//
// MakefileData.cs
//
// Author:
//   Ankit Jain <jankit@novell.com>
//
// Copyright (C) 2007 Novell, Inc (http://www.novell.com)
//
// Permission is hereby granted, free of charge, to any person obtaining
// a copy of this software and associated documentation files (the
// "Software"), to deal in the Software without restriction, including
// without limitation the rights to use, copy, modify, merge, publish,
// distribute, sublicense, and/or sell copies of the Software, and to
// permit persons to whom the Software is furnished to do so, subject to
// the following conditions:
// 
// The above copyright notice and this permission notice shall be
// included in all copies or substantial portions of the Software.
// 
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
// EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
// NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
// LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
// OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
// WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
//

using System;
using System.IO;
using System.Collections.Generic;
using System.Reflection;
using System.Text;
using System.Text.RegularExpressions;

using MonoDevelop.Core;
using MonoDevelop.Core.Serialization;
using MonoDevelop.Projects;
using MonoDevelop.Core.Assemblies;
using MonoDevelop.Ide;

namespace MonoDevelop.Autotools
{
	[DataItem ("MakefileInfo")]
	public class MakefileData : ICloneable
	{
		bool integrationEnabled;
		string relativeMakefileName;
		string buildTargetName;
		string cleanTargetName;
		string executeTargetName;
		Project ownerProject;
		CustomMakefile makefile;
		
		[ItemProperty ("ExcludedFiles")]
		[ProjectPathItemProperty("File", Scope="*")]
		List<string> excludedFiles = new List<string> ();
		
		IAssemblyContext assemblyContext;

		public MakefileData ()
		{
			relativeMakefileName = String.Empty;
			buildTargetName = "all";
			cleanTargetName = "clean";
			executeTargetName = String.Empty;
			ParallelProcesses = 1;
			
			assemblyContext = GetMonoRuntimeContext ();
			if (assemblyContext == null)
				integrationEnabled = false;
		}
		
		internal static IAssemblyContext GetMonoRuntimeContext ()
		{
			if (Runtime.SystemAssemblyService.CurrentRuntime.RuntimeId == "Mono")
				return Runtime.SystemAssemblyService.CurrentRuntime.AssemblyContext;
			else {
				foreach (TargetRuntime r in Runtime.SystemAssemblyService.GetTargetRuntimes ("Mono"))
					return r.AssemblyContext;
			}
			return null;
		}

		public Project OwnerProject {
			get { return ownerProject; }
			set {
				if (!Object.ReferenceEquals (ownerProject, value) && value != null) {
					//Setup handlers
					ProjectReferenceEventHandler refhandler = delegate {
						if (SyncReferences)
							dirty = true;
					};
					
					if (value is DotNetProject) {
						((DotNetProject)value).ReferenceRemovedFromProject += refhandler;
						((DotNetProject)value).ReferenceAddedToProject += refhandler;
					}

					ProjectFileEventHandler filehandler = delegate (object sender, ProjectFileEventArgs e) {
						MakefileVar var = null;
						switch (e.ProjectFile.BuildAction) {
						case "Compile":
							var = BuildFilesVar;
							break;
						case "Content":
							var = DeployFilesVar;
							break;
						case "EmbeddedResource":
							var = ResourcesVar;
							break;
						case "None":
							var = OthersVar;
							break;
						}
						if (var != null && var.Sync)
							dirty = true;
					};

					value.FileRemovedFromProject += filehandler;
					value.FileAddedToProject += filehandler;

					value.FilePropertyChangedInProject += delegate {
						dirty = true;
					};

					value.FileRenamedInProject += delegate {
						dirty = true;
					};
				}
				ownerProject = value;
				InitBuildVars ();
			}
		}

		[ItemProperty (DefaultValue = false)]
		public bool IntegrationEnabled {
			get { return integrationEnabled; }
			set { integrationEnabled = value;}
		}

		public bool SupportsIntegration {
			get { return IntegrationEnabled && !PropertyService.IsWindows; }
		}
		
		[ItemProperty (DefaultValue = "")]
		public string RelativeMakefileName {
			get {
				if (ownerProject == null)
					return relativeMakefileName;
				return ownerProject.GetRelativeChildPath (relativeMakefileName);
			}
			set {
				if (String.Compare (relativeMakefileName, value) == 0)
					return;

				relativeMakefileName = value;
				makefile = null;
				InitBuildVars ();
			}
		}

		public string AbsoluteMakefileName {
			get {
				if (ownerProject == null)
					return relativeMakefileName;
				return ownerProject.GetAbsoluteChildPath (relativeMakefileName);
			}
		}

		public string BaseDirectory {
			get {
				//FIXME: Check for AbsoluteMakefileName == null or empty
				return Path.GetDirectoryName (AbsoluteMakefileName);
			}
		}

		[ItemProperty (DefaultValue = "all")]
		public string BuildTargetName {
			get { return buildTargetName; }
			set { buildTargetName = value;}
		}

		[ItemProperty (DefaultValue = "clean")]
		public string CleanTargetName {
			get { return cleanTargetName; }
			set { cleanTargetName = value;}
		}

		[ItemProperty (DefaultValue = "")]
		public string ExecuteTargetName {
			get { return executeTargetName; }
			set { executeTargetName = value;}
		}
		
		/// <summary>
		/// The number of parallel build processes to use
		/// </summary>
		[ItemProperty (DefaultValue = 1)]
		public int ParallelProcesses { get; set; }

		//Makefile variables
		MakefileVar buildFilesVar;
		[ItemProperty]
		public MakefileVar BuildFilesVar {
			get {
				if (buildFilesVar == null)
					buildFilesVar = new MakefileVar ();
				return buildFilesVar;
			}
			set { buildFilesVar = value; }
		}

		MakefileVar deployFilesVar;
		[ItemProperty]
		public MakefileVar DeployFilesVar {
			get {
				if (deployFilesVar == null)
					deployFilesVar = new MakefileVar ();
				return deployFilesVar;
			}
			set { deployFilesVar = value; }
		}

		MakefileVar resourcesVar;
		[ItemProperty]
		public MakefileVar ResourcesVar {
			get {
				if (resourcesVar == null)
					resourcesVar = new MakefileVar ();
				return resourcesVar;
			}
			set { resourcesVar = value; }
		}

		MakefileVar othersVar;
		[ItemProperty]
		public MakefileVar OthersVar {
			get {
				if (othersVar == null)
					othersVar = new MakefileVar ();
				return othersVar;
			}
			set { othersVar = value; }
    		}

		//Individual Sync of *RefVar is ignored, instead
		//SyncReferences is used
		bool syncReferences = false;
		[ItemProperty (DefaultValue = false)]
		public bool SyncReferences {
			get { return syncReferences; }
			set {
				GacRefVar.Sync = value;
				AsmRefVar.Sync = value;
				ProjectRefVar.Sync =value;
				syncReferences = value;
			}
		}

		bool SaveReferences = true;

		bool isAutotoolsProject;
		[ItemProperty (DefaultValue = false)]
		public bool IsAutotoolsProject {
			get { return isAutotoolsProject; }
			set {
				if (isAutotoolsProject == value)
					return;
				isAutotoolsProject = value;
				configuredPackages = null;
			}
		}

		public bool UseAutotools {
			get { return ConfiguredPackages != null; }
		}

		MakefileVar gacRefVar;
		[ItemProperty]
		public MakefileVar GacRefVar {
			get {
				if (gacRefVar == null)
					gacRefVar = new MakefileVar ();
				return gacRefVar;
			}
			set { gacRefVar = value; }
		}

		MakefileVar asmRefVar;
		[ItemProperty]
		public MakefileVar AsmRefVar {
			get {
				if (asmRefVar == null)
					asmRefVar = new MakefileVar ();
				return asmRefVar;
			}
			set { asmRefVar = value; }
		}

