Update to build model.

- ablility to add configs to target and set options on configs.

9 files changed, 289 insertions, 172 deletions

diff --git a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/IBuildObject.java b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/IBuildObject.java
index 335c2239c7e..1cce486b013 100644
--- a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/IBuildObject.java
+++ b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/IBuildObject.java
@@ -16,10 +16,6 @@ public interface IBuildObject {
 
 	public String getId();
 
-	public void setId(String id);
-	
 	public String getName();
 	
-	public void setName(String name);
-		
 }
diff --git a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/IConfiguration.java b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/IConfiguration.java
index 5f03a2d9808..da26cb1afeb 100644
--- a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/IConfiguration.java
+++ b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/IConfiguration.java
@@ -37,4 +37,19 @@ public interface IConfiguration extends IBuildObject {
 	 */
 	public ITool[] getTools();
 	
+	/**
+	 * Sets an option value for this configuration.
+	 * 
+	 * @param option
+	 * @param value
+	 */
+	public void setOption(IOption option, String value)
+		throws BuildException;
+	
+	/**
+	 * Sets an option value for this configuration.
+	 * @param option
+	 */
+	public void setOption(IOption option, String[] value)
+		throws BuildException;
 }
diff --git a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/IOption.java b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/IOption.java
index e3fa082a65c..7926ed79cb8 100644
--- a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/IOption.java
+++ b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/IOption.java
@@ -34,13 +34,6 @@ public interface IOption extends IBuildObject {
 	public IOptionCategory getCategory();
 	
 	/**
-	 * Set the option category for this option.
-	 * 
-	 * @param category
-	 */
-	public void setCategory(IOptionCategory category);
-	
-	/**
 	 * Returns the name of this option.
 	 * 
 	 * @return
@@ -68,35 +61,13 @@ public interface IOption extends IBuildObject {
 	 * 
 	 * @return
 	 */
-	public String getStringValue();
+	public String getStringValue() throws BuildException;
 	
 	/**
 	 * Returns the current value for this option if it is a List of Strings.
 	 * 
 	 * @return
 	 */
-	public String [] getStringListValue();
+	public String [] getStringListValue() throws BuildException;
 	
-	/**
-	 * Sets the value for this option in a given configuration.
-	 * A new instance of the option for the configuration may be created.
-	 * The appropriate new option is returned.
-	 * 
-	 * @param config
-	 * @param value
-	 */
-	public IOption setValue(IConfiguration config, String value)
-		throws BuildException;
-
-	/**
-	 * Sets the value for this option in a given configuration.
-	 * A new instance of the option for the configuration may be created.
-	 * The appropriate new option is returned.
-	 * 
-	 * @param config
-	 * @param value
-	 */
-	public IOption setValue(IConfiguration config, String[] value)
-		throws BuildException;
-
 }
diff --git a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/ITarget.java b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/ITarget.java
index cb2c9dd479c..c1afcc8a8e3 100644
--- a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/ITarget.java
+++ b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/ITarget.java
@@ -45,4 +45,24 @@ public interface ITarget extends IBuildObject {
 	 */
 	public IConfiguration[] getConfigurations();
 
+	/**
+	 * Creates a new configuration for the target.  It is populated with
+	 * the tools defined for that target and options set at their defaults.
+	 * 
+	 * @param id id for this configuration.
+	 * @return
+	 */
+	public IConfiguration createConfiguration(String id);
+	
+	/**
+	 * Creates a configuration for the target populated with the tools and
+	 * options settings from the parent configuration.  As options and tools
+	 * change in the parent, unoverridden values are updated in the child
+	 * config as well.
+	 * 
+	 * @param parent
+	 * @param id
+	 * @return
+	 */
+	public IConfiguration createConfiguration(IConfiguration parent, String id);
 }
diff --git a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/ManagedBuildManager.java b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/ManagedBuildManager.java
index e98142f39a8..25605d1648d 100644
--- a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/ManagedBuildManager.java
+++ b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/core/build/managed/ManagedBuildManager.java
@@ -123,7 +123,7 @@ public class ManagedBuildManager {
 	}
 
