Use remote file and launch proxies.

	*
src/org/eclipse/linuxtools/internal/cdt/autotools/core/configure/AutotoolsConfigurationManager.java
(applyConfigs):
	Use remote file proxy to save .autotools file.
	(getSavedConfigs): Use remote file proxy to access .autotools file.
	*
src/org/eclipse/linuxtools/internal/cdt/autotools/core/AutotoolsNewMakeGenerator.java
(runScript): Use
	remote launch proxy.
	(getWinOSType): Ditto.
	(runCommand): Ditto.
	(makefileCvsExists): Use remote file proxy.
	(regenerateMakefiles): Ditto.
	(createDirectory): Ditto.
	(initialize): Get remote file proxy for current project.
	*
src/org/eclipse/linuxtools/internal/cdt/autotools/core/PkgconfigErrorResolution.java
(run): Use
	remote command launch proxy.
	*
src/org/eclipse/linuxtools/internal/cdt/autotools/core/RemoteProxyManager.java:
New class.

8 files changed, 183 insertions, 93 deletions

diff --git a/autotools/org.eclipse.linuxtools.cdt.autotools.core/ChangeLog b/autotools/org.eclipse.linuxtools.cdt.autotools.core/ChangeLog
index a7818f5c4d..08a7a097f4 100644
--- a/autotools/org.eclipse.linuxtools.cdt.autotools.core/ChangeLog
+++ b/autotools/org.eclipse.linuxtools.cdt.autotools.core/ChangeLog
@@ -1,3 +1,20 @@
+2011-09-08  Jeff Johnston  <jjohnstn@redhat.com>
+
+	* src/org/eclipse/linuxtools/internal/cdt/autotools/core/configure/AutotoolsConfigurationManager.java (applyConfigs):
+	Use remote file proxy to save .autotools file.
+	(getSavedConfigs): Use remote file proxy to access .autotools file.
+	* src/org/eclipse/linuxtools/internal/cdt/autotools/core/AutotoolsNewMakeGenerator.java (runScript): Use
+	remote launch proxy.
+	(getWinOSType): Ditto.
+	(runCommand): Ditto.
+	(makefileCvsExists): Use remote file proxy.
+	(regenerateMakefiles): Ditto.
+	(createDirectory): Ditto.
+	(initialize): Get remote file proxy for current project.
+	* src/org/eclipse/linuxtools/internal/cdt/autotools/core/PkgconfigErrorResolution.java (run): Use
+	remote command launch proxy.
+	* src/org/eclipse/linuxtools/internal/cdt/autotools/core/RemoteProxyManager.java: New class.
+
 2011-08-18  Jeff Johnston  <jjohnstn@redhat.com>
 
 	* src/org/eclipse/linuxtools/internal/cdt/autotools/core/LocalFileProxy.java: New file.
diff --git a/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/AutotoolsNewMakeGenerator.java b/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/AutotoolsNewMakeGenerator.java
index 9ac79d5d3b..be1189ad74 100644
--- a/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/AutotoolsNewMakeGenerator.java
+++ b/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/AutotoolsNewMakeGenerator.java
@@ -26,7 +26,6 @@ import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
 import org.eclipse.cdt.core.CCorePlugin;
-import org.eclipse.cdt.core.CommandLauncher;
 import org.eclipse.cdt.core.ConsoleOutputStream;
 import org.eclipse.cdt.core.ICDescriptor;
 import org.eclipse.cdt.core.envvar.IEnvironmentVariable;
@@ -153,7 +152,7 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
 	public void initialize(IProject project, IManagedBuildInfo info,
 			IProgressMonitor monitor) {
 		this.project = project;
-		proxy = FileProxyManager.getInstance().getFileProxy(project);
+		proxy = RemoteProxyManager.getInstance().getFileProxy(project);
 		ICProjectDescription pdesc = CCorePlugin.getDefault().getProjectDescription(project);
 		this.cdesc = pdesc.getActiveConfiguration();
 		this.cfg = info.getDefaultConfiguration();
@@ -777,7 +776,8 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
 		consoleOutStream.flush();
 