		MakefileVar projectRefVar;
		[ItemProperty]
		public MakefileVar ProjectRefVar {
			get {
				if (projectRefVar == null)
					projectRefVar = new MakefileVar ();
				return projectRefVar;
			}
			set { projectRefVar = value; }
		}
		
		string errorRegex = String.Empty;
		[ItemProperty (Name = "MessageRegex/Error", DefaultValue = "")]
		public string CustomErrorRegex {
			get {
				if (MessageRegexName != "Custom")
					return String.Empty;
				return errorRegex;
			}
			set { errorRegex = value; }
		}
		
		string warningRegex = String.Empty;
		[ItemProperty (Name = "MessageRegex/Warning", DefaultValue = "")]
		public string CustomWarningRegex {
			get {
				if (MessageRegexName != "Custom")
					return String.Empty;
				return warningRegex;
			}
			set { warningRegex = value; }			
		}
		
		string messageRegexName = "C# (mcs)";
		[ItemProperty (Name = "MessageRegex/Name", DefaultValue = "C# (mcs)")]
		public string MessageRegexName {
			get { return messageRegexName; }
			set {
				if (value != "Custom") {
					// !Custom
					if (CompilerMessageRegex.ContainsKey (value)) {
						errorRegex = CompilerMessageRegex [value][0];
						warningRegex = CompilerMessageRegex [value][1];
					} else {
						LoggingService.LogError ("Invalid value for MessageRegexName : {0}", value);
						//FIXME: If !valid then throw
					}
				}
				messageRegexName = value;
			}
		}
		
		// Custom is not stored in this list!
		static Dictionary<string, string []> compilerMessageRegex;
		static public Dictionary<string, string[]> CompilerMessageRegex {
			get {
				if (compilerMessageRegex == null)
					InitCompilerMessageRegex ();
				return compilerMessageRegex;
			}
		}

		static Regex [] customRegex = null;

		// Regex(string) to Regex object
		static Dictionary<string, Regex> regexTable;
		static Dictionary<string, Regex> RegexTable {
			get {
				if (regexTable == null)
					regexTable = new Dictionary<string, Regex> ();
				return regexTable;
			}
		}

		string relativeConfigureInPath = String.Empty;
		[ItemProperty (DefaultValue = "")]
		//FIXME: Sanitize usage .. relative required or absolute ??
		public string RelativeConfigureInPath {
			get {
				return relativeConfigureInPath;
			}
			set {
				if (String.Compare (relativeConfigureInPath, value) == 0)
					return;

				relativeConfigureInPath = value;
				configuredPackages = null;

				if (String.IsNullOrEmpty (relativeConfigureInPath))
					return;

				relativeConfigureInPath = GetRelativePath (relativeConfigureInPath);
				InitBuildVars ();
			}
		}

		public string AbsoluteConfigureInPath {
			get { return GetAbsolutePath (RelativeConfigureInPath); }
		}

		ConfiguredPackagesManager configuredPackages = null;
		public ConfiguredPackagesManager ConfiguredPackages {
			get { return configuredPackages; }
		}

		string outputDirVar;
		[ItemProperty (DefaultValue = "")]
		public string OutputDirVar {
			get { return outputDirVar; }
			set { outputDirVar = value;}
    		}

		string assemblyNameVar;
		[ItemProperty (DefaultValue = "")]
		public string AssemblyNameVar {
			get { return assemblyNameVar; }
			set { assemblyNameVar = value;}
    		}

		public CustomMakefile Makefile {
			get {
				if (makefile == null)
					makefile = new CustomMakefile (AbsoluteMakefileName);
				return makefile;
			}
		}

		Dictionary <string, string> unresolvedReferences;
		Dictionary <string, string> UnresolvedReferences {
			get { 
				if (unresolvedReferences == null)
					unresolvedReferences = new Dictionary <string, string> ();
				return unresolvedReferences;
			}
 		}

		Dictionary<string, string> buildVariables ;
		public Dictionary<string, string> BuildVariables  {
			get {
				if (buildVariables == null)
					buildVariables = new Dictionary<string, string> ();
				return buildVariables;
			}
		}
		
		public bool IsFileIntegrationEnabled (string buildAction)
		{
			if (IntegrationEnabled) {
				if (buildAction == BuildAction.Compile)
					return BuildFilesVar.Sync;
				else if (buildAction == BuildAction.EmbeddedResource)
					return ResourcesVar.Sync;
				else if (buildAction == BuildAction.Content)
					return DeployFilesVar.Sync;
				else
					return OthersVar.Sync;
			}
			return false;
		}
		
		public bool IsFileExcluded (string fileName)
		{
			return excludedFiles.Contains (fileName);
		}
		
		public void SetFileExcluded (string fileName, bool exclude)
		{
			if (exclude)
				excludedFiles.Add (fileName);
			else
				excludedFiles.Remove (fileName);
			dirty = true;
		}

		bool dirty = false;

		public object Clone ()
		{
			MakefileData data = new MakefileData ();
			data.OwnerProject = this.OwnerProject;
			data.IntegrationEnabled = this.IntegrationEnabled;
			data.RelativeMakefileName = this.RelativeMakefileName;
			data.BuildTargetName = this.BuildTargetName;
			data.CleanTargetName = this.CleanTargetName;
			data.ExecuteTargetName = this.ExecuteTargetName;
			data.ParallelProcesses = this.ParallelProcesses;
			
			data.BuildFilesVar = new MakefileVar (this.BuildFilesVar);
			data.DeployFilesVar = new MakefileVar (this.DeployFilesVar);
			data.ResourcesVar = new MakefileVar (this.ResourcesVar);
			data.OthersVar = new MakefileVar (this.OthersVar);
			data.GacRefVar = new MakefileVar (this.GacRefVar);
			data.AsmRefVar = new MakefileVar (this.AsmRefVar);
			data.ProjectRefVar = new MakefileVar (this.ProjectRefVar);

			data.SyncReferences = this.SyncReferences;
			data.IsAutotoolsProject = this.IsAutotoolsProject;
			data.RelativeConfigureInPath = this.RelativeConfigureInPath;
			data.OutputDirVar = this.OutputDirVar;
			data.AssemblyNameVar = this.AssemblyNameVar;

			data.CustomErrorRegex = this.CustomErrorRegex;
			data.CustomWarningRegex = this.CustomWarningRegex;
			data.MessageRegexName = this.MessageRegexName;
			// This shouldn't be required
			//data.unresolvedReferences = new List<string> (this.UnresolvedReferences);

			return data;
		}

		static void InitCompilerMessageRegex ()
		{
			compilerMessageRegex = new Dictionary<string, string[]> ();
			compilerMessageRegex ["C# (mcs)"] = new string [] {
				@"(^\s*(?<file>.*)\((?<line>\d*){1}(,(?<column>\d*[\+]*))?\)(:|)\s+)*error\s*(?<number>.*):\s(?<message>.*)",
				@"(^\s*(?<file>.*)\((?<line>\d*){1}(,(?<column>\d*[\+]*))?\)(:|)\s+)*warning\s*(?<number>.*):\s(?<message>.*)"
			};
			
			compilerMessageRegex ["gcc"] = new string [] {
				@"^\s*(?<file>[^:]*):(?<line>\d*){1}(:(?<column>\d*))?\s*:\s*error\s*:\s(?<message>.*)",
				@"^\s*(?<file>[^:]*):(?<line>\d*){1}(:(?<column>\d*))?\s*:\s*warning\s*:\s(?<message>.*)"
			};
			
