Switched Doxygen to generate in 'doc' (not in build/doc)

Doxyfile

@@ -1,4 +1,4 @@
-# Doxyfile 1.7.3
+# Doxyfile 1.7.5.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project
@@ -22,8 +22,9 @@
 
 DOXYFILE_ENCODING      = UTF-8
 
-# The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
+# The PROJECT_NAME tag is a single word (or sequence of words) that should 
-# by quotes) that should identify the project.
+# identify the project. Note that if you do not use Doxywizard you need 
+# to put quotes around the project name if it contains spaces.
 
 PROJECT_NAME           = gtsam
 
@@ -33,8 +34,8 @@ PROJECT_NAME           = gtsam
 
 PROJECT_NUMBER         = 0.9.3
 
-# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# Using the PROJECT_BRIEF tag one can provide an optional one line description 
-# for a project that appears at the top of each page and should give viewer
+# 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          = gtsam
@@ -51,7 +52,7 @@ PROJECT_LOGO           =
 # If a relative path is entered, it will be relative to the location 
 # where doxygen was started. If left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = build/doc
+OUTPUT_DIRECTORY       = doc
 
 # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 
 # 4096 sub-directories (in 2 levels) under the output directory of each output 
@@ -286,6 +287,22 @@ DISTRIBUTE_GROUP_DOC   = NO
 
 SUBGROUPING            = YES
 
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and 
+# unions are shown inside the group in which they are included (e.g. using 
+# @ingroup) instead of on a separate page (for HTML and Man pages) or 
+# section (for LaTeX and RTF).
+
+INLINE_GROUPED_CLASSES = NO
+
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and 
+# unions with only public data fields will be shown inline in the documentation 
+# of the scope in which they are defined (i.e. file, namespace, or group 
+# documentation), provided this scope is documented. If set to NO (the default), 
+# structs, classes, and unions are shown on a separate page (for HTML and Man 
+# pages) or section (for LaTeX and RTF).
+
+INLINE_SIMPLE_STRUCTS  = NO
+
 # When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum 
 # is documented as struct, union, or enum with the name of the typedef. So 
 # typedef struct TypeS {} TypeT, will appear in the documentation as a struct 
@@ -461,10 +478,10 @@ SORT_GROUP_NAMES       = NO
 
 SORT_BY_SCOPE_NAME     = NO
 
-# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to 
 # do proper type resolution of all parameters of a function it will reject a 
-# match between the prototype and the implementation of a member function even
+# match between the prototype and the implementation of a member function even 
-# if there is only one candidate or it is obvious which candidate to choose
+# if there is only one candidate or it is obvious which candidate to choose 
 # by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen 
 # will still accept a match between prototype and implementation in such cases.
 
@@ -552,6 +569,15 @@ FILE_VERSION_FILTER    =
 
 LAYOUT_FILE            = DoxygenLayout.xml
 
+# The CITE_BIB_FILES tag can be used to specify one or more bib files 
+# containing the references data. This must be a list of .bib files. The 
+# .bib extension is automatically appended if omitted. Using this command 
+# requires the bibtex tool to be installed. See also 
+# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style 
+# of the bibliography can be controlled using LATEX_BIB_STYLE.
+
+CITE_BIB_FILES         = 
+
 #---------------------------------------------------------------------------
 # configuration options related to warning and progress messages
 #---------------------------------------------------------------------------
@@ -676,7 +702,8 @@ RECURSIVE              = NO
 
 # The EXCLUDE tag can be used to specify files and/or directories that should 
 # excluded from the INPUT source files. This way you can easily exclude a 
-# subdirectory from a directory tree whose root is specified with the INPUT tag.
+# subdirectory from a directory tree whose root is specified with the INPUT tag. 
+# Note that relative paths are relative to directory from which doxygen is run.
 
 EXCLUDE                = 
 
@@ -862,7 +889,14 @@ HTML_FILE_EXTENSION    = .html
 
 # The HTML_HEADER tag can be used to specify a personal HTML header for 
 # each generated HTML page. If it is left blank doxygen will generate a 
-# standard header.
+# standard header. Note that when using a custom header you are responsible  
+# for the proper inclusion of any scripts and style sheets that doxygen 
+# needs, which is dependent on the configuration options used. 
+# It is adviced to generate a default header using "doxygen -w html 
+# header.html footer.html stylesheet.css YourConfigFile" and then modify 
+# that header. Note that the header is subject to change so you typically 
+# have to redo this when upgrading to a newer version of doxygen or when 
+# changing the value of configuration settings such as GENERATE_TREEVIEW!
 
 HTML_HEADER            = 
 
@@ -881,6 +915,15 @@ HTML_FOOTER            =
 
 HTML_STYLESHEET        = 
 
+# 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 
+# that these files will be copied to the base HTML output directory. Use the 
+# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these 
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that 
+# the files will be copied as-is; there are no commands or markers available.
+
+HTML_EXTRA_FILES       = 
+
 # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. 
 # Doxygen will adjust the colors in the stylesheet and background images 
 # according to this color. Hue is specified as an angle on a colorwheel, 
@@ -924,7 +967,7 @@ HTML_ALIGN_MEMBERS     = YES
 # JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox 
 # Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
 
-HTML_DYNAMIC_SECTIONS  = NO
+HTML_DYNAMIC_SECTIONS  = YES
 
 # If the GENERATE_DOCSET tag is set to YES, additional index files 
 # will be generated that can be used as input for Apple's Xcode 3 
@@ -1083,10 +1126,10 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 
 DISABLE_INDEX          = NO
 
-# This tag can be used to set the number of enum values (range [0,1..20]) 
+# 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. 
+# (range [0,1..20]) that doxygen will group on one line in the generated HTML 
-# Note that a value of 0 will completely suppress the enum values from
+# documentation. Note that a value of 0 will completely suppress the enum 
-# appearing in the overview section.
+# values from appearing in the overview section.
 