 		// Get a launcher for the config command
-		CommandLauncher launcher = new CommandLauncher();
+		IRemoteCommandLauncher launcher = RemoteProxyManager.getInstance().getLauncher(project);
+		
 		// Set the environment
 		IEnvironmentVariable variables[] = 
 			CCorePlugin.getDefault().getBuildEnvironmentManager().getVariables(cdesc, true);
@@ -800,7 +800,7 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
 		OutputStream stdout = epm.getOutputStream();
 		OutputStream stderr = stdout;
 
-		launcher.showCommand(true);
+//		launcher.showCommand(true);
 		Process proc = launcher.execute(commandPath, configTargets, env,
 				runPath, new NullProgressMonitor());
 		if (proc != null) {
@@ -812,7 +812,7 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
 			}
 
 			if (launcher.waitAndRead(stdout, stderr, new SubProgressMonitor(
-					monitor, IProgressMonitor.UNKNOWN)) != CommandLauncher.OK) {
+					monitor, IProgressMonitor.UNKNOWN)) != IRemoteCommandLauncher.OK) {
 				errMsg = launcher.getErrorMessage();
 			}
 
@@ -889,7 +889,7 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
 	private String getWinOSType() {
 		if (winOSType.equals("")) {
 			try {
-				CommandLauncher launcher = new CommandLauncher();
+				IRemoteCommandLauncher launcher = RemoteProxyManager.getInstance().getLauncher(project);
 				ByteArrayOutputStream out = new ByteArrayOutputStream();
 				launcher.execute(
 						new Path(SHELL_COMMAND), //$NON-NLS-1$
@@ -897,7 +897,7 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
 						new String[0],
 						new Path("."), //$NON-NLS-1$
 						new NullProgressMonitor());
-				if (launcher.waitAndRead(out, out) == CommandLauncher.OK)
+				if (launcher.waitAndRead(out, out, new NullProgressMonitor()) == IRemoteCommandLauncher.OK)
 					winOSType = out.toString().trim();
 			} catch (CoreException e) {
 				// do nothing
@@ -911,7 +911,7 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
     // doesn't cause Makefile to choke. For Cygwin we use /cygdrive/C/a/b
     private String getPathString(IPath path) {
             String s = path.toString();
-            if (Platform.getOS().equals(Platform.OS_WIN32)) {
+            if (RemoteProxyManager.getInstance().getOS(project).equals(Platform.OS_WIN32)) {
             	if (getWinOSType().equals("cygwin")) {
                     s = s.replaceAll("^([A-Z])(:)", "/cygdrive/$1");            		
             	} else {
@@ -946,8 +946,9 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
         configTargets[0] = getPathString(commandPath);
 
         // Fix for bug #343731
-        if (Platform.getOS().equals(Platform.OS_WIN32)
-                || Platform.getOS().equals(Platform.OS_MACOSX)) {
+        RemoteProxyManager rpm = RemoteProxyManager.getInstance();
+        if (rpm.getOS(project).equals(Platform.OS_WIN32)
+                || rpm.getOS(project).equals(Platform.OS_MACOSX)) {
         	removePWD = true;
             // Neither Mac or Windows support calling scripts directly.
             String command = null;
@@ -1004,7 +1005,7 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
 		consoleOutStream.flush();
 
 		// Get a launcher for the config command
-		CommandLauncher launcher = new CommandLauncher();
+		IRemoteCommandLauncher launcher = RemoteProxyManager.getInstance().getLauncher(project);
 		// Set the environment
 		IEnvironmentVariable variables[] = 
 			CCorePlugin.getDefault().getBuildEnvironmentManager().getVariables(cdesc, true);
@@ -1033,7 +1034,7 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
 		OutputStream stdout = epm.getOutputStream();
 		OutputStream stderr = stdout;
 