			compilerMessageRegex ["Boo"] = new string [] {
				@"(^\s*(?<file>.*)\((?<line>\d*){1}(,(?<column>\d*[\+]*))?\)(:|)\s+)*(?=BCE)(?<number>.*?):\s(?<message>.*)",
				@"(^\s*(?<file>.*)\((?<line>\d*){1}(,(?<column>\d*[\+]*))?\)(:|)\s+)*(?=BCW)(?<number>.*?):\sWARNING:\s(?<message>.*)"
			};

			compilerMessageRegex ["Vala"] = new string [] {
				@"((^\s*(?<file>.*):(?<line>\d*)\.(?<column>\d*)-\d*\.\d*: error: (?<message>.*))|(^\s*(?<file>[^:]*):(?<line>\d*){1}(:(?<column>\d*))?\s*:\s*error\s*:\s(?<message>.*)))",
				@"((^\s*(?<file>.*):(?<line>\d*)\.(?<column>\d*)-\d*\.\d*: warning: (?<message>.*))|(^\s*(?<file>[^:]*):(?<line>\d*){1}(:(?<column>\d*))?\s*:\s*warning\s*:\s(?<message>.*)))"
			};
		}

		void InitBuildVars ()
		{
			if (!String.IsNullOrEmpty (RelativeConfigureInPath)) {
				BuildVariables ["top_srcdir"] = RelativeConfigureInPath;
				BuildVariables ["top_builddir"] = RelativeConfigureInPath;
			}

			if (!String.IsNullOrEmpty (AbsoluteMakefileName))
				BuildVariables ["srcdir"] = BaseDirectory;
		}

		public string GetRelativePath (string path)
		{
			if (Path.IsPathRooted (path))
				return FileService.AbsoluteToRelativePath (BaseDirectory, path);
			else
				return path;
		}

		public string GetAbsolutePath (string path)
		{
			if (Path.IsPathRooted (path))
				return path;
			else
				return FileService.RelativeToAbsolutePath (BaseDirectory, path);
		}

		public void Save ()
		{
			Makefile.Save ();
		}

		public Regex GetErrorRegex (bool throwOnError)
		{
			return GetCompilerMessageRegex (0, throwOnError);
		}

		public Regex GetWarningRegex (bool throwOnError)
		{
			return GetCompilerMessageRegex (1, throwOnError);
		}

		Regex GetCompilerMessageRegex (int index, bool throwOnError)
		{
			if (index < 0 || index > 1)
				throw new ArgumentException ("index");

			string str = null;
			if (MessageRegexName != "Custom") {
				str = CompilerMessageRegex [MessageRegexName][index];
				if (!RegexTable.ContainsKey (str))
					RegexTable [str] = new Regex (str, RegexOptions.Compiled | RegexOptions.ExplicitCapture);

				return RegexTable [str];
			}

			// Custom
			if (customRegex == null)
				customRegex = new Regex [2];

			str = index == 0 ? CustomErrorRegex : CustomWarningRegex;
			if (customRegex [index] == null || customRegex [index].ToString () != str) {
				try {
					customRegex [index] = new Regex (str, RegexOptions.Compiled | RegexOptions.ExplicitCapture);
				} catch (ArgumentException) {
					// Invalid regex string
					LoggingService.LogError ("Invalid {0}Regex '{1}' specified for project '{2}'.",
						(index == 0 ? "Error" : "Warning"), str, OwnerProject.Name);
					customRegex [index] = null;
					if (throwOnError)
						throw;
				}
			}

			return customRegex [index];
		}

		IProgressMonitor monitor = null;

		// VarName -> Encode filenames Eg. $(srcdir)
		Dictionary<string, bool> encodeValues;
		Dictionary<string, bool> EncodeValues {
			get {
				if (encodeValues == null) {
					encodeValues = new Dictionary<string, bool> ();

					// Default is false!
					encodeValues [BuildFilesVar.Name] = false;
					encodeValues [DeployFilesVar.Name] = false;
					encodeValues [OthersVar.Name] = false;
					encodeValues [ResourcesVar.Name] = false;

					encodeValues [GacRefVar.Name] = false;
					encodeValues [AsmRefVar.Name] = false;
					encodeValues [ProjectRefVar.Name] = false;
				}

				return encodeValues;
			}
		}

		// Global table for keeping weak references to ConfiguredPackagesManager objects,
		// one per configure.in file. A strong reference to the object is kept in
		// every project's ExtendedProperties, this ensures that it won't get collected
		// too early.
		static Dictionary<string, WeakReference> pkgManagerTable = null;
		static Dictionary<string, WeakReference> PkgManagerTable {
			get {
				if (pkgManagerTable == null)
					pkgManagerTable = new Dictionary<string, WeakReference> ();
				return pkgManagerTable;
			}
		}

		//use events.. 
		public void UpdateProject (IProgressMonitor monitor, bool promptForRemoval)
		{
			if (!IntegrationEnabled)
				return;

			if (ownerProject == null)
				throw new InvalidOperationException ("Internal Error: ownerProject not set");

			this.monitor = monitor;

			try {
				Makefile.GetVariables ();
			} catch (Exception e) {
				monitor.ReportError (GettextCatalog.GetString (
					"Invalid Makefile '{0}'. Disabling Makefile integration.", AbsoluteMakefileName), e);
				IntegrationEnabled = false;

				return;
			}

			//FIXME: Improve the message
			if (promptForRemoval) {
				AlertButton projectButton = new AlertButton ("_Project");
				AlertButton makefileButton = new AlertButton ("_Makefile");
				AlertButton choice = MessageService.AskQuestion (GettextCatalog.GetString ("Enabling Makefile integration. You can choose to have either the Project or the Makefile be used as the master copy. This is done only when enabling this feature. After this, the Makefile will be taken as the master copy."),
				                                                 projectButton, makefileButton);
				if (choice == projectButton) {
					//Sync Project --> Makefile
					dirty = true;
					return;
				}
			}

			dirty = true;
			encodeValues = null;

			try {
				if (IsAutotoolsProject) {
					string path = Path.Combine (AbsoluteConfigureInPath, "configure.in");
					if (!File.Exists (path))
						path = Path.Combine (AbsoluteConfigureInPath, "configure.ac");
					
					configuredPackages = null;
					WeakReference weakref;
					if (PkgManagerTable.TryGetValue (path, out weakref)) {
						if (weakref.IsAlive) {
							configuredPackages = (ConfiguredPackagesManager) weakref.Target;
							FileInfo finfo = new FileInfo (path);
							if (finfo.LastWriteTime > configuredPackages.LastWriteTime)
								// file has changed since last time we parsed it!
								configuredPackages = null;
						}
					}

					// no entry in table or it got collected or file has changed
					if (configuredPackages == null) {
						configuredPackages = new ConfiguredPackagesManager (path);
						PkgManagerTable [path] = new WeakReference (configuredPackages);
						ownerProject.ExtendedProperties ["MonoDevelop.Autotools.ConfiguredPackagesManager"] = configuredPackages;
					}
				}
			} catch (Exception e) {
				LoggingService.LogWarning (
					"Error trying to read configure.in ('{0}') for project '{1}':\n{2}",
					AbsoluteConfigureInPath, OwnerProject.Name, e.ToString ());

				monitor.ReportWarning (GettextCatalog.GetString (
					"Error trying to read configure.in ('{0}') for project '{1}':\n{2}",
					AbsoluteConfigureInPath, OwnerProject.Name, e.Message));
			}

			ReadFiles (BuildFilesVar, BuildAction.Compile, "Build", promptForRemoval);
			ReadFiles (DeployFilesVar, BuildAction.Content, "Deploy", promptForRemoval);
			ReadFiles (OthersVar, BuildAction.None, "Others", promptForRemoval);
			ReadFiles (ResourcesVar, BuildAction.EmbeddedResource, "Resources", promptForRemoval);

			if (!SyncReferences)
				return;

			try {
				SaveReferences = true;

