 
 # If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
-# potential errors in the documentation, such as not documenting some parameters
-# in a documented function, or documenting parameters that don't exist or using
-# markup commands wrongly.
+# potential errors in the documentation, such as documenting some parameters in
+# a documented function twice, or documenting parameters that don't exist or
+# using markup commands wrongly.
 # The default value is: YES.
 
 WARN_IF_DOC_ERROR      = YES
 
+# If WARN_IF_INCOMPLETE_DOC is set to YES, doxygen will warn about incomplete
+# function parameter documentation. If set to NO, doxygen will accept that some
+# parameters have no documentation without warning.
+# The default value is: YES.
+
+WARN_IF_INCOMPLETE_DOC = YES
+
 # This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
 # are documented, but have no documentation for their parameters or return
-# value. If set to NO, doxygen will only warn about wrong or incomplete
-# parameter documentation, but not about the absence of documentation. If
-# EXTRACT_ALL is set to YES then this flag will automatically be disabled.
+# value. If set to NO, doxygen will only warn about wrong parameter
+# documentation, but not about the absence of documentation. If EXTRACT_ALL is
+# set to YES then this flag will automatically be disabled. See also
+# WARN_IF_INCOMPLETE_DOC
 # The default value is: NO.
 
 WARN_NO_PARAMDOC       = NO
@@ -850,7 +857,10 @@ WARN_FORMAT            = "$file:$line: $text"
 
 # The WARN_LOGFILE tag can be used to specify a file to which warning and error
 # messages should be written. If left blank the output is written to standard
-# error (stderr).
+# error (stderr). In case the file specified cannot be opened for writing the
+# warning and error messages are written to standard error. When as file - is
+# specified the warning and error messages are written to standard output
+# (stdout).
 
 WARN_LOGFILE           =
 
@@ -892,10 +902,10 @@ INPUT_ENCODING         = UTF-8
 #
 # If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
 # *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
-# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
-# *.m, *.markdown, *.md, *.mm, *.dox (to be provided as doxygen C comment),
-# *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f18, *.f, *.for, *.vhd, *.vhdl,
-# *.ucf, *.qsf and *.ice.
+# *.hh, *.hxx, *.hpp, *.h++, *.l, *.cs, *.d, *.php, *.php4, *.php5, *.phtml,
+# *.inc, *.m, *.markdown, *.md, *.mm, *.dox (to be provided as doxygen C
+# comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f18, *.f, *.for, *.vhd,
+# *.vhdl, *.ucf, *.qsf and *.ice.
 
 FILE_PATTERNS          = *.c \
                          *.cc \
@@ -978,7 +988,7 @@ EXCLUDE_PATTERNS       =
 # (namespaces, classes, functions, etc.) that should be excluded from the
 # output. The symbol name can be a fully qualified name, a word, or if the
 # wildcard * is used, a substring. Examples: ANamespace, AClass,
-# AClass::ANamespace, ANamespace::*Test
+# ANamespace::AClass, ANamespace::*Test
 #
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories use the pattern */test/*
@@ -1091,19 +1101,19 @@ INLINE_SOURCES         = YES
 # Fortran comments will always remain visible.
 # The default value is: YES.
 
-STRIP_CODE_COMMENTS    = YES
+STRIP_CODE_COMMENTS    = NO
 
 # If the REFERENCED_BY_RELATION tag is set to YES then for each documented
 # entity all documented functions referencing it will be listed.
 # The default value is: NO.
 
-REFERENCED_BY_RELATION = NO
+REFERENCED_BY_RELATION = YES
 
 # If the REFERENCES_RELATION tag is set to YES then for each documented function
 # all documented entities called/used by that function will be listed.
 # The default value is: NO.
 
-REFERENCES_RELATION    = NO
+REFERENCES_RELATION    = YES
 
 # If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
 # to YES then the hyperlinks from functions in REFERENCES_RELATION and
@@ -1121,7 +1131,7 @@ REFERENCES_LINK_SOURCE = YES
 # The default value is: YES.
 # This tag requires that the tag SOURCE_BROWSER is set to YES.
 