-		launcher.showCommand(true);
+//		launcher.showCommand(true);
 		// Run the shell script via shell command.
 		Process proc = launcher.execute(new Path(SHELL_COMMAND), configTargets, env,
 				runPath, new NullProgressMonitor());
@@ -1046,7 +1047,7 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
 			}
 
 			if (launcher.waitAndRead(stdout, stderr, new SubProgressMonitor(
-					monitor, IProgressMonitor.UNKNOWN)) != CommandLauncher.OK) {
+					monitor, IProgressMonitor.UNKNOWN)) != IRemoteCommandLauncher.OK) {
 				errMsg = launcher.getErrorMessage();
 			}
 
diff --git a/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/FileProxyManager.java b/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/FileProxyManager.java
deleted file mode 100644
index 4fd67c7da2..0000000000
--- a/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/FileProxyManager.java
+++ /dev/null
@@ -1,30 +0,0 @@
-package org.eclipse.linuxtools.internal.cdt.autotools.core;
-
-import org.eclipse.core.resources.IProject;
-
-public class FileProxyManager {
-	
-	private static FileProxyManager manager;
-	private LocalFileProxy lfp;
-	
-	private FileProxyManager() {
-		// do nothing
-	}
-	
-	public static FileProxyManager getInstance() {
-		if (manager == null)
-			manager = new FileProxyManager();
-		return manager;
-	}
-	
-	LocalFileProxy getLocalFileProxy() {
-		if (lfp == null)
-			lfp = new LocalFileProxy();
-		return lfp;
-	}
-	
-	IRemoteFileProxy getFileProxy(IProject project) {
-		return getLocalFileProxy();
-	}
-
-}
diff --git a/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/IRemoteCommandLauncher.java b/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/IRemoteCommandLauncher.java
new file mode 100644
index 0000000000..880af09e33
--- /dev/null
+++ b/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/IRemoteCommandLauncher.java
@@ -0,0 +1,17 @@
+package org.eclipse.linuxtools.internal.cdt.autotools.core;
+
+import java.io.OutputStream;
+
+import org.eclipse.core.runtime.CoreException;
+import org.eclipse.core.runtime.IPath;
+import org.eclipse.core.runtime.IProgressMonitor;
+
+public interface IRemoteCommandLauncher {
+	
+	public final static int OK = 0;
+	
+	public Process execute(IPath commandPath, String[] args, String[] env, IPath changeToDirectory, IProgressMonitor monitor) throws CoreException;
+	public int waitAndRead(OutputStream output, OutputStream err, IProgressMonitor monitor);
+	public String getErrorMessage();
+	
+}
\ No newline at end of file
diff --git a/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/LocalLauncher.java b/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/LocalLauncher.java
new file mode 100644
index 0000000000..eead59b831
--- /dev/null
+++ b/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/LocalLauncher.java
@@ -0,0 +1,34 @@
+package org.eclipse.linuxtools.internal.cdt.autotools.core;
+
+import java.io.OutputStream;
+
+import org.eclipse.cdt.core.CommandLauncher;
+import org.eclipse.core.runtime.CoreException;
+import org.eclipse.core.runtime.IPath;
+import org.eclipse.core.runtime.IProgressMonitor;
+
+public class LocalLauncher implements IRemoteCommandLauncher {
+
+	private CommandLauncher launcher;
+	
+	public LocalLauncher() {
+		launcher = new CommandLauncher();
+	}
+	
+	public Process execute(IPath commandPath, String[] args, String[] env,
+			IPath changeToDirectory, IProgressMonitor monitor)
+			throws CoreException {
+		launcher.showCommand(true);
+		return launcher.execute(commandPath, args, env, changeToDirectory, monitor);
+	}
+
+	public int waitAndRead(OutputStream output, OutputStream err,
+			IProgressMonitor monitor) {