				//Do these for DotNetProject only
				DotNetProject dotnetProject = ownerProject as DotNetProject;
				if (dotnetProject != null) {
					GacRefVar.Extra.Clear ();
					AsmRefVar.Extra.Clear ();
					ProjectRefVar.Extra.Clear ();

					existingGacRefs = new Dictionary<string, ProjectReference> ();
					requiredPackageVersions = new Dictionary<string,string> ();
					newGacRefs = new Dictionary<string, ProjectReference> ();

					List<ProjectReference> toRemove = new List<ProjectReference> ();
					foreach (ProjectReference pref in dotnetProject.References) {
						if (pref.ReferenceType == ReferenceType.Gac) {
							string [] files = pref.GetReferencedFileNames (ConfigurationSelector.Default);
							if (files == null)
								continue;

							if (pref.ReferenceType == ReferenceType.Gac) {
								// Store the package version required by this reference. We'll use
								// the same version when trying to match references coming from the makefile
								SystemAssembly asm = assemblyContext.GetAssemblyFromFullName (pref.StoredReference, pref.Package != null ? pref.Package.Name : null, dotnetProject.TargetFramework);
								if (asm != null && asm.Package != null)
									requiredPackageVersions [asm.Package.Name] = asm.Package.Version;
							}
							// this should help normalize paths like /foo//bar/../
							string fullpath = Path.GetFullPath (files [0]);
							if (existingGacRefs.ContainsKey (fullpath))
								toRemove.Add (pref);
							else
								existingGacRefs [fullpath] = pref;
						}
					}

					// Remove the repeats
					foreach (ProjectReference pref in toRemove)
						dotnetProject.References.Remove (pref);

					ReadReferences (GacRefVar, ReferenceType.Gac, "Gac References", dotnetProject);

					// !SaveReferences indicates that previous ref reading failed
					if (SaveReferences && String.Compare (AsmRefVar.Name, GacRefVar.Name) != 0)
						ReadReferences (AsmRefVar, ReferenceType.Assembly, "Asm References", dotnetProject);
					if (SaveReferences && (String.Compare (ProjectRefVar.Name, GacRefVar.Name) != 0) && 
						(String.Compare (ProjectRefVar.Name, AsmRefVar.Name) != 0))
						ReadReferences (ProjectRefVar, ReferenceType.Project, "Project References", dotnetProject);
					
					//Resolve References
					//Required when UpdateProject gets called by ui
					if (ownerProject.ParentSolution != null)
						ResolveProjectReferences (ownerProject.ParentSolution.RootFolder, monitor);

					foreach (ProjectReference pr in existingGacRefs.Values)
						dotnetProject.References.Remove (pr);

					existingGacRefs.Clear ();
					newGacRefs.Clear ();
				}
			} catch (Exception e) {
				string msg = GettextCatalog.GetString (
					"Error in loading references: {0}. Skipping syncing of references", e.Message);
				LoggingService.LogWarning (msg);
				monitor.ReportWarning (msg);

				SaveReferences = false;
			}

			this.monitor = null;
		}

		void ReadFiles (MakefileVar fileVar, string buildAction, string id, bool promptForRemoval)
		{
			try { 
				fileVar.SaveEnabled = true;
				ReadFilesActual (fileVar, buildAction, id, promptForRemoval);
			} catch (Exception e) {
				string msg = GettextCatalog.GetString ("Error in loading files for '{0}'. Skipping.", id);
				LoggingService.LogError (msg, e);
				monitor.ReportWarning (msg);
				fileVar.SaveEnabled = false;
			}
		}

		void ReadFilesActual (MakefileVar fileVar, string buildAction, string id, bool promptForRemoval)
		{
			fileVar.Extra.Clear ();
			if (!fileVar.Sync || String.IsNullOrEmpty (fileVar.Name))
				return;

			//All filenames are treated as relative to the Makefile path
			List<string> files = Makefile.GetListVariable (fileVar.Name);
			if (files == null) {
				//FIXME: Move this to the caller, try-catch there
				string msg = GettextCatalog.GetString (
					"Makefile variable '{0}' not found. Skipping syncing of '{1}' file list for project '{2}'.",
					fileVar.Name, id, ownerProject.Name);
				LoggingService.LogWarning (msg);
				monitor.ReportWarning (msg);

				fileVar.SaveEnabled = false;
				return;
			}

			//FIXME: Trim?
			bool usePrefix = !String.IsNullOrEmpty (fileVar.Prefix);
			int len = 0;
			if (fileVar.Prefix != null)
				len = fileVar.Prefix.Length;

			Dictionary<string, ProjectFile> existingFiles = new Dictionary<string, ProjectFile> ();
			foreach (ProjectFile pf in ownerProject.Files) {
				if (pf.BuildAction == buildAction)
					existingFiles [ownerProject.GetAbsoluteChildPath (pf.FilePath)] = pf;
			}

			// True if the user has been warned that filenames contain Variables
			// but no configure.in path is set
			bool autotoolsWarned = false;
			bool varFound = false;

			foreach (string f in files) { 
				string fname = f.Trim ();
				
				try { 
					if (usePrefix && String.Compare (fileVar.Prefix, 0, fname, 0, len) == 0)
						//FIXME: If it doesn't match, then?
						fname = fname.Substring (len);

					fname = FromMakefilePath (fname);

					string resourceId = null;
					if (buildAction == BuildAction.EmbeddedResource && fname.IndexOf (',') >= 0) {
						string [] tmp = fname.Split (new char [] {','}, 2);
						fname = tmp [0];
						if (tmp.Length > 1)
							resourceId = tmp [1];
					}

					if ((fname.Length > 2 && fname [0] == '$' && fname [1] == '(') && !UseAutotools) {
						fileVar.Extra.Add (f);
						if (!autotoolsWarned) {
							string msg = GettextCatalog.GetString (
								"Files in variable '{0}' contains variables which cannot be parsed without the path " +
								"to configure.in being set. Ignoring such files.", fileVar.Name);
							LoggingService.LogWarning (msg);
							monitor.ReportWarning (msg);
							autotoolsWarned = true;
						}
						continue;
					}

					varFound = false;
					fname = ResolveBuildVars (fname, ref varFound);
					EncodeValues [fileVar.Name] |= varFound;

					//File path in the makefile are relative to the makefile,
					//but have to be added to the project as relative to project.BaseDirectory
					string absPath = Path.GetFullPath (Path.Combine (BaseDirectory, fname));

					if (existingFiles.ContainsKey (absPath)) {
						existingFiles.Remove (absPath);
						continue;
					}

					if (!File.Exists (absPath)) {
						//Invalid file, maybe we couldn't parse it correctly!
						string msg = GettextCatalog.GetString (
							"Ignoring invalid file '{0}' found in '{1}' for project '{2}'.", f,
							relativeMakefileName, OwnerProject.Name);
						LoggingService.LogWarning (msg);
						monitor.ReportWarning (msg);
						fileVar.Extra.Add (f);
						continue;
					}

					ProjectFile pf = ownerProject.AddFile (absPath, buildAction);
					if (buildAction == BuildAction.EmbeddedResource && resourceId != null)
						pf.ResourceId = resourceId;
				} catch (Exception e) {
					LoggingService.LogError (e.ToString ());
					fileVar.Extra.Add (f);
				}
			}

			if (existingFiles.Count > 0) {
				foreach (ProjectFile file in existingFiles.Values) {
					if (!IsFileExcluded (file.FilePath))
						ownerProject.Files.Remove (file);
				}
			}
		}

