Reflow documentation

1. Clean up as much useless whitespace as I can. 2. Swap tabs for whitespace. 3. Reflow the doxygen comments (leaving redundancy). 4. Reformat doxygen so that the '*' flower box is removed. This does *not* include plugins. That will be done at some later date.
janx8r · Apr 11, 2019 · 3a5d13d · 3a5d13d
1 parent 7f8da84
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diff --git a/doc/Menge.cfg b/doc/Menge.cfg
@@ -672,7 +672,7 @@ FILE_VERSION_FILTER    =
 # DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
 # tag is left empty.
 
-LAYOUT_FILE            =	doc/MengeDoxygenLayout.xml
+LAYOUT_FILE            =  doc/MengeDoxygenLayout.xml
 
 # The CITE_BIB_FILES tag can be used to specify one or more bib files containing
 # the reference definitions. This must be a list of .bib files. The .bib
@@ -871,7 +871,7 @@ EXAMPLE_RECURSIVE      = NO
 # that contain images that are to be included in the documentation (see the
 # \image command).
 
-IMAGE_PATH             =	doc/images
+IMAGE_PATH             =  doc/images
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program
@@ -1094,7 +1094,7 @@ HTML_FILE_EXTENSION    = .html
 # of the possible markers and block names see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_HEADER            =	doc/header.html
+HTML_HEADER            =  doc/header.html
 
 # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
 # generated HTML page. If the tag is left blank doxygen will generate a standard
@@ -1104,7 +1104,7 @@ HTML_HEADER            =	doc/header.html
 # that doxygen normally uses.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_FOOTER            =	doc/footer.html
+HTML_FOOTER            =  doc/footer.html
 
 # The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
 # sheet that is used by each HTML page. It can be used to fine-tune the look of
@@ -1127,7 +1127,7 @@ HTML_STYLESHEET        =
 # see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_STYLESHEET  =	doc/customdoxygen.css 
+HTML_EXTRA_STYLESHEET  =  doc/customdoxygen.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
@@ -1990,7 +1990,7 @@ INCLUDE_FILE_PATTERNS  =
 # recursively expanded use the := operator instead of the = operator.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-PREDEFINED             =	DOXYGEN_SHOULD_SKIP_THIS
+PREDEFINED             =  DOXYGEN_SHOULD_SKIP_THIS
 
 # 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
@@ -2029,8 +2029,8 @@ SKIP_FUNCTION_MACROS   = YES
 # run, you must also specify the path to the tagfile here.
 
 TAGFILES               = doc/tags/MengeCore.tag \
-						 doc/tags/MengeVis.tag \
-						 doc/tags/PedPlugins.tag
+             doc/tags/MengeVis.tag \
+             doc/tags/PedPlugins.tag
 
 # When a file name is specified after GENERATE_TAGFILE, doxygen will create a
 # tag file that is based on the input files it reads. See section "Linking to

diff --git a/doc/MengeCore.cfg b/doc/MengeCore.cfg
@@ -672,7 +672,7 @@ FILE_VERSION_FILTER    =
 # DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
 # tag is left empty.
 
-LAYOUT_FILE            =	doc/MengeDoxygenLayout.xml
+LAYOUT_FILE            =  doc/MengeDoxygenLayout.xml
 
 # The CITE_BIB_FILES tag can be used to specify one or more bib files containing
 # the reference definitions. This must be a list of .bib files. The .bib
@@ -1066,7 +1066,7 @@ HTML_FILE_EXTENSION    = .html
 # of the possible markers and block names see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_HEADER            =	doc/header.html
+HTML_HEADER            =  doc/header.html
 
 # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
 # generated HTML page. If the tag is left blank doxygen will generate a standard
@@ -1076,7 +1076,7 @@ HTML_HEADER            =	doc/header.html
 # that doxygen normally uses.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_FOOTER            =	doc/footer.html
+HTML_FOOTER            =  doc/footer.html
 
 # The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
 # sheet that is used by each HTML page. It can be used to fine-tune the look of
@@ -1099,7 +1099,7 @@ HTML_STYLESHEET        =
 # see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_STYLESHEET  =	doc/customdoxygen.css 
+HTML_EXTRA_STYLESHEET  =  doc/customdoxygen.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
@@ -1962,7 +1962,7 @@ INCLUDE_FILE_PATTERNS  =
 # recursively expanded use the := operator instead of the = operator.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-PREDEFINED             =	DOXYGEN_SHOULD_SKIP_THIS
+PREDEFINED             =  DOXYGEN_SHOULD_SKIP_THIS
 
 # 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

diff --git a/doc/MengeFull.cfg b/doc/MengeFull.cfg
@@ -672,7 +672,7 @@ FILE_VERSION_FILTER    =
 # DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
 # tag is left empty.
 