-SOURCE_TOOLTIPS        = YES
+SOURCE_TOOLTIPS        = NO
 
 # If the USE_HTAGS tag is set to YES then the references to source code will
 # point to the HTML generated by the htags(1) tool instead of doxygen built-in
@@ -1143,7 +1153,7 @@ SOURCE_TOOLTIPS        = YES
 # The default value is: NO.
 # This tag requires that the tag SOURCE_BROWSER is set to YES.
 
-USE_HTAGS              = YES
+USE_HTAGS              = NO
 
 # If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
 # verbatim copy of the header file for each class for which an include is
@@ -1164,9 +1174,11 @@ VERBATIM_HEADERS       = YES
 
 CLANG_ASSISTED_PARSING = NO
 
-# If clang assisted parsing is enabled and the CLANG_ADD_INC_PATHS tag is set to
-# YES then doxygen will add the directory of each input to the include path.
+# If the CLANG_ASSISTED_PARSING tag is set to YES and the CLANG_ADD_INC_PATHS
+# tag is set to YES then doxygen will add the directory of each input to the
+# include path.
 # The default value is: YES.
+# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
 
 CLANG_ADD_INC_PATHS    = YES
 
@@ -1301,7 +1313,7 @@ HTML_EXTRA_FILES       =
 
 # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
 # will adjust the colors in the style sheet and background images according to
-# this color. Hue is specified as an angle on a colorwheel, see
+# this color. Hue is specified as an angle on a color-wheel, see
 # https://en.wikipedia.org/wiki/Hue for more information. For instance the value
 # 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
 # purple, and 360 is red again.
@@ -1311,7 +1323,7 @@ HTML_EXTRA_FILES       =
 HTML_COLORSTYLE_HUE    = 220
 
 # 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 grayscales only. A
+# in the HTML output. For a value of 0 the output will use gray-scales only. A
 # value of 255 will produce the most vivid colors.
 # Minimum value: 0, maximum value: 255, default value: 100.
 # This tag requires that the tag GENERATE_HTML is set to YES.
@@ -1393,6 +1405,13 @@ GENERATE_DOCSET        = NO
 
 DOCSET_FEEDNAME        = "Doxygen generated docs"
 
+# This tag determines the URL of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_FEEDURL         =
+
 # This tag specifies a string that should uniquely identify the documentation
 # set bundle. This should be a reverse domain-name style string, e.g.
 # com.mycompany.MyDocSet. Doxygen will append .docset to the name.
@@ -1418,8 +1437,12 @@ DOCSET_PUBLISHER_NAME  = Publisher
 # If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
 # additional HTML index files: index.hhp, index.hhc, and index.hhk. The
 # index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
-# (see:
-# https://www.microsoft.com/en-us/download/details.aspx?id=21138) on Windows.
+# on Windows. In the beginning of 2021 Microsoft took the original page, with
+# a.o. the download links, offline the HTML help workshop was already many years
+# in maintenance mode). You can download the HTML help workshop from the web
+# archives at Installation executable (see:
+# http://web.archive.org/web/20160201063255/http://download.microsoft.com/downlo
+# ad/0/A/9/0A939EF6-E31C-430F-A3DF-DFAE7960D564/htmlhelp.exe).
 #
 # The HTML Help Workshop contains a compiler that can convert all HTML output
 # generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
@@ -1578,16 +1601,28 @@ DISABLE_INDEX          = NO
 # to work a browser that supports JavaScript, DHTML, CSS and frames is required
 # (i.e. any modern browser). Windows users are probably better off using the
 # HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
-# further fine-tune the look of the index. As an example, the default style
-# sheet generated by doxygen has an example that shows how to put an image at
-# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
-# the same information as the tab index, you could consider setting
-# DISABLE_INDEX to YES when enabling this option.
+# further fine tune the look of the index (see "Fine-tuning the output"). As an
+# example, the default style sheet generated by doxygen has an example that
+# shows how to put an image at the root of the tree instead of the PROJECT_NAME.
+# Since the tree basically has the same information as the tab index, you could
+# consider setting DISABLE_INDEX to YES when enabling this option.
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
 GENERATE_TREEVIEW      = NO
 