		Dictionary<string, ProjectReference> existingGacRefs = null;
		Dictionary<string, ProjectReference> newGacRefs = null;
		Dictionary<string, string> requiredPackageVersions = null;

		void ReadReferences (MakefileVar refVar, ReferenceType refType, string id, DotNetProject project)
		{
			if (String.IsNullOrEmpty (refVar.Name) || project == null)
				return;

			//All filenames are treated as relative to the Makefile path
			List<string> references = Makefile.GetListVariable (refVar.Name);
			if (references == null) {
				string msg = GettextCatalog.GetString (
					"Makefile variable '{0}' not found. Skipping syncing of all '{1}' references for project {2}.",
					refVar.Name, id, project.Name);
				LoggingService.LogWarning (msg);
				monitor.ReportWarning (msg);
				SaveReferences = false;
				return;
			}
			//FIXME: Trim?
			bool usePrefix = !String.IsNullOrEmpty (refVar.Prefix);
			int len = 0;
			if (refVar.Prefix != null)
				len = refVar.Prefix.Length;

			ReferencedPackages.Clear ();
			foreach (string r in references) {
				//Handle -r:System,System.Data also
				try { 
					ParseReference (r, usePrefix, refVar, len, refType, project);
				} catch (Exception e) {
					string msg = GettextCatalog.GetString ("Unable to parse reference '{0}' for project '{1}'. Ignoring.", r, project.Name);
					LoggingService.LogWarning (msg, e);
					monitor.ReportWarning (msg);
					refVar.Extra.Add (r);
				}
			}

			referencedPackages = null;
		}

		List<string> referencedPackages;
		List<string> ReferencedPackages  {
			get {
				if (referencedPackages == null)
					referencedPackages = new List<string> ();
				return referencedPackages;
			}
    		}

		//FIXME: change return type to bool, on false, extra.Add (reference)
		void ParseReference (string reference, bool usePrefix, MakefileVar refVar, int len, ReferenceType refType, 
				DotNetProject project)
		{
			string rname = reference;
			// .StartsWith "$("
			if (rname.Length > 3 && rname [0] == '$' && rname [1] == '(' && rname [rname.Length - 1] == ')') {
				if (!UseAutotools) {
					refVar.Extra.Add (reference);
					return;
				}

				// Autotools based project

				if (!rname.EndsWith ("_LIBS)")) {
					//Not a pkgconfig *_LIBS var
					refVar.Extra.Add (reference);
					return;
				}

				string pkgVarName = rname.Substring (2, rname.Length - 3).Replace ("_LIBS", String.Empty);
				List<PackageContent> pkgNames = ConfiguredPackages.GetPackageContentFromVarName (pkgVarName);
				if (pkgNames == null) {
					 LoggingService.LogWarning  ("Package named '{0}' not found in configure.in. Ignoring reference to '{1}'.",
						pkgVarName, rname);
					refVar.Extra.Add (reference);
					return;
				}

				bool added = false;
				foreach (PackageContent packageContent in pkgNames) {
					if (ReferencedPackages.Contains (packageContent.Name)) {
						added = true;
						continue;
					}

					// Add all successfully added packages to ReferencedPackages
					foreach (string referencedName in packageContent.AllReferencedNames) {
						if (LoadPackageReference (referencedName, project, refVar.Prefix)) {
							ReferencedPackages.Add (referencedName);
							added = true;
						}
					}
				}

				// none of the packages could be added
				if (!added)
					refVar.Extra.Add (reference);

				return;
			}

			// .StartsWith "-pkg:"
			if (rname.Length >= 5 && rname [0] == '-' && rname [1] == 'p' && rname [2] == 'k' && rname [3] == 'g' && rname [4] == ':') {
				string pkgName = rname.Substring (5);
				//-pkg:foo,bar
				foreach (string s in pkgName.Split (new char [] {','}, StringSplitOptions.RemoveEmptyEntries)) {
					if (ReferencedPackages.Contains (s))
						continue;

					if (LoadPackageReference (s, project, refVar.Prefix))
						ReferencedPackages.Add (s);
					else
						refVar.Extra.Add ("-pkg:" + s);
				}

				return;
			}

			if (usePrefix && String.Compare (refVar.Prefix, 0, rname, 0, len) == 0)
				rname = rname.Substring (len);

			//FIXME: try/catch around the split refs ?
			bool varFound = false;
			foreach (string r in rname.Split (new char [] {','}, StringSplitOptions.RemoveEmptyEntries)) {
				string refname = r;
				if (refname.Length >= 2 && refname [0] == '$' && refname [1] == '(' && !UseAutotools) {
					//Eg. -r:$(top_builddir)/foo.dll
					refVar.Extra.Add (reference);
					continue;
				}

				varFound = false;
				refname = ResolveBuildVars (refname, ref varFound);
				EncodeValues [refVar.Name] |= varFound;

				string fullpath = Path.GetFullPath (Path.Combine (BaseDirectory, refname));
				
				// if refname is part of a package then add as gac
				// but don't do it if the refname exactly matches a file name in the project dir
				if (refname.IndexOf (Path.DirectorySeparatorChar) < 0 && !File.Exists (fullpath) &&
					ParseReferenceAsGac (refname, project) != null)
					continue;
				
				if (TryGetExistingGacRef (fullpath) != null)
					continue;

				if (refname.IndexOf (Path.DirectorySeparatorChar) < 0) {
					// Check that its a valid assembly
					string fullname = null;
					try {
						fullname = AssemblyName.GetAssemblyName (fullpath).FullName;
					} catch (FileNotFoundException) {
					} catch (BadImageFormatException) {
					}

					// Valid assembly, From a package, add as Gac
					SystemPackage pkg = assemblyContext.GetPackageFromPath (fullpath);
					if (fullname != null && pkg != null) {
						SystemAssembly sa = assemblyContext.GetAssemblyFromFullName (fullname, pkg.Name, project.TargetFramework);
						if (sa != null) {
							AddNewGacReference (project, sa);
							continue;
						}
					}
				}

				//Else add to unresolved project refs, avoid repeats
				if (!UnresolvedReferences.ContainsKey (fullpath))
					UnresolvedReferences [fullpath] = fullpath;
			}
		}

		bool LoadPackageReference (string pkgName, DotNetProject project, string prefix)
		{
			SystemPackage pkg = null;
			string packageVersion;
			if (requiredPackageVersions.TryGetValue (pkgName, out packageVersion))
				pkg = assemblyContext.GetPackage (pkgName, packageVersion);
			if (pkg == null)
				pkg = assemblyContext.GetPackage (pkgName);
			
			if (pkg == null) {
				LoggingService.LogWarning ("No package named '{0}' found. Ignoring.", pkgName);
				return false;
			}

			foreach (SystemAssembly sa in pkg.Assemblies) {
				if (TryGetExistingGacRef (sa.Location) != null)
					continue;

				//Get fullname of the assembly
				AddNewGacReference (project, sa);
			}

			return true;
		}

		ProjectReference ParseReferenceAsGac (string rname, DotNetProject project)
		{
			string aname = rname;
			if (rname.EndsWith (".dll", StringComparison.InvariantCultureIgnoreCase))
				//-r:Mono.Posix.dll
				aname = rname.Substring (0, rname.Length - 4);

			string fullname = assemblyContext.GetAssemblyFullName (aname, project.TargetFramework);
			if (fullname == null)
				return null;

			SystemAssembly asm = assemblyContext.GetAssemblyForVersion (fullname, null, project.TargetFramework);
			if (asm == null)
				return null;