 	/**
-	 * Adds a new target to the resource based on the parentTarget.
+	 * Creates a new target for the resource based on the parentTarget.
 	 * 
 	 * @param resource
 	 * @param parentTarget
@@ -156,6 +156,26 @@ public class ManagedBuildManager {
 	}
 	
 	/**
+	 * Set the string value for an option for a given config.
+	 * 
+	 * @param config
+	 * @param option
+	 * @param value
+	 */
+	public static void setOption(IConfiguration config, IOption option, String value) {
+	}
+	
+	/**
+	 * Set the string array value for an option for a given config.
+	 * 
+	 * @param config
+	 * @param option
+	 * @param value
+	 */
+	public static void setOption(IConfiguration config, IOption option, String[] value) {
+		
+	}
+	/**
 	 * Saves the build information associated with a project and all resources
 	 * in the project to the build info file.
 	 * 
diff --git a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/internal/core/build/managed/Configuration.java b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/internal/core/build/managed/Configuration.java
index 4b3cd43176b..5978512cefb 100644
--- a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/internal/core/build/managed/Configuration.java
+++ b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/internal/core/build/managed/Configuration.java
@@ -13,11 +13,15 @@ package org.eclipse.cdt.internal.core.build.managed;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.eclipse.cdt.core.build.managed.BuildException;
 import org.eclipse.cdt.core.build.managed.IConfiguration;
+import org.eclipse.cdt.core.build.managed.IOption;
 import org.eclipse.cdt.core.build.managed.ITarget;
 import org.eclipse.cdt.core.build.managed.ITool;
 import org.eclipse.core.resources.IResource;
 import org.eclipse.core.runtime.IConfigurationElement;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
 
 /**
  * 
@@ -27,17 +31,29 @@ public class Configuration extends BuildObject implements IConfiguration {
 	private ITarget target;
 	private IConfiguration parent;
 	private List toolReferences;
-	
-	public Configuration(Target target) {
+
+	/**
+	 * A fresh new configuration for a target.
+	 * @param target
+	 * @param id
+	 */	
+	public Configuration(Target target, String id) {
+		this.id = id;
 		this.target = target;
+		
+		target.addConfiguration(this);
 	}
 
-	public Configuration(IConfiguration parent) {
+	public Configuration(Target target, IConfiguration parent, String id) {
+		this.id = id;
+		this.target = target;
 		this.parent = parent;
+		
+		target.addConfiguration(this);
 	}
 
 	public Configuration(Target target, IConfigurationElement element) {
-		this(target);
+		this.target = target;
 		
 		// id
 		setId(element.getAttribute("id"));
@@ -57,6 +73,20 @@ public class Configuration extends BuildObject implements IConfiguration {
 		}
 	}
 	
+	public void serealize(Document doc, Element element) {
+		element.setAttribute("id", id);
+		element.setAttribute("name", name);
+		if (parent != null)
+			element.setAttribute("parent", parent.getId());
+		
+		if (toolReferences != null)
+			for (int i = 0; i < toolReferences.size(); ++i) {
+				ToolReference toolRef = (ToolReference)toolReferences.get(i);
+				Element toolRefElement = doc.createElement("toolRef");
+				toolRef.serealize(doc, toolRefElement);
+			}
+	}
+	
 	/* (non-Javadoc)
 	 * @see org.eclipse.cdt.core.build.managed.IConfiguration#getName()
 	 */
@@ -124,4 +154,37 @@ public class Configuration extends BuildObject implements IConfiguration {
 			toolReferences = new ArrayList();
 		toolReferences.add(toolRef);
 	}
+	
+	public OptionReference createOptionReference(IOption option) {
+		if (option instanceof OptionReference) {
+			OptionReference optionRef = (OptionReference)option;
+			ToolReference toolRef = optionRef.getToolReference();
+			if (toolRef.getConfiguration().equals(this))
+				return optionRef;
+			else {
+				toolRef = new ToolReference(this, toolRef);
+				return toolRef.createOptionReference(option);
+			}
+		} else {
+			ToolReference toolRef = getToolReference(option.getTool());
+			if (toolRef == null)
+				toolRef = new ToolReference(this, option.getTool());
+			return toolRef.createOptionReference(option);
+		}
+	}
+
+	/* (non-Javadoc)
+	 * @see org.eclipse.cdt.core.build.managed.IConfiguration#setOption(org.eclipse.cdt.core.build.managed.IOption, java.lang.String)
+	 */
+	public void setOption(IOption option, String value) throws BuildException {
+		createOptionReference(option).setValue(value);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.eclipse.cdt.core.build.managed.IConfiguration#setOption(org.eclipse.cdt.core.build.managed.IOption, java.lang.String[])
+	 */
+	public void setOption(IOption option, String[] value) throws BuildException {
+		createOptionReference(option).setValue(value);
+	}
+
 }
diff --git a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/internal/core/build/managed/OptionReference.java b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/internal/core/build/managed/OptionReference.java
index 16e4b7b715a..9043afcb529 100644
--- a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/internal/core/build/managed/OptionReference.java
+++ b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/internal/core/build/managed/OptionReference.java
@@ -10,11 +10,13 @@
  **********************************************************************/
 package org.eclipse.cdt.internal.core.build.managed;
 