+		return launcher.waitAndRead(output, err, monitor);
+	}
+	
+	public String getErrorMessage() {
+		return launcher.getErrorMessage();
+	}
+
+}
diff --git a/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/PkgconfigErrorResolution.java b/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/PkgconfigErrorResolution.java
index 0c91aad758..dae20e9c2d 100644
--- a/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/PkgconfigErrorResolution.java
+++ b/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/PkgconfigErrorResolution.java
@@ -14,9 +14,10 @@ import java.io.IOException;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.eclipse.cdt.core.CommandLauncher;
 import org.eclipse.cdt.core.ConsoleOutputStream;
 import org.eclipse.core.resources.IMarker;
+import org.eclipse.core.resources.IProject;
+import org.eclipse.core.resources.IResource;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IPath;
 import org.eclipse.core.runtime.NullProgressMonitor;
@@ -56,7 +57,9 @@ public class PkgconfigErrorResolution implements IMarkerResolution {
 		IPath pkgconfigPath = 
 			new Path("/usr/lib/pkgconfig").append(pkgName+".pc"); //$NON-NLS-1$ //$NON-NLS-2$
 		// Get a launcher for the config command
-		CommandLauncher launcher = new CommandLauncher();
+		IResource resource = marker.getResource();
+		IProject project = resource.getProject();
+		IRemoteCommandLauncher launcher = RemoteProxyManager.getInstance().getLauncher(project);
 		IPath commandPath = new Path("rpm"); //$NON-NLS-1$
 		String[] commandArgs = 
 			new String[] {"-q", //$NON-NLS-1$
@@ -78,7 +81,7 @@ public class PkgconfigErrorResolution implements IMarkerResolution {
 				} catch (IOException e) {
 				}
 				if (launcher.waitAndRead(output, output, new NullProgressMonitor())
-						!= CommandLauncher.OK) {
+						!= IRemoteCommandLauncher.OK) {
 					AutotoolsPlugin.logErrorMessage(launcher.getErrorMessage());
 				} else {
 					String result = output.readBuffer();
diff --git a/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/RemoteProxyManager.java b/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/RemoteProxyManager.java
new file mode 100644
index 0000000000..63c815c394
--- /dev/null
+++ b/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/RemoteProxyManager.java
@@ -0,0 +1,38 @@
+package org.eclipse.linuxtools.internal.cdt.autotools.core;
+
+import org.eclipse.cdt.utils.Platform;
+import org.eclipse.core.resources.IProject;
+
+public class RemoteProxyManager {
+	
+	private static RemoteProxyManager manager;
+	private LocalFileProxy lfp;
+	
+	private RemoteProxyManager() {
+		// do nothing
+	}
+	
+	public static RemoteProxyManager getInstance() {
+		if (manager == null)
+			manager = new RemoteProxyManager();
+		return manager;
+	}
+	
+	LocalFileProxy getLocalFileProxy() {
+		if (lfp == null)
+			lfp = new LocalFileProxy();
+		return lfp;
+	}
+	
+	public IRemoteFileProxy getFileProxy(IProject project) {
+		return getLocalFileProxy();
+	}
+	
+	public IRemoteCommandLauncher getLauncher(IProject project) {
+		return new LocalLauncher();
+	}
+
+	public String getOS(IProject project) {
+		return Platform.getOS();
+	}
+}
diff --git a/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/configure/AutotoolsConfigurationManager.java b/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/configure/AutotoolsConfigurationManager.java
index 95c04bbccb..4fe5b4bc1a 100644
--- a/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/configure/AutotoolsConfigurationManager.java
+++ b/autotools/org.eclipse.linuxtools.cdt.autotools.core/src/org/eclipse/linuxtools/internal/cdt/autotools/core/configure/AutotoolsConfigurationManager.java