			ProjectReference pref = TryGetExistingGacRef (asm.Location);
			if (pref != null)
				return pref;

			return AddNewGacReference (project, asm);
		}

		ProjectReference TryGetExistingGacRef (string fullpath)
		{
			if (existingGacRefs.ContainsKey (fullpath)) {
				ProjectReference ret = existingGacRefs [fullpath];
				existingGacRefs.Remove (fullpath);
				newGacRefs [fullpath] = ret;

				return ret;
			}

			if (newGacRefs.ContainsKey (fullpath))
				return newGacRefs [fullpath];

			return null;
		}

		ProjectReference AddNewGacReference (DotNetProject project, SystemAssembly sa)
		{
			ProjectReference pref = new ProjectReference (sa);
			project.References.Add (pref);
			newGacRefs [sa.Location] = pref;

			return pref;
		}

		public static void ResolveProjectReferences (SolutionFolder folder, IProgressMonitor monitor)
		{
			Dictionary<string, DotNetProject> projects = new Dictionary<string, DotNetProject> ();
			foreach (DotNetProject p in folder.GetAllItems<DotNetProject> ()) {
				string filename = p.GetOutputFileName (ConfigurationSelector.Default);
				// Can be null for Generic projects
				if (!String.IsNullOrEmpty (filename))
					projects [filename] = p;
			}

			foreach (DotNetProject sproj in projects.Values) {
				MakefileData mdata = sproj.ExtendedProperties ["MonoDevelop.Autotools.MakefileInfo"] as MakefileData;
				if (mdata == null)
					continue;

				if (mdata.UnresolvedReferences.Count != 0) {
				
					Dictionary<string, ProjectReference> asmProjectRefs =
						new Dictionary<string, ProjectReference> ();

					foreach (ProjectReference pr in sproj.References) {
						if (pr.ReferenceType != ReferenceType.Assembly &&
							pr.ReferenceType != ReferenceType.Project)
							continue;
						
						string [] files = pr.GetReferencedFileNames (ConfigurationSelector.Default);
						if (files.Length > 0)
							asmProjectRefs [files [0]] = pr;
					}

					List<string> toRemove = new List<string> ();
					foreach (string refstr in mdata.UnresolvedReferences.Keys) {
						if (asmProjectRefs.ContainsKey (refstr)) {
							// ref already exists in the project
							toRemove.Add (refstr);
							asmProjectRefs.Remove (refstr);
						} else {
							// Try as a project ref
							if (projects.ContainsKey (refstr)) {
								sproj.References.Add (new ProjectReference (projects [refstr]));
								toRemove.Add (refstr);
							}
						}
					}

					foreach (string s in toRemove)
						mdata.UnresolvedReferences.Remove (s);

					// Add all remaining unresolved refs as Assembly refs
					foreach (string s in mdata.UnresolvedReferences.Keys)
						sproj.References.Add (new ProjectReference (ReferenceType.Assembly, s));
						
					// Remove asm/project refs not found in UnresolvedReferences
					foreach (ProjectReference pr in asmProjectRefs.Values)
						sproj.References.Remove (pr);

					mdata.UnresolvedReferences.Clear ();
				}

				mdata.UpdateMakefile (monitor);
			}
		}

		string ResolveBuildVars (string filename, ref bool varFound)
		{   
			varFound = false;
			if (filename.IndexOf ('$') < 0)
				return filename;

			StringBuilder sb = new StringBuilder ();
			char c;
			int len = filename.Length;
			for (int i = 0; i < len; i ++) {
				c = filename [i];
				if (c != '$' || (i + 3 >= len)) {
					sb.Append (c);
					continue;
				}

				if (filename [i + 1] == '(') {
					int j = i + 2;
					while (j < len && filename [j] != ')')
						j ++;

					if (j >= len) {
						sb.Append (filename.Substring (i));
						break;
					}

					string varname = filename.Substring (i + 2, j - (i + 2));

					if (BuildVariables.ContainsKey (varname)) {
						sb.Append (BuildVariables [varname]);
						varFound = true;
					}
					else
						sb.Append ("$(" + varname + ")");
					i = j;
				}
			}

			return sb.ToString ();
		}

		//Converts a absolute filename to use the specified buildvar like top_builddir,
		//if applicable
		string EncodeFileName (string filename, string varname, bool isAbsolute)
		{
			if (!UseAutotools)
				return filename;

			string varpath = null;
			if (isAbsolute)
				varpath = GetAbsolutePath (BuildVariables [varname]);
			else
				varpath = GetRelativePath (BuildVariables [varname]);

			if (filename.StartsWith (varpath)) {
				string suffix = filename.Substring (varpath.Length);
				if (suffix [0] == Path.DirectorySeparatorChar)
					return String.Format ("$({0}){1}", varname, suffix);
				else
					return String.Format ("$({0}){1}{2}", varname, Path.DirectorySeparatorChar, suffix);
			}

			return filename;
		}
		

		string NormalizeFileName (string fileName)
		{
			// Cosmetic fix: remove the "./" prefix
			
			if (! (fileName [0] == '.' && fileName [1] == '/'))
				return fileName;
				
			do {
				if (fileName [0] == '.' && fileName [1] == '/')
					fileName = fileName.Substring (2);
				else if (fileName [0] == '/')
					fileName = fileName.Substring (1);
				else
					return fileName;
			} while (true);
		}

		//Writing methods

		public void UpdateMakefile (IProgressMonitor monitor)
		{
			//FIXME: AssemblyName & OutputDir

			if (!dirty || !IntegrationEnabled)
				return;

			this.monitor = monitor;
			bool makeRelative = (OwnerProject.BaseDirectory != BaseDirectory);

			//FIXME: If anything fails while writing, skip completely
			//FIXME: All the file vars must be distinct
			WriteFiles (BuildFilesVar, BuildAction.Compile, makeRelative, "Build");
			WriteFiles (DeployFilesVar, BuildAction.Content, makeRelative, "Deploy");
			WriteFiles (OthersVar, BuildAction.None, makeRelative, "Others");
			WriteFiles (ResourcesVar, BuildAction.EmbeddedResource, makeRelative, "Resources");

			if (SyncReferences && SaveReferences) {
				Makefile.ClearVariableValue (GacRefVar.Name);
				Makefile.ClearVariableValue (AsmRefVar.Name);
				Makefile.ClearVariableValue (ProjectRefVar.Name);

				WriteReferences (GacRefVar, ReferenceType.Gac, makeRelative, "Gac");
				WriteReferences (AsmRefVar, ReferenceType.Assembly, makeRelative, "Assembly");
				WriteReferences (ProjectRefVar, ReferenceType.Project, makeRelative, "Project");
			
				// Sort list of references in the makefile,
				// but sort only once per distinct var
				// (Required as we are comparing the full makefile as a string,
				//  to detect changes!)
				List<string> list = Makefile.GetListVariable (GacRefVar.Name);
				if (list != null)
					list.Sort (System.StringComparer.InvariantCulture);

				if (String.Compare (AsmRefVar.Name, GacRefVar.Name) != 0) {
					list = Makefile.GetListVariable (AsmRefVar.Name);
					if (list != null)
						list.Sort (System.StringComparer.InvariantCulture);
				}

				if ((String.Compare (ProjectRefVar.Name, GacRefVar.Name) != 0) && 
					(String.Compare (ProjectRefVar.Name, AsmRefVar.Name) != 0)) {
					list = Makefile.GetListVariable (ProjectRefVar.Name);
					if (list != null)
						list.Sort (System.StringComparer.InvariantCulture);
				}
			}

			Save ();
			dirty = false;

			this.monitor = null;
		}

		bool WriteFiles (MakefileVar fileVar, string buildAction, bool makeRelative, string id)
		{
			if (!fileVar.Sync || !fileVar.SaveEnabled)
				return false;

			if (Makefile.GetListVariable (fileVar.Name) == null) {
				//Var not found, skip
				string msg = GettextCatalog.GetString (
                                        "Makefile variable '{0}' not found. Skipping writing of '{1}' files to the Makefile.", fileVar.Name, id);
                                LoggingService.LogWarning (msg);
                                monitor.ReportWarning (msg);
				return false;
			}