-LAYOUT_FILE            =	doc/MengeDoxygenLayout.xml
+LAYOUT_FILE            =  doc/MengeDoxygenLayout.xml
 
 # The CITE_BIB_FILES tag can be used to specify one or more bib files containing
 # the reference definitions. This must be a list of .bib files. The .bib
@@ -875,7 +875,7 @@ EXAMPLE_RECURSIVE      = NO
 # that contain images that are to be included in the documentation (see the
 # \image command).
 
-IMAGE_PATH             =	doc/images
+IMAGE_PATH             =  doc/images
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program
@@ -1098,7 +1098,7 @@ HTML_FILE_EXTENSION    = .html
 # of the possible markers and block names see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_HEADER            =	doc/header.html
+HTML_HEADER            =  doc/header.html
 
 # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
 # generated HTML page. If the tag is left blank doxygen will generate a standard
@@ -1108,7 +1108,7 @@ HTML_HEADER            =	doc/header.html
 # that doxygen normally uses.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_FOOTER            =	doc/footer.html
+HTML_FOOTER            =  doc/footer.html
 
 # The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
 # sheet that is used by each HTML page. It can be used to fine-tune the look of
@@ -1131,7 +1131,7 @@ HTML_STYLESHEET        =
 # see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_STYLESHEET  =	doc/customdoxygen.css 
+HTML_EXTRA_STYLESHEET  =  doc/customdoxygen.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
@@ -1994,7 +1994,7 @@ INCLUDE_FILE_PATTERNS  =
 # recursively expanded use the := operator instead of the = operator.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-PREDEFINED             =	DOXYGEN_SHOULD_SKIP_THIS
+PREDEFINED             =  DOXYGEN_SHOULD_SKIP_THIS
 
 # 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

diff --git a/doc/Plugins.cfg b/doc/Plugins.cfg
@@ -672,7 +672,7 @@ FILE_VERSION_FILTER    =
 # DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
 # tag is left empty.
 
-LAYOUT_FILE            = 	doc/MengeDoxygenLayout.xml
+LAYOUT_FILE            =   doc/MengeDoxygenLayout.xml
 
 # The CITE_BIB_FILES tag can be used to specify one or more bib files containing
 # the reference definitions. This must be a list of .bib files. The .bib
@@ -755,8 +755,8 @@ WARN_LOGFILE           =
 # Note: If this tag is empty the current directory is searched.
 
 INPUT                  = doc/pluginDetails/mainpage.md \
-						 doc/pluginDetails/examples.md \
-						 src\Plugins\aircraft \
+             doc/pluginDetails/examples.md \
+             src\Plugins\aircraft \
                          src\Plugins\Formations \
                          src\Plugins\FundamentalDiagram \
                          src\Plugins\AgtDummy \
@@ -765,7 +765,7 @@ INPUT                  = doc/pluginDetails/mainpage.md \
                          src\Plugins\AgtKaramouzas \
                          src\Plugins\AgtZanlungo \
                          src\Plugins\Terrain \
-						 src\Plugins\StressGas
+             src\Plugins\StressGas
 
 
 # This tag can be used to specify the character encoding of the source files
@@ -1077,7 +1077,7 @@ HTML_FILE_EXTENSION    = .html
 # of the possible markers and block names see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_HEADER            =	doc/header.html
+HTML_HEADER            =  doc/header.html
 
 # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
 # generated HTML page. If the tag is left blank doxygen will generate a standard
@@ -1087,7 +1087,7 @@ HTML_HEADER            =	doc/header.html
 # that doxygen normally uses.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_FOOTER            =	doc/footer.html
+HTML_FOOTER            =  doc/footer.html
 
 # The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
 # sheet that is used by each HTML page. It can be used to fine-tune the look of
@@ -1110,7 +1110,7 @@ HTML_STYLESHEET        =
 # see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_STYLESHEET  =	doc/customdoxygen.css 
+HTML_EXTRA_STYLESHEET  =  doc/customdoxygen.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
@@ -2012,7 +2012,7 @@ SKIP_FUNCTION_MACROS   = YES
 # run, you must also specify the path to the tagfile here.
 