@@ -14,6 +14,8 @@ import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -35,6 +37,8 @@ import org.eclipse.cdt.managedbuilder.core.IOption;
 import org.eclipse.cdt.managedbuilder.core.ITool;
 import org.eclipse.cdt.managedbuilder.core.IToolChain;
 import org.eclipse.cdt.managedbuilder.core.ManagedBuildManager;
+import org.eclipse.core.filesystem.EFS;
+import org.eclipse.core.filesystem.IFileStore;
 import org.eclipse.core.resources.IProject;
 import org.eclipse.core.resources.IResource;
 import org.eclipse.core.resources.IResourceChangeEvent;
@@ -42,8 +46,12 @@ import org.eclipse.core.resources.IResourceChangeListener;
 import org.eclipse.core.resources.IResourceDelta;
 import org.eclipse.core.resources.IWorkspaceRoot;
 import org.eclipse.core.resources.ResourcesPlugin;
+import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IPath;
+import org.eclipse.core.runtime.NullProgressMonitor;
 import org.eclipse.linuxtools.cdt.autotools.core.AutotoolsPlugin;
+import org.eclipse.linuxtools.internal.cdt.autotools.core.IRemoteFileProxy;
+import org.eclipse.linuxtools.internal.cdt.autotools.core.RemoteProxyManager;
 import org.eclipse.linuxtools.internal.cdt.autotools.core.configure.AutotoolsConfiguration.Option;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -177,12 +185,14 @@ public class AutotoolsConfigurationManager implements IResourceChangeListener {
 		if (list == null) {
 			try {
 				IPath fileLocation = project.getLocation().append(CFG_FILE_NAME);
-				File dirFile = fileLocation.toFile();
+				IRemoteFileProxy proxy = RemoteProxyManager.getInstance().getFileProxy(project);
+				IFileStore f = proxy.getResource(fileLocation.toString());
 				Map<String, IAConfiguration> cfgList = new HashMap<String, IAConfiguration>();
 				DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
 				DocumentBuilder db = dbf.newDocumentBuilder();
-				if (dirFile.exists()) {
-					Document d = db.parse(dirFile);
+				if (f.fetchInfo().exists()) {
+					InputStream is = f.openInputStream(EFS.NONE, new NullProgressMonitor());
+					Document d = db.parse(is);
 					Element e = d.getDocumentElement();
 					// Get the stored configuration data
 					NodeList cfgs = e.getElementsByTagName("configuration"); // $NON-NLS-1$
@@ -235,6 +245,9 @@ public class AutotoolsConfigurationManager implements IResourceChangeListener {
 			} catch (IOException e) {
 				// TODO Auto-generated catch block
 				e.printStackTrace();
+			} catch (CoreException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
 			}
 		}
 		return list;
@@ -399,27 +412,44 @@ public class AutotoolsConfigurationManager implements IResourceChangeListener {
 			}
 			IProject project = (IProject)res;
 			IPath output = project.getLocation().append(CFG_FILE_NAME);
-			File f = output.toFile();
-			if (!f.exists())
-				f.createNewFile();
-			if (f.exists()) {
-				PrintWriter p = new PrintWriter(new BufferedWriter(new FileWriter(f)));
-				Map<String, IAConfiguration> cfgs = getSavedConfigs(project);
-				if (cfgs == null)
-					return;
-				p.println("<?xml version=\"1.0\" encoding=\"UTF-8\"?>"); //$NON-NLS-1$
-				p.println("<configurations>"); // $NON-NLS-1$
-				Option[] optionList = AutotoolsConfiguration.getOptionList();
-				HashSet<String> savedIds = new HashSet<String>();
-				setSyncing(true);
-				for (int x = 0; x < cfgds.length; ++x) {
-					ICConfigurationDescription cfgd = cfgds[x];
-					@SuppressWarnings("unused")
-					CConfigurationData data = cfgd.getConfigurationData();
-					String id = cfgd.getId();
-					savedIds.add(id);
-					IAConfiguration cfg = getTmpConfiguration(project, cfgd);