			List<string> files = new List<string> ();
			foreach (ProjectFile pf in OwnerProject.Files) {
				if (pf.Subtype != Subtype.Code)
					continue;
				if (IsFileExcluded (pf.FilePath))
					continue;
				if (pf.BuildAction == buildAction) {
					string str = null;
					if (makeRelative)
						//Files are relative to the Makefile
						str = GetRelativePath (pf.FilePath);
					else
						str = pf.FilePath.ToRelative (pf.Project.BaseDirectory);

					string unescapedFileName = Path.GetFileName (str);

					if (EncodeValues [fileVar.Name]) {
						if (pf.IsExternalToProject)
							str = EncodeFileName (str, "top_srcdir", false);
						else
							str = EncodeFileName (str, "srcdir", false);
					}
					str = ToMakefilePath (str);

					// Emit the resource ID only when it is different from the file name
					if (pf.BuildAction == BuildAction.EmbeddedResource && pf.ResourceId != null && pf.ResourceId.Length > 0 && pf.ResourceId != unescapedFileName)
						str = String.Format ("{0}{1},{2}", fileVar.Prefix, str, EscapeString (pf.ResourceId));
					else
						str = String.Format ("{0}{1}", fileVar.Prefix, str);

					str = NormalizeFileName (str);
					files.Add (str);
				}
			}

			foreach (string s in fileVar.Extra)
				files.Add (s);

			// Keep the file list sorted in the makefile
			files.Sort (System.StringComparer.InvariantCulture);
			
			Makefile.SetListVariable (fileVar.Name, files);
			return true;
		}

		bool WriteReferences (MakefileVar refVar, ReferenceType refType, bool makeRelative, string id)
		{
			//Reference vars can be shared too, so use existing list
			//Eg. REF for both Gac and Asm ref
			List<string> references = Makefile.GetListVariable (refVar.Name);
			if (references == null) {
				//Var not found, skip
				string msg = GettextCatalog.GetString (
                                        "Makefile variable '{0}' not found. Skipping syncing of '{1}' references.", refVar.Name, id);
				LoggingService.LogWarning (msg);
				monitor.ReportWarning (msg);
				return false;
			}

			//if .Value is true
			//	key -> Varname, Emit as $key_LIBS
			//if .Value is false
			//	key -> pkgname, emit as -pkg:$key
			Dictionary<string, bool> hasAcSubstPackages = new Dictionary<string, bool> ();

			foreach (ProjectReference pr in ((DotNetProject)OwnerProject).References) {
				if (pr.ReferenceType != refType)
					continue;

				string refstr = String.Empty;
				switch (refType) {
				case ReferenceType.Gac:
					//Assemblies coming from packages are always added as Gac
					refstr = GacRefToString (pr, hasAcSubstPackages, refVar);
					if (refstr == null)
						continue;
					break;
				case ReferenceType.Assembly:
					refstr = AsmRefToString (pr.Reference, refVar, false);
					break;
				case ReferenceType.Project:
					refstr = ProjectRefToString (pr, refVar);
					if (refstr == null)
						continue;
					break;
				default:
					//not supported
					continue;
				}

				references.Add (String.Format ("{0}{1}", refVar.Prefix, refstr));
			}

			//Add packages
			foreach (KeyValuePair<string, bool> pair in hasAcSubstPackages) {
				if (pair.Value)
					references.Add (String.Format ("$({0}_LIBS)", pair.Key));
				else
					references.Add (String.Format ("-pkg:{0}", pair.Key));
			}

			foreach (string s in refVar.Extra)
				references.Add (s);

			Makefile.SetListVariable (refVar.Name, references);
			return true;
		}

		string GacRefToString (ProjectReference pr, Dictionary<string, bool> hasAcSubstPackages, MakefileVar refVar)
		{
			//Gac ref can be a full name OR a path!
			//FIXME: Use GetReferencedFileName and GetPackageFromPath ?
			string fullname = pr.Reference;
			SystemPackage pkg = pr.Package;
			if (pkg == null) {
				//reference could be a path
				pkg = assemblyContext.GetPackageFromPath (Path.GetFullPath (pr.Reference));
				if (pkg != null) {
					//Path
					try {
						fullname = AssemblyName.GetAssemblyName (pr.Reference).FullName;
						//If this throws : Invalid assembly!
						//let it fall through and be emitted as a asm ref
					} catch (FileNotFoundException) {
						pkg = null;
					} catch (BadImageFormatException) {
						pkg = null;
					}
				}
			}

			if (pkg == null)
				return AsmRefToString (pr.GetReferencedFileNames (ConfigurationSelector.Default) [0], refVar, false);

			// Reference is from a package

			if (pkg.IsCorePackage)
				//pkg:mono, Eg. System, System.Data etc
				return fullname.Split (new char [] {','}, 2) [0];

			//Ref is from a non-core package
			string varname = null;
			if (UseAutotools)
				//Check whether ref'ed in configure.in
				varname = ConfiguredPackages.GetVarNameFromName (pkg.Name);
			
			if (varname == null) {
				//Package not referenced in configure.in
				//Or not a autotools based project,
				//so emit -pkg:

				if (!hasAcSubstPackages.ContainsKey (pkg.Name)) {
					if (UseAutotools) {
						//Warn only if UseAutotools
						string msg = GettextCatalog.GetString (
							"A reference to the pkg-config package '{0}' is being emitted to the Makefile, " +
							"because at least one assembly from the package is used in the project '{1}'. However, " +
							"this dependency is not specified in the configure.in file, so you might need to " +
							"add it to ensure that the project builds successfully on other systems.", pkg.Name, pr.OwnerProject.Name);
						LoggingService.LogWarning (msg);
						monitor.ReportWarning (msg);
					}

					hasAcSubstPackages [pkg.Name] = false;
				}
			} else {
				// If the package as AC_SUBST(FOO_LIBS) defined, then
				// emit FOO_LIBS, else emit -pkg:foo
				if (ConfiguredPackages.HasAcSubst (varname + "_LIBS")) {
					hasAcSubstPackages [varname] = true;
				} else {
					hasAcSubstPackages [pkg.Name] = false;
				}
			}

			return null;
		}

		string AsmRefToString (string reference, MakefileVar refVar, bool isBuiltAssembly)
		{
			if (EncodeValues [refVar.Name]) {
				if (!isBuiltAssembly)
					return ToMakefilePath (EncodeFileName (reference, "top_srcdir", true));
				else if (!reference.StartsWith (BaseDirectory))
					//Reference is external to this project
					return ToMakefilePath (EncodeFileName (reference, "top_builddir", true));
			}

			// !external and !encode
			return ToMakefilePath (GetRelativePath (reference));
		}

		string ProjectRefToString (ProjectReference pr, MakefileVar refVar)
		{
			string [] tmp = pr.GetReferencedFileNames (ConfigurationSelector.Default);
			if (tmp == null || tmp.Length == 0)
				//Reference not found, ignoring
				return null;

			return AsmRefToString (tmp [0], refVar, true);
		}

		public static string GetUnixPath (string path)
		{
			if (Path.DirectorySeparatorChar != '/')
				return path.Replace (Path.DirectorySeparatorChar, '/');
			else
				return path;
		}

		public static string FromUnixPath (string path)
		{
			if (Path.DirectorySeparatorChar != '/')
				return path.Replace (Path.DirectorySeparatorChar, '/');
			else
				return path;
		}

		public static string ToMakefilePath (string str)
		{
			return EscapeString (GetUnixPath (str));
		}

		public static string FromMakefilePath (string str)
		{
			return FromUnixPath (UnescapeString (str));
		}

		public static string EscapeString (string str)
		{
			StringBuilder sb = new StringBuilder ();
			int len = str.Length;
			for (int i = 0; i < len; i ++) {
				char c = str [i];
				if (c == '\\' || c == '#' || c == ' ')
					sb.Append ("\\");
				
				sb.Append (c);
			}
			
			return sb.ToString ();
		}
		
		static string UnescapeString (string str)
		{
			if (str.IndexOf ('\\') < 0)
				return str;
			