+# When both GENERATE_TREEVIEW and DISABLE_INDEX are set to YES, then the
+# FULL_SIDEBAR option determines if the side bar is limited to only the treeview
+# area (value NO) or if it should extend to the full height of the window (value
+# YES). Setting this to YES gives a layout similar to
+# https://docs.readthedocs.io with more room for contents, but less room for the
+# project logo, title, and description. If either GENERATE_TREEVIEW or
+# DISABLE_INDEX is set to NO, this option has no effect.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FULL_SIDEBAR           = NO
+
 # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
 # doxygen will group on one line in the generated HTML documentation.
 #
@@ -1612,6 +1647,13 @@ TREEVIEW_WIDTH         = 250
 
 EXT_LINKS_IN_WINDOW    = NO
 
+# If the OBFUSCATE_EMAILS tag is set to YES, doxygen will obfuscate email
+# addresses.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+OBFUSCATE_EMAILS       = YES
+
 # If the HTML_FORMULA_FORMAT option is set to svg, doxygen will use the pdf2svg
 # tool (see https://github.com/dawbarton/pdf2svg) or inkscape (see
 # https://inkscape.org) to generate formulas as SVG images instead of PNGs for
@@ -1660,11 +1702,29 @@ FORMULA_MACROFILE      =
 
 USE_MATHJAX            = NO
 
+# 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
+# regards to the different settings, so it is possible that also other MathJax
+# settings have to be changed when switching between the different MathJax
+# versions.
+# Possible values are: MathJax_2 and MathJax_3.
+# The default value is: MathJax_2.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_VERSION        = MathJax_2
+
 # When MathJax is enabled you can set the default output format to be used for
-# the MathJax output. See the MathJax site (see:
-# http://docs.mathjax.org/en/v2.7-latest/output.html) for more details.
+# the MathJax output. For more details about the output format see MathJax
+# version 2 (see:
+# http://docs.mathjax.org/en/v2.7-latest/output.html) and MathJax version 3
+# (see:
+# http://docs.mathjax.org/en/latest/web/components/output.html).
 # Possible values are: HTML-CSS (which is slower, but has the best
-# compatibility), NativeMML (i.e. MathML) and SVG.
+# compatibility. This is the name for Mathjax version 2, for MathJax version 3
+# this will be translated into chtml), NativeMML (i.e. MathML. Only supported
+# for NathJax 2. For MathJax version 3 chtml will be used instead.), chtml (This
+# is the name for Mathjax version 3, for MathJax version 2 this will be
+# translated into HTML-CSS) and SVG.
 # The default value is: HTML-CSS.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
@@ -1677,15 +1737,21 @@ MATHJAX_FORMAT         = HTML-CSS
 # MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
 # Content Delivery Network so you can quickly see the result without installing
 # MathJax. However, it is strongly recommended to install a local copy of
-# MathJax from https://www.mathjax.org before deployment.
-# The default value is: https://cdn.jsdelivr.net/npm/mathjax@2.
+# MathJax from https://www.mathjax.org before deployment. The default value is:
+# - in case of MathJax version 2: https://cdn.jsdelivr.net/npm/mathjax@2
+# - in case of MathJax version 3: https://cdn.jsdelivr.net/npm/mathjax@3
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
 MATHJAX_RELPATH        = https://cdn.jsdelivr.net/npm/mathjax@2
 
 # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
 # extension names that should be enabled during MathJax rendering. For example
+# for MathJax version 2 (see
+# https://docs.mathjax.org/en/v2.7-latest/tex.html#tex-and-latex-extensions):
 # MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# For example for MathJax version 3 (see
+# http://docs.mathjax.org/en/latest/input/tex/extensions/index.html):
+# MATHJAX_EXTENSIONS = ams
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
 MATHJAX_EXTENSIONS     =
@@ -1865,29 +1931,31 @@ PAPER_TYPE             = a4
 