 ENUM_VALUES_PER_LINE   = 4
 
@@ -1145,12 +1188,17 @@ USE_MATHJAX            = NO
 # HTML output directory using the MATHJAX_RELPATH option. The destination 
 # directory should contain the MathJax.js script. For instance, if the mathjax 
 # directory is located at the same level as the HTML output directory, then 
-# MATHJAX_RELPATH should be ../mathjax. The default value points to the
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the 
 # mathjax.org site, so you can quickly see the result without installing 
 # MathJax, but it is strongly recommended to install a local copy of MathJax 
 # before deployment.
 
-MATHJAX_RELPATH        = http://www.mathjax.org/mathjax
+MATHJAX_RELPATH        = http://cdn.mathjax.org/mathjax/latest
+
+# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension 
+# names that should be enabled during MathJax rendering.
+
+MATHJAX_EXTENSIONS     = 
 
 # When the SEARCHENGINE tag is enabled doxygen will generate a search box 
 # for the HTML output. The underlying search engine uses javascript 
@@ -1160,7 +1208,7 @@ MATHJAX_RELPATH        = http://www.mathjax.org/mathjax
 # typically be disabled. For large projects the javascript based search engine 
 # can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
 
-SEARCHENGINE           = NO
+SEARCHENGINE           = YES
 
 # When the SERVER_BASED_SEARCH tag is enabled the search engine will be 
 # implemented using a PHP enabled web server instead of at the web client 
@@ -1225,6 +1273,13 @@ EXTRA_PACKAGES         =
 
 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. Notice: only use this tag if you know what you are doing!
+
+LATEX_FOOTER           = 
+
 # If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated 
 # is prepared for conversion to pdf (using ps2pdf). The pdf file will 
 # contain links (just like the HTML output) instead of page references 
@@ -1258,6 +1313,12 @@ LATEX_HIDE_INDICES     = NO
 
 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. The default style is "plain". See 
+# http://en.wikipedia.org/wiki/BibTeX for more info.
+
+LATEX_BIB_STYLE        = plain
+
 #---------------------------------------------------------------------------
 # configuration options related to the RTF output
 #---------------------------------------------------------------------------
@@ -1432,7 +1493,7 @@ MACRO_EXPANSION        = NO
 EXPAND_ONLY_PREDEF     = NO
 
 # If the SEARCH_INCLUDES tag is set to YES (the default) the includes files 
-# in the INCLUDE_PATH (see below) will be search if a #include is found.
+# pointed to by INCLUDE_PATH will be searched when a #include is found.
 
 SEARCH_INCLUDES        = YES
 
@@ -1462,7 +1523,7 @@ PREDEFINED             =
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then 
 # this tag can be used to specify a list of macro names that should be expanded. 
 # The macro definition that is found in the sources will be used. 
-# Use the PREDEFINED tag if you want to use a different macro definition that
+# Use the PREDEFINED tag if you want to use a different macro definition that 
 # overrules the definition found in the source code.
 
 EXPAND_AS_DEFINED      = 
@@ -1559,13 +1620,12 @@ HAVE_DOT               = NO
 
 DOT_NUM_THREADS        = 0
 
-# By default doxygen will write a font called Helvetica to the output 
+# By default doxygen will use the Helvetica font for all dot files that 
-# directory and reference it in all dot files that doxygen generates. 
+# doxygen generates. When you want a differently looking font you can specify 
-# When you want a differently looking font you can specify the font name 
+# the font name using DOT_FONTNAME. You need to make sure dot is able to find 
-# using DOT_FONTNAME. You need to make sure dot is able to find the font, 
+# the font, which can be done by putting it in a standard location or by setting 
-# which can be done by putting it in a standard location or by setting the 
+# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the 
-# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory 
+# directory containing the font.
-# containing the font.
 
 DOT_FONTNAME           = Helvetica
 
@@ -1574,10 +1634,9 @@ DOT_FONTNAME           = Helvetica
 
 DOT_FONTSIZE           = 10
 
-# By default doxygen will tell dot to use the output directory to look for the 
+# By default doxygen will tell dot to use the Helvetica font. 
-# FreeSans.ttf font (which doxygen will put there itself). If you specify a 
+# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to 
-# different font using DOT_FONTNAME you can set the path where dot 
+# set the path where dot can find it.
-# can find it using this tag.
 
 DOT_FONTPATH           = 
 
@@ -1654,11 +1713,22 @@ GRAPHICAL_HIERARCHY    = YES
 DIRECTORY_GRAPH        = YES
 
 # The DOT_IMAGE_FORMAT tag can be used to set the image format of the images 
-# generated by dot. Possible values are png, svg, gif or svg. 
+# generated by dot. Possible values are svg, png, jpg, or gif. 
-# If left blank png will be used.
+# If left blank png will be used. If you choose svg you need to set 
+# HTML_FILE_EXTENSION to xhtml in order to make the SVG files 
+# visible in IE 9+ (other browsers do not have this requirement).
 
 DOT_IMAGE_FORMAT       = png
 
+# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to 
+# enable generation of interactive SVG images that allow zooming and panning. 
+# Note that this requires a modern browser other than Internet Explorer. 
+# Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you 
+# need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files 
+# visible. Older versions of IE do not have SVG support.
+
+INTERACTIVE_SVG        = NO
+
 # The tag DOT_PATH can be used to specify the path where the dot tool can be 
 # found. If left blank, it is assumed the dot tool can be found in the path.