-import org.eclipse.cdt.core.build.managed.IConfiguration;
+import org.eclipse.cdt.core.build.managed.BuildException;
 import org.eclipse.cdt.core.build.managed.IOption;
 import org.eclipse.cdt.core.build.managed.IOptionCategory;
 import org.eclipse.cdt.core.build.managed.ITool;
 import org.eclipse.core.runtime.IConfigurationElement;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
 
 /**
  * 
@@ -22,121 +24,127 @@ import org.eclipse.core.runtime.IConfigurationElement;
 public class OptionReference implements IOption {
 
 	private IOption option;
-	private ITool tool;
-
-	public OptionReference(IOption option, ITool tool) {
+	private ToolReference owner;
+	private Object value;
+
+	/**
+	 * Created internally.
+	 * 
+	 * @param owner
+	 * @param option
+	 */
+	public OptionReference(ToolReference owner, IOption option) {
+		this.owner = owner;
 		this.option = option;
-		this.tool = tool;
+		
+		owner.addOptionReference(this);
 	}
 
+	/**
+	 * Created from extension.
+	 * 
+	 * @param owner
+	 * @param element
+	 */
 	public OptionReference(ToolReference owner, IConfigurationElement element) {
-		this.tool = owner;
+		this.owner = owner;
+		option = owner.getOption(element.getAttribute("id"));
 		
-		option = tool.getOption(element.getAttribute("id"));
+		owner.addOptionReference(this);
 	}
 
+	/**
+	 * Created from project file.
+	 * 
+	 * @param owner
+	 * @param element
+	 */
+	public OptionReference(ToolReference owner, Element element) {
+		this.owner = owner;	
+		option = owner.getOption(element.getAttribute("id"));
+		
+		owner.addOptionReference(this);
+	}
+	
+	/**
+	 * Write out to project file.
+	 * 
+	 * @param doc
+	 * @param element
+	 */
+	public void serealize(Document doc, Element element) {
+		element.setAttribute("id", option.getId());
+		option = owner.getOption(element.getAttribute("id"));
+	}
+	
 	/* (non-Javadoc)
 	 * @see org.eclipse.cdt.core.build.managed.IOption#getApplicableValues()
 	 */
 	public String[] getApplicableValues() {
-		// TODO Auto-generated method stub
-		return null;
+		return option.getApplicableValues();
 	}
 
 	/* (non-Javadoc)
 	 * @see org.eclipse.cdt.core.build.managed.IOption#getCategory()
 	 */
 	public IOptionCategory getCategory() {
-		// TODO Auto-generated method stub
-		return null;
+		return option.getCategory();
 	}
 
 	/* (non-Javadoc)
 	 * @see org.eclipse.cdt.core.build.managed.IBuildObject#getName()
 	 */
 	public String getName() {
-		// TODO Auto-generated method stub
-		return null;
+		return option.getName();
 	}
 