 TAGFILES               =  doc/tags/MengeCore.tag \
-						  doc/tags/MengeVis.tag
+              doc/tags/MengeVis.tag
 
 # When a file name is specified after GENERATE_TAGFILE, doxygen will create a
 # tag file that is based on the input files it reads. See section "Linking to

diff --git a/doc/mengeDetails/elements.md b/doc/mengeDetails/elements.md
@@ -8,44 +8,44 @@ Elements                {#page_Elements}
 @section sec_elemTypes Element Types
 
 The element types are as follows:
-	- Agent initial conditions
-	
-		Each agent's initial condition is uniquely defined by where it is in space, its properties, and its current behavior state.  These three characteristics are defined by three elements: the agent generator, the profile selector, and the state selector, respectively.  		
-		+ [Agent Generators](@ref page_AgentGen): Mechanism by which the number and position of all agents in the scene are determined.
-		+ [Profile Selectors](@ref page_ProSelect): Mechanism by which agent properties (defined by an "agent profile") are assigned to the agents created by the Agent Generator.
-		+ [State Selectors](@ref page_StateSelect): Mechanism by which each agent is assigned an initial state in the [Behavioral Finite State Machine (BFSM)](@ref sec_Arch_BFSM).
-	- Simulator Components
-	
-		The simulator uses various elements to satisfy queries and define the domain.  
-		
-		+ [Elevations](@ref page_Elevation): Mechanism by which agents can move in domains that are not flat planes.
-		+ [Obstacle Sets](@ref page_ObstSet): Mechanism by which obstacles are introduced into the scene.
-		+ [Spatial Queries](@ref page_SpatialQuery): Mechanism by which spatial queries (e.g., k-nearest neighbors) are satisfied.
-		+ [Tasks](@ref page_Tasks): Mechanism by which arbitrary computation can be introduced into the %Menge paradigm.  
-		
-	- [Behavioral Finite State Machine](@ref sec_Arch_BFSM)
-	
-		The behavior of each agent can change as the simulation progresses.  We accomplish this by use of a finite state machine.  An agent exists in a single state at any given time.  The state defines the agent's *preferred velocity*.  As the agent moves from state to state, its preferred velocity (and even how it is computed) can radically change.  Agents can transition from one state to another state based on FSM *structural* transitions or external events.  As agents enter and leave states, actions can be applied to the agent, changing (permanently *or* temporarily) properties of the agent.
-		
-		+ [Actions](@ref page_Actions): Actions assigned to a state are applied to agents upon entering that state and can optionally be undone when the agent leaves the state.
-		+ [Events](@ref page_EventSystem)
+  - Agent initial conditions
+
+    Each agent's initial condition is uniquely defined by where it is in space, its properties, and its current behavior state.  These three characteristics are defined by three elements: the agent generator, the profile selector, and the state selector, respectively.      
+    + [Agent Generators](@ref page_AgentGen): Mechanism by which the number and position of all agents in the scene are determined.
+    + [Profile Selectors](@ref page_ProSelect): Mechanism by which agent properties (defined by an "agent profile") are assigned to the agents created by the Agent Generator.
+    + [State Selectors](@ref page_StateSelect): Mechanism by which each agent is assigned an initial state in the [Behavioral Finite State Machine (BFSM)](@ref sec_Arch_BFSM).
+  - Simulator Components
+
+    The simulator uses various elements to satisfy queries and define the domain.  
+
+	+ [Elevations](@ref page_Elevation): Mechanism by which agents can move in domains that are not flat planes.
+	+ [Obstacle Sets](@ref page_ObstSet): Mechanism by which obstacles are introduced into the scene.
+	+ [Spatial Queries](@ref page_SpatialQuery): Mechanism by which spatial queries (e.g., k-nearest neighbors) are satisfied.
+	+ [Tasks](@ref page_Tasks): Mechanism by which arbitrary computation can be introduced into the %Menge paradigm.  
+
+  - [Behavioral Finite State Machine](@ref sec_Arch_BFSM)
+
+    The behavior of each agent can change as the simulation progresses.  We accomplish this by use of a finite state machine.  An agent exists in a single state at any given time.  The state defines the agent's *preferred velocity*.  As the agent moves from state to state, its preferred velocity (and even how it is computed) can radically change.  Agents can transition from one state to another state based on FSM *structural* transitions or external events.  As agents enter and leave states, actions can be applied to the agent, changing (permanently *or* temporarily) properties of the agent.
+
+	+ [Actions](@ref page_Actions): Actions assigned to a state are applied to agents upon entering that state and can optionally be undone when the agent leaves the state.
+	+ [Events](@ref page_EventSystem)
 		
