added working code

CombineArchive.sln

@@ -0,0 +1,32 @@
+
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio 2012
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "LibCombine", "LibCombine\LibCombine.csproj", "{FA52A855-38B5-4110-9C69-D62FC7D9EF7B}"
+EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "CombineCLI", "CombineCLI\CombineCLI.csproj", "{1CA41C80-EE9C-4C32-B7F0-621801257429}"
+EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "FormsCombineArchive", "FormsCombineArchive\FormsCombineArchive.csproj", "{A2D55519-57E2-497A-912F-3D857823E4B9}"
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Any CPU = Debug|Any CPU
+		Release|Any CPU = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(ProjectConfigurationPlatforms) = postSolution
+		{FA52A855-38B5-4110-9C69-D62FC7D9EF7B}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{FA52A855-38B5-4110-9C69-D62FC7D9EF7B}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{FA52A855-38B5-4110-9C69-D62FC7D9EF7B}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{FA52A855-38B5-4110-9C69-D62FC7D9EF7B}.Release|Any CPU.Build.0 = Release|Any CPU
+		{1CA41C80-EE9C-4C32-B7F0-621801257429}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{1CA41C80-EE9C-4C32-B7F0-621801257429}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{1CA41C80-EE9C-4C32-B7F0-621801257429}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{1CA41C80-EE9C-4C32-B7F0-621801257429}.Release|Any CPU.Build.0 = Release|Any CPU
+		{A2D55519-57E2-497A-912F-3D857823E4B9}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{A2D55519-57E2-497A-912F-3D857823E4B9}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{A2D55519-57E2-497A-912F-3D857823E4B9}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{A2D55519-57E2-497A-912F-3D857823E4B9}.Release|Any CPU.Build.0 = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	EndGlobalSection
+EndGlobal

CombineCLI/App.config

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<configuration>
+    <startup> 
+        <supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.5" />
+    </startup>
+</configuration>

CombineCLI/CombineCLI.csproj

@@ -0,0 +1,64 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Project ToolsVersion="4.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+  <Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
+  <PropertyGroup>
+    <Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
+    <Platform Condition=" '$(Platform)' == '' ">AnyCPU</Platform>
+    <ProjectGuid>{1CA41C80-EE9C-4C32-B7F0-621801257429}</ProjectGuid>
+    <OutputType>Exe</OutputType>
+    <AppDesignerFolder>Properties</AppDesignerFolder>
+    <RootNamespace>CombineCLI</RootNamespace>
+    <AssemblyName>CombineCLI</AssemblyName>
+    <TargetFrameworkVersion>v4.5</TargetFrameworkVersion>
+    <FileAlignment>512</FileAlignment>
+  </PropertyGroup>
+  <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
+    <PlatformTarget>AnyCPU</PlatformTarget>
+    <DebugSymbols>true</DebugSymbols>
+    <DebugType>full</DebugType>
+    <Optimize>false</Optimize>
+    <OutputPath>bin\Debug\</OutputPath>
+    <DefineConstants>DEBUG;TRACE</DefineConstants>
+    <ErrorReport>prompt</ErrorReport>
+    <WarningLevel>4</WarningLevel>
+  </PropertyGroup>
+  <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
+    <PlatformTarget>AnyCPU</PlatformTarget>
+    <DebugType>pdbonly</DebugType>
+    <Optimize>true</Optimize>
+    <OutputPath>bin\Release\</OutputPath>
+    <DefineConstants>TRACE</DefineConstants>
+    <ErrorReport>prompt</ErrorReport>
+    <WarningLevel>4</