-					cfgs.put(id, cfg); // add to list in case we have a new configuration not yet added to Project Description
+			IRemoteFileProxy proxy = RemoteProxyManager.getInstance().getFileProxy(project);
+			IFileStore f = proxy.getResource(output.toString());
+			PrintWriter p = new PrintWriter(new BufferedWriter(new OutputStreamWriter(f.openOutputStream(EFS.NONE, new NullProgressMonitor()))));
+			Map<String, IAConfiguration> cfgs = getSavedConfigs(project);
+			if (cfgs == null)
+				return;
+			p.println("<?xml version=\"1.0\" encoding=\"UTF-8\"?>"); //$NON-NLS-1$
+			p.println("<configurations>"); // $NON-NLS-1$
+			Option[] optionList = AutotoolsConfiguration.getOptionList();
+			HashSet<String> savedIds = new HashSet<String>();
+			setSyncing(true);
+			for (int x = 0; x < cfgds.length; ++x) {
+				ICConfigurationDescription cfgd = cfgds[x];
+				@SuppressWarnings("unused")
+				CConfigurationData data = cfgd.getConfigurationData();
+				String id = cfgd.getId();
+				savedIds.add(id);
+				IAConfiguration cfg = getTmpConfiguration(project, cfgd);
+				cfgs.put(id, cfg); // add to list in case we have a new configuration not yet added to Project Description
+				p.println("<configuration id=\"" + id + "\">"); //$NON-NLS-1$ //$NON-NLS-2$ 
+				for (int j = 0; j < optionList.length; ++j) {
+					Option option = optionList[j];
+					IConfigureOption opt = cfg.getOption(option.getName());
+					if (!opt.isCategory())
+						p.println("<option id=\"" + option.getName() + "\" value=\"" + opt.getValue() + "\"/>"); //$NON-NLS-1$ //$NON-NLS-2$ // $NON-NLS-3$
+				}
+				p.println("</configuration>"); //$NON-NLS-1$
+				syncNameField(cfgd);
+			}
+			setSyncing(false);
+
+			// Put all the remaining configurations already saved back into the file.
+			// These represent deleted configurations, but confirmation has not occurred.
+			for (Iterator<String> i = cfgs.keySet().iterator(); i.hasNext(); ) {
+				String id = i.next();
+				// A remaining id won't appear in our savedIds list.
+				if (!savedIds.contains(id)) {
+					IAConfiguration cfg = cfgs.get(id);
 					p.println("<configuration id=\"" + id + "\">"); //$NON-NLS-1$ //$NON-NLS-2$ 
 					for (int j = 0; j < optionList.length; ++j) {
 						Option option = optionList[j];
@@ -428,31 +458,11 @@ public class AutotoolsConfigurationManager implements IResourceChangeListener {
 							p.println("<option id=\"" + option.getName() + "\" value=\"" + opt.getValue() + "\"/>"); //$NON-NLS-1$ //$NON-NLS-2$ // $NON-NLS-3$
 					}
 					p.println("</configuration>"); //$NON-NLS-1$
-					syncNameField(cfgd);
 				}
-				setSyncing(false);
-
-				// Put all the remaining configurations already saved back into the file.
-				// These represent deleted configurations, but confirmation has not occurred.
-				for (Iterator<String> i = cfgs.keySet().iterator(); i.hasNext(); ) {
-					String id = i.next();
-					// A remaining id won't appear in our savedIds list.
-					if (!savedIds.contains(id)) {
-						IAConfiguration cfg = cfgs.get(id);
-						p.println("<configuration id=\"" + id + "\">"); //$NON-NLS-1$ //$NON-NLS-2$ 
-						for (int j = 0; j < optionList.length; ++j) {
-							Option option = optionList[j];
-							IConfigureOption opt = cfg.getOption(option.getName());
-							if (!opt.isCategory())
-								p.println("<option id=\"" + option.getName() + "\" value=\"" + opt.getValue() + "\"/>"); //$NON-NLS-1$ //$NON-NLS-2$ // $NON-NLS-3$
-						}
-						p.println("</configuration>"); //$NON-NLS-1$
-					}
-				}
-				p.println("</configurations>");
-				p.close();
 			}
-		} catch (IOException e) {
+			p.println("</configurations>");
+			p.close();
+		} catch (CoreException e) {
 			AutotoolsPlugin.log(e);
 		}
 	}