 	/* (non-Javadoc)
 	 * @see org.eclipse.cdt.core.build.managed.IOption#getStringListValue()
 	 */
-	public String[] getStringListValue() {
-		// TODO Auto-generated method stub
-		return null;
+	public String[] getStringListValue() throws BuildException {
+		if (value == null)
+			return option.getStringListValue();
+		else if (getValueType() == IOption.STRING_LIST)
+			return (String[])value;
+		else
+			throw new BuildException("bad value type");
 	}
 
 	/* (non-Javadoc)
 	 * @see org.eclipse.cdt.core.build.managed.IOption#getStringValue()
 	 */
-	public String getStringValue() {
-		// TODO Auto-generated method stub
-		return null;
+	public String getStringValue() throws BuildException {
+		if (value == null)
+			return option.getStringValue();
+		else if (getValueType() == IOption.STRING)
+			return (String)value;
+		else
+			throw new BuildException("bad value type");
 	}
 
 	/* (non-Javadoc)
 	 * @see org.eclipse.cdt.core.build.managed.IOption#getTool()
 	 */
 	public ITool getTool() {
-		// TODO Auto-generated method stub
-		return null;
+		return owner;
 	}
 
+	public ToolReference getToolReference() {
+		return owner;
+	}
+	
 	/* (non-Javadoc)
 	 * @see org.eclipse.cdt.core.build.managed.IOption#getValueType()
 	 */
 	public int getValueType() {
-		// TODO Auto-generated method stub
-		return 0;
-	}
-
-	/* (non-Javadoc)
-	 * @see org.eclipse.cdt.core.build.managed.IOption#setCategory(org.eclipse.cdt.core.build.managed.IOptionCategory)
-	 */
-	public void setCategory(IOptionCategory category) {
-		// TODO Auto-generated method stub
-
-	}
-
-	/* (non-Javadoc)
-	 * @see org.eclipse.cdt.core.build.managed.IOption#setStringValue(org.eclipse.cdt.core.build.managed.IConfiguration, java.lang.String)
-	 */
-	public IOption setValue(IConfiguration config, String value) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	/* (non-Javadoc)
-	 * @see org.eclipse.cdt.core.build.managed.IOption#setStringValue(org.eclipse.cdt.core.build.managed.IConfiguration, java.lang.String[])
-	 */
-	public IOption setValue(IConfiguration config, String[] value) {
-		// TODO Auto-generated method stub
-		return null;
+		return option.getValueType();
 	}
 
 	/* (non-Javadoc)
 	 * @see org.eclipse.cdt.core.build.managed.IBuildObject#getId()
 	 */
 	public String getId() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	/* (non-Javadoc)
-	 * @see org.eclipse.cdt.core.build.managed.IBuildObject#setId(java.lang.String)
-	 */
-	public void setId(String id) {
-		// TODO Auto-generated method stub
-
-	}
-
-	/* (non-Javadoc)
-	 * @see org.eclipse.cdt.core.build.managed.IBuildObject#setName(java.lang.String)
-	 */
-	public void setName(String name) {
-		// TODO Auto-generated method stub
-
+		return option.getId();
 	}
 
 	public boolean references(IOption target) {
@@ -151,4 +159,17 @@ public class OptionReference implements IOption {
 			return option.equals(target);
 	}
 
+	public void setValue(String value) throws BuildException {
+		if (getValueType() == IOption.STRING)
+			this.value = value;
+		else
+			throw new BuildException("bad value type");
+	}
+	
+	public void setValue(String [] value) throws BuildException {
+		if (getValueType() == IOption.STRING_LIST)
+			this.value = value;
+		else
+			throw new BuildException("bad value type");
+	}
 }
diff --git a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/internal/core/build/managed/Target.java b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/internal/core/build/managed/Target.java
index 3eab91f50f6..4799b0dc6d5 100644
--- a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/internal/core/build/managed/Target.java
+++ b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/internal/core/build/managed/Target.java
@@ -15,12 +15,10 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import org.eclipse.cdt.core.build.managed.BuildException;
 import org.eclipse.cdt.core.build.managed.IConfiguration;
 import org.eclipse.cdt.core.build.managed.ITarget;
 import org.eclipse.cdt.core.build.managed.ITool;
 import org.eclipse.cdt.core.build.managed.ManagedBuildManager;
-import org.eclipse.core.resources.IProject;
 import org.eclipse.core.resources.IResource;
 import org.eclipse.core.runtime.IConfigurationElement;
 import org.w3c.dom.Document;
@@ -45,15 +43,15 @@ public class Target extends BuildObject implements ITarget {
 	}
 	