			StringBuilder sb = new StringBuilder ();
			int len = str.Length;
			for (int i = 0; i < len; i ++) {
				char c = str [i];
				if (c != '\\' || i == len - 1) {
					sb.Append (c);
					continue;
				}
				char next = str [i + 1];
				if (next != '\\' && next != '#' && next != ' ')
					sb.Append ("\\");
				
				sb.Append (next);
				i ++;
			}
			
			return sb.ToString ();
		}

	}

	public class ConfiguredPackagesManager
	{
		Dictionary<string, List<PackageContent>> pkgVarNameToPkgName;
		Dictionary<string, string> pkgNameToPkgVarName;

		//This dict has entries for all vars that have a
		//AC_SUBST(VARNAME_LIBS) defined
		Dictionary<string, string> varNameAcSubst;

		string fullpath;
		DateTime lastWriteTime;

		public ConfiguredPackagesManager (string fullpath)
		{
			this.fullpath = fullpath;
			
			if (!File.Exists (fullpath) || (Path.GetFileName (fullpath) != "configure.in" && Path.GetFileName (fullpath) != "configure.ac"))
				//FIXME: Exception type?
				throw new ArgumentException (GettextCatalog.GetString ("Unable to find configure.in at '{0}'.", fullpath));

			FileInfo finfo = new FileInfo (fullpath);
			lastWriteTime = finfo.LastWriteTime;
			ReadPackagesList ();
		}

		//Gets the pkg-config name from the makefile (or autoconf?) var name
		// TODO: Remove me, if unused.
		[Obsolete("Use 'GetPackageContentFromVarName' instead.")]
		public List<string> GetNamesFromVarName (string varname)
		{
			if (!pkgVarNameToPkgName.ContainsKey (varname)) {
				LoggingService.LogDebug ("pkg-config variable {0} not found in pkgVarNameToPkgName.", varname);
				return null;
			}
			List<string> result = new List<string> ();
			foreach (PackageContent content in pkgVarNameToPkgName [varname]) {
				result.Add (content.Name);
			}
			return result;
		}
		
		//Gets the pkg-config PackageContent from the makefile (or autoconf?) var name
		public List<PackageContent> GetPackageContentFromVarName (string varname)
		{
			if (!pkgVarNameToPkgName.ContainsKey (varname)) {
				LoggingService.LogDebug ("pkg-config variable {0} not found in pkgVarNameToPkgName.", varname);
				return null;
			}
			
			return pkgVarNameToPkgName [varname];
		}

		//Gets the pkg-config varname from a package name (info comes from configure.in)
		public string GetVarNameFromName (string name)
		{
			if (!pkgNameToPkgVarName.ContainsKey (name)) {
				LoggingService.LogDebug ("Package named '{0}' not specified in configure.in", name);
				return null;
			}

			return pkgNameToPkgVarName [name];
		}

		public bool HasAcSubst (string varname)
		{
			return varNameAcSubst.ContainsKey (varname);
		}
		
		
		void ReadPackagesList ()
		{
			pkgVarNameToPkgName = new Dictionary<string, List<PackageContent>> ();
			pkgNameToPkgVarName = new Dictionary<string, string> ();
			varNameAcSubst = new Dictionary<string, string> ();

			string content = null;
			using (StreamReader sr = new StreamReader (fullpath))
				content = sr.ReadToEnd ();
			var assemblyContext = MakefileData.GetMonoRuntimeContext ();

			foreach (Match match in PkgCheckModulesRegex.Matches (content)) {
				if (!match.Success)
					continue;

				List<PackageContent> pkgs = new List<PackageContent> ();
				string pkgId = match.Groups ["pkgId"].Value;
				if (pkgId.Length > 2 && pkgId [0] == '[' && pkgId [pkgId.Length - 1] == ']')
					// Remove [] used for quoting
					pkgId = pkgId.Substring (1, pkgId.Length - 2);

				foreach (Capture c in match.Groups ["content"].Captures) {
					string s = c.Value.Trim ();
					if (s.Length == 0)
						continue;

					if (s.Length > 2 && s [0] == '[' && s [s.Length - 1] == ']')
						// Remove [] used for quoting
						s = s.Substring (1, s.Length - 2);
					PackageContent packageContent = new PackageContent (s);
					pkgs.Add (packageContent);
					pkgNameToPkgVarName [s] = pkgId;
					AddRequiredPackages (assemblyContext, pkgId, s, packageContent);
				}
				pkgVarNameToPkgName [pkgId] = pkgs;
			}
			
			foreach (Match match in AcSubstRegex.Matches (content)) {
				if (!match.Success)
					continue;

				string s = match.Groups [1].Value;
				if (!s.EndsWith ("_LIBS"))
					continue;

				string pkgVarName = s.Replace ("_LIBS", String.Empty);
				List<PackageContent> l = GetPackageContentFromVarName (pkgVarName);
				
				IAssemblyContext r = MakefileData.GetMonoRuntimeContext ();
				if (l != null && l.Count == 1 && r.GetPackage (l [0].Name) != null) {
					//PKG_CHECK_MODULES for pkgVarName was found
					//and it references only a single managed package
					//
					//This ensures that we don't emit $(FOO_LIBS)
					//for pkgVarName's that reference > 1 package or
					//for unmanaged packages
					varNameAcSubst [s] = s;
				}
			}
		}

		void AddRequiredPackages (IAssemblyContext assemblyContext, string variableName, string packageName, PackageContent packageContent)
		{
			SystemPackage package = assemblyContext.GetPackage (packageName);
			if (package != null && !string.IsNullOrEmpty (package.Requires)) {
				foreach (string requiredPackageName in package.Requires.Split (' ')) {
					if (!pkgNameToPkgVarName.ContainsKey (requiredPackageName)) {
						pkgNameToPkgVarName[requiredPackageName] = variableName;
						packageContent.RequiredPackages.Add (requiredPackageName);
					}
					AddRequiredPackages (assemblyContext, variableName, requiredPackageName, packageContent);
				}
			}
		}
		
		public DateTime LastWriteTime {
			get { return lastWriteTime; }
		}

		static Regex pkgCheckModulesRegex = null;
		static Regex PkgCheckModulesRegex {
			get {
				if (pkgCheckModulesRegex == null)
					pkgCheckModulesRegex = new Regex (
						@".*PKG_CHECK_MODULES\(\s*(?<pkgId>[^,\) \t]*)\s*,(\s*(?<content>[^,\) \t]*)\s*([><=]+\s*[^,\) \t]+|))*");
				return pkgCheckModulesRegex;
			}
		}

		static Regex acsubstRegex = null;
		static Regex AcSubstRegex {
			get {
				if (acsubstRegex == null)
					acsubstRegex = new Regex (@"AC_SUBST\(\s*([^\)\s]+)\s*\)");
				return acsubstRegex;
			}
		}
	}
	
	public class PackageContent
	{
		public string Name { get; set; }
		
		System.Collections.Generic.List<string> requiredPackages = new System.Collections.Generic.List<string> ();
		public List<string> RequiredPackages { 
			get {
				return requiredPackages; 
			}
		}
		
		public IEnumerable<string> AllReferencedNames {
			get {
				yield return Name;
				foreach (string name in requiredPackages) {
					yield return name;
				}
			}
		}
		
		public PackageContent (string name)
		{
			this.Name = name;
		}
	}
}