 EXTRA_PACKAGES         =
 
-# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
-# generated LaTeX document. The header should contain everything until the first
-# chapter. If it is left blank doxygen will generate a standard header. See
-# section "Doxygen usage" for information on how to let doxygen write the
-# default header to a separate file.
+# The LATEX_HEADER tag can be used to specify a user-defined LaTeX header for
+# the generated LaTeX document. The header should contain everything until the
+# first chapter. If it is left blank doxygen will generate a standard header. It
+# is highly recommended to start with a default header using
+# doxygen -w latex new_header.tex new_footer.tex new_stylesheet.sty
+# and then modify the file new_header.tex. See also section "Doxygen usage" for
+# information on how to generate the default header that doxygen normally uses.
 #
-# Note: Only use a user-defined header if you know what you are doing! The
-# following commands have a special meaning inside the header: $title,
-# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
-# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
-# string, for the replacement values of the other commands the user is referred
-# to HTML_HEADER.
+# Note: Only use a user-defined header if you know what you are doing!
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. The following
+# commands have a special meaning inside the header (and footer): For a
+# description of the possible markers and block names see the documentation.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_HEADER           =
 
-# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
-# generated LaTeX document. The footer should contain everything after the last
-# chapter. If it is left blank doxygen will generate a standard footer. See
+# The LATEX_FOOTER tag can be used to specify a user-defined LaTeX footer for
+# the generated LaTeX document. The footer should contain everything after the
+# last chapter. If it is left blank doxygen will generate a standard footer. See
 # LATEX_HEADER for more information on how to generate a default footer and what
-# special commands can be used inside the footer.
-#
-# Note: Only use a user-defined footer if you know what you are doing!
+# special commands can be used inside the footer. See also section "Doxygen
+# usage" for information on how to generate the default footer that doxygen
+# normally uses. Note: Only use a user-defined footer if you know what you are
+# doing!
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_FOOTER           =
@@ -1932,8 +2000,7 @@ USE_PDFLATEX           = YES
 
 # If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
 # command to the generated LaTeX files. This will instruct LaTeX to keep running
-# if errors occur, instead of asking the user for help. This option is also used
-# when generating formulas in HTML.
+# if errors occur, instead of asking the user for help.
 # The default value is: NO.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
@@ -1946,16 +2013,6 @@ LATEX_BATCHMODE        = NO
 
 LATEX_HIDE_INDICES     = NO
 
-# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
-# code with syntax highlighting in the LaTeX output.
-#
-# Note that which sources are shown also depends on other settings such as
-# SOURCE_BROWSER.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_SOURCE_CODE      = NO
-
 # The LATEX_BIB_STYLE tag can be used to specify the style to use for the
 # bibliography, e.g. plainnat, or ieeetr. See
 # https://en.wikipedia.org/wiki/BibTeX and \cite for more info.
@@ -2036,16 +2093,6 @@ RTF_STYLESHEET_FILE    =
 
 RTF_EXTENSIONS_FILE    =
 
-# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
-# with syntax highlighting in the RTF output.
-#
-# Note that which sources are shown also depends on other settings such as
-# SOURCE_BROWSER.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_SOURCE_CODE        = NO
-
 #---------------------------------------------------------------------------
 # Configuration options related to the man page output
 #---------------------------------------------------------------------------
@@ -2142,15 +2189,6 @@ GENERATE_DOCBOOK       = NO
 
 DOCBOOK_OUTPUT         = docbook
 
-# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
-# program listings (including syntax highlighting and cross-referencing
-# information) to the DOCBOOK output. Note that enabling this will significantly
-# increase the size of the DOCBOOK output.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
-
-DOCBOOK_PROGRAMLISTING = NO
-
 #---------------------------------------------------------------------------
 # Configuration options for the AutoGen Definitions output
 #---------------------------------------------------------------------------
@@ -2333,15 +2371,6 @@ EXTERNAL_PAGES         = YES
 # Configuration options related to the dot tool
 #---------------------------------------------------------------------------
 
-# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram
-# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
-# NO turns the diagrams off. Note that this option also works with HAVE_DOT
-# disabled, but it is recommended to install and use dot, since it yields more
-# powerful graphs.
-# The default value is: YES.
-
-CLASS_DIAGRAMS         = YES
-
 # You can include diagrams made with dia in doxygen documentation. Doxygen will
 # then run dia to produce the diagram and insert it in the documentation. The
 # DIA_PATH tag allows you to specify the directory where the dia binary resides.
@@ -2398,11 +2427,14 @@ DOT_FONTSIZE           = 10
 