 	/**
-	 * Create a target owned by a resource based on a parent target 
+	 * Create a target owned by a resource based on a parent target
+	 * 
+	 * @param owner 
 	 * @param parent
 	 */
 	public Target(IResource owner, ITarget parent) {
 		this(owner);
 		this.parent = parent;
 
-		inheritConfigs();
-
 		// Copy the parent's identity
 		setId(parent.getId());		
 		setName(parent.getName());
@@ -80,13 +78,9 @@ public class Target extends BuildObject implements ITarget {
 
 		// parent
 		String parentId = element.getAttribute("parent");
-		if (parentId != null) {
+		if (parentId != null)
 			parent = ManagedBuildManager.getTarget(null, parentId);
 
-			// Inherit the configs from the parent
-			inheritConfigs();
-		}
-
 		// isAbstract
 		if ("true".equals(element.getAttribute("isAbstract")))
 			isAbstract = true;
@@ -103,6 +97,12 @@ public class Target extends BuildObject implements ITarget {
 
 	}
 
+	/**
+	 * Create target from project file
+	 * 
+	 * @param buildInfo
+	 * @param element
+	 */
 	public Target(ResourceBuildInfo buildInfo, Element element) {
 		this(buildInfo.getOwner());
 		
@@ -117,27 +117,30 @@ public class Target extends BuildObject implements ITarget {
 
 		// parent
 		String parentId = element.getAttribute("parent");
-		if (parentId != null) {
+		if (parentId != null)
 			parent = ManagedBuildManager.getTarget(null, parentId);
 
-			// Inherit the configs from the parent
-			inheritConfigs();
-		}
-
 		// isAbstract
 		if ("true".equals(element.getAttribute("isAbstract")))
 			isAbstract = true;
 
 	}
-	private void inheritConfigs() {
-		IConfiguration[] parentConfigs = parent.getConfigurations();
-		if (parentConfigs.length > 0)
-			configurations = new ArrayList(parentConfigs.length);
-		for (int i = 0; i < parentConfigs.length; ++i)
-			configurations.add(new Configuration(parentConfigs[i]));
+	
+	public void serialize(Document doc, Element element) {
+		element.setAttribute("id", getId());
+		element.setAttribute("name", getName());
+		if (parent != null)
+			element.setAttribute("parent", parent.getId());
+		element.setAttribute("isAbstract", isAbstract ? "true" : "false");
 		
+		if (configurations != null)
+			for (int i = 0; i < configurations.size(); ++i) {
+				Configuration config = (Configuration)configurations.get(i);
+				Element configElement = doc.createElement("configuration");
+				config.serealize(doc, configElement);
+			}
 	}
-	
+
 	public String getName() {
 		return (name == null && parent != null) ? parent.getName() : name;
 	}
@@ -209,47 +212,25 @@ public class Target extends BuildObject implements ITarget {
 		configurations.add(configuration);
 	}
 	