-			%Menge supports an event system for affecting agent behaviors.  The event system is comprised of three elements: an event trigger, effect, and target.
-			- [Event Triggers](@ref page_EventTrigger): The definition of a condition on simulation state which causes an event to be applied to the simulation.
-			- [Event Effects](@ref page_EventEffect): The definition of a response to an event (such as changing agent states, changing the simulation domain, etc.)
-			- [Event Targets](@ref page_EventTarget): The definition of the simulation entity that will be affected by the Event Effect.
-
-		+ [Goals](@ref page_Goal): The definition of a region in space the agent wants to reach.
-		+ [Goal Selectors](@ref page_GoalSelect): The mechanism by which the agent selects a goal.
-		+ Transitions
-			
-			These are the FSM transitions.  They define the circumstances, based on agent state, which cause an agent to transition from one state to another.
-			- [Conditions](@ref sec_Trans_Condition): The definition of the condition which causes an agent to move to a connected state.
-			- [Targets](@ref sec_Trans_Target): The definition of the connected state to which an agent moves.
-		+ [Velocity Components](@ref page_VelComp): The mechanism which computes an agent's instantaneous preferred velocity.
-		+ [Velocity Modifiers](@ref page_VelMod): A mechanism through which an agent's preferred velocity can be modified based on aribtrary simulation state.
+		%Menge supports an event system for affecting agent behaviors.  The event system is comprised of three elements: an event trigger, effect, and target.
+		- [Event Triggers](@ref page_EventTrigger): The definition of a condition on simulation state which causes an event to be applied to the simulation.
+		- [Event Effects](@ref page_EventEffect): The definition of a response to an event (such as changing agent states, changing the simulation domain, etc.)
+		- [Event Targets](@ref page_EventTarget): The definition of the simulation entity that will be affected by the Event Effect.
+
+	+ [Goals](@ref page_Goal): The definition of a region in space the agent wants to reach.
+	+ [Goal Selectors](@ref page_GoalSelect): The mechanism by which the agent selects a goal.
+	+ Transitions
+
+		These are the FSM transitions.  They define the circumstances, based on agent state, which cause an agent to transition from one state to another.
+		- [Conditions](@ref sec_Trans_Condition): The definition of the condition which causes an agent to move to a connected state.
+		- [Targets](@ref sec_Trans_Target): The definition of the connected state to which an agent moves.
+	+ [Velocity Components](@ref page_VelComp): The mechanism which computes an agent's instantaneous preferred velocity.
+	+ [Velocity Modifiers](@ref page_VelMod): A mechanism through which an agent's preferred velocity can be modified based on aribtrary simulation state.
 	- Future Elements
 
 		There are plans to extend %Menge's expressive ability by adding new element types.  We are always open to suggestions which will increase %Menge's usefulness.
 		
-		- Agent Sources: Entities which can dynamically introduce new agents into the simulation at arbitrary times rather than purely as initial conditions.
+		- Agent Sources: Entities which can dynamically introduce new agents into the simulation at arbitrary times rather than purely as initial conditions.
diff --git a/doc/mengeDetails/elements/agentGen.md b/doc/mengeDetails/elements/agentGen.md
@@ -32,7 +32,7 @@ This version of Menge includes the following implementations of the agent genera
 - The [rectangular grid generator](@ref Menge::Agents::RectGridGenerator).
 - The [hexagonal lattice generator](@ref Menge::Agents::HexLatticeGenerator).
 - The [explicit navigation mesh generator](@ref Menge::Agents::NavMeshGenerator).
-	
+
 See the class documentation for details on their semantics and how to instantiate this profile
 selector.
 

diff --git a/doc/mengeDetails/elements/velMod.md b/doc/mengeDetails/elements/velMod.md
@@ -21,12 +21,12 @@ The preferred velocity computed by the Velocity Component is fed into the single
 
 Multiple velocity modifiers can be provided.  For example, an agent profile could specify two velocity modifiers as follows:
 
-	<AgentProfile>
-		...
-		<VelModifer type="firstMod" ... />
-		<VelModifer type="secondMod" ... />
-	</AgentProfile>
-	
+  <AgentProfile>
+    ...
+    <VelModifer type="firstMod" ... />
+    <VelModifer type="secondMod" ... />
+  </AgentProfile>
+
 In this case, the velocity modifiers are composed in the order given:
 
 \image html specification/velMod_doubleEval.png