 DOT_FONTPATH           =
 
-# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for
-# each documented class showing the direct and indirect inheritance relations.
-# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO.
+# If the CLASS_GRAPH tag is set to YES (or GRAPH) then doxygen will generate a
+# graph for each documented class showing the direct and indirect inheritance
+# relations. In case HAVE_DOT is set as well dot will be used to draw the graph,
+# otherwise the built-in generator will be used. If the CLASS_GRAPH tag is set
+# to TEXT the direct and indirect inheritance relations will be shown as texts /
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@@ -2531,6 +2563,13 @@ GRAPHICAL_HIERARCHY    = YES
 
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+# path where java can find the plantuml.jar file or to the filename of jar file
+# to be used. If left blank, it is assumed PlantUML is not used or called during
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README.md

@@ -1,6 +1,7 @@
 # Theodosius - Jit linker, Mapper, Mutator, and Obfuscator 
 
 Theodosius (Theo for short) is a jit linker created for obfuscation. The project is extremely modular in design and supports both kernel and usermode projects. 
+Theo works with static libraries rather than completely compiled binaries. This allows it to easily position, obfuscate, and scatter symbols anywhere as the project takes the place of the linker.
 
 ### Table Of Contents
 

doxygen/html/annotated.html

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+<meta name="generator" content="Doxygen 1.9.3"/>
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-<title>Theodosius: Class List</title>
+<title>Theodosius: Data Structures</title>
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-  <td id="projectalign" style="padding-left: 0.5em;">
-   <div id="projectname">Theodosius
-   &#160;<span id="projectnumber">v3.0</span>
+ <tr id="projectrow">
+  <td id="projectlogo"><img alt="Logo" src="icon.png"/></td>
+  <td id="projectalign">
+   <div id="projectname">Theodosius<span id="projectnumber">&#160;v3.0</span>
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-   <div id="projectbrief">Jit linker, mapper, obfuscator, and mutator</div>
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+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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@@ -63,42 +64,41 @@ $(function() {
 </div>
 
 <div class="header">
-  <div class="headertitle">
-<div class="title">Class List</div>  </div>
+  <div class="headertitle"><div class="title">Data Structures</div></div>
 </div><!--header-->
 <div class="contents">
-<div class="textblock">Here are the classes, structs, unions and interfaces with brief descriptions:</div><div class="directory">
+<div class="textblock">Here are the data structures with brief descriptions:</div><div class="directory">
 <div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</span><span onclick="javascript:toggleLevel(3);">3</span><span onclick="javascript:toggleLevel(4);">4</span>]</div><table class="directory">
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+<tr id="row_0_1_0_1_" class="even"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="d7/de2/classtheo_1_1obf_1_1transform_1_1operation__t.html" target="_self">operation_t</a></td><td class="desc"><a class="el" href="d7/de2/classtheo_1_1obf_1_1transform_1_1operation__t.html" title="operation_t is the base class for all types of transformations. classes that inherit this class are s...">operation_t</a> is the base class for all types of transformations. classes that inherit this class are singleton and simply call the super constructor (<a class="el" href="d7/de2/classtheo_1_1obf_1_1transform_1_1operation__t.html#a3876ca1c7904aed54940e1519fc9fdf4" title="explicit constructor for operation_t">operation_t::operation_t</a>). </td></tr>
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 <tr id="row_0_1_0_4_"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="d6/d52/classtheo_1_1obf_1_1transform_1_1sub__op__t.html" target="_self">sub_op_t</a></td><td class="desc"></td></tr>
 <tr id="row_0_1_0_5_" class="even"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="da/db7/classtheo_1_1obf_1_1transform_1_1xor__op__t.html" target="_self">xor_op_t</a></td><td class="desc"></td></tr>
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+<tr id="row_0_1_2_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="d5/d6a/classtheo_1_1obf_1_1hello__world__pass__t.html" target="_self">hello_world_pass_t</a></td><td class="desc">hello world pass example of how to inherit <a class="el" href="d4/dad/classtheo_1_1obf_1_1pass__t.html" title="the pass_t class is a base clase for all passes made. you must override the pass_t::run virtual funct...">pass_t</a>. </td></tr>
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 <tr id="row_0_2_0_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="d5/d05/classtheo_1_1recomp_1_1recomp__t.html" target="_self">recomp_t</a></td><td class="desc">the main class responsible for recomposition </td></tr>
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