-	public IConfiguration createConfiguration()
-		throws BuildException
-	{
-		IConfiguration config = new Configuration(this);
-		addLocalConfiguration(config);
-		return config;
-	}
-
-	public IConfiguration createConfiguration(IConfiguration parentConfig)
-		throws BuildException
-	{
-		IResource parentOwner = parentConfig.getOwner();
-		
-		if (owner instanceof IProject) {
-			// parent must be owned by the same project
-			if (!owner.equals(parentOwner))
-				throw new BuildException("addConfiguration: parent must be in same project");
-		} else {
-			// parent must be owned by the project
-			if (!owner.getProject().equals(parentOwner))
-				throw new BuildException("addConfiguration: parent must be in owning project");
-		}
-
-		// Validation passed
-		IConfiguration config = new Configuration(parentConfig);
-		addLocalConfiguration(config);
-		return config;
-	}
-
 	/* (non-Javadoc)
 	 * @see org.eclipse.cdt.core.build.managed.ITarget#isAbstract()
 	 */
 	public boolean isAbstract() {
 		return isAbstract;
 	}
-	
-	public void serialize(Document doc, Element element) {
-		element.setAttribute("id", getId());
-		element.setAttribute("name", getName());
-		if (parent != null)
-			element.setAttribute("parent", parent.getId());
+
+	/* (non-Javadoc)
+	 * @see org.eclipse.cdt.core.build.managed.ITarget#createConfiguration()
+	 */
+	public IConfiguration createConfiguration(String id) {
+		return new Configuration(this, id);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.eclipse.cdt.core.build.managed.ITarget#createConfiguration(org.eclipse.cdt.core.build.managed.IConfiguration)
+	 */
+	public IConfiguration createConfiguration(IConfiguration parent, String id) {
+		return new Configuration(this, parent, id);
 	}
 
 }
diff --git a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/internal/core/build/managed/ToolReference.java b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/internal/core/build/managed/ToolReference.java
index f261c89cdd6..ff1efc8761f 100644
--- a/core/org.eclipse.cdt.core/build/org/eclipse/cdt/internal/core/build/managed/ToolReference.java
+++ b/core/org.eclipse.cdt.core/build/org/eclipse/cdt/internal/core/build/managed/ToolReference.java
@@ -20,6 +20,8 @@ import org.eclipse.cdt.core.build.managed.IOptionCategory;
 import org.eclipse.cdt.core.build.managed.ITarget;
 import org.eclipse.cdt.core.build.managed.ITool;
 import org.eclipse.core.runtime.IConfigurationElement;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
 
 /**
  * 
@@ -31,11 +33,25 @@ public class ToolReference implements ITool {
 	private List optionReferences;
 	private Map optionRefMap;
 	
-	public ToolReference(ITool parent, IConfiguration owner) {
-		this.parent = parent;
+	/**
+	 * Created on the fly.
+	 * 
+	 * @param owner
+	 * @param parent
+	 */
+	public ToolReference(Configuration owner, ITool parent) {
 		this.owner = owner;
+		this.parent = parent;
+		
+		owner.addToolReference(this);
 	}
 	
+	/**
+	 * Created from extension.
+	 * 
+	 * @param owner
+	 * @param element
+	 */
 	public ToolReference(Configuration owner, IConfigurationElement element) {
 		this.owner = owner;
 		
@@ -51,6 +67,24 @@ public class ToolReference implements ITool {
 			}
 		}
 	}
+
+	public ToolReference(Configuration owner, Element element) {
+	}
+
+	public void serealize(Document doc, Element element) {
+		element.setAttribute("id", parent.getId());
+		
+		if (optionReferences != null)
+			for (int i = 0; i < optionReferences.size(); ++i) {
+				OptionReference optionRef = (OptionReference)optionReferences.get(i);
+				Element optionRefElement = doc.createElement("optionRef");
+				optionRef.serealize(doc, optionRefElement);
+			}
+	}
+
+	public IConfiguration getConfiguration() {
+		return owner;
+	}
 	
 	public ITool getTool() {
 		return parent;
@@ -144,6 +178,10 @@ public class ToolReference implements ITool {
 		return null;
 	}
 	
+	public OptionReference createOptionReference(IOption option) {
+		return new OptionReference(this, option);
+	}
+	
 	public void addOptionReference(OptionReference optionRef) {
 		if (optionReferences == null)
 			optionReferences = new ArrayList();
@@ -158,12 +196,4 @@ public class ToolReference implements ITool {
 		return null;
 	}
 
-	/* (non-Javadoc)
-	 * @see org.eclipse.cdt.core.build.managed.ITool#createOption(org.eclipse.cdt.core.build.managed.IConfiguration)
-	 */
-	public IOption createOption(IConfiguration config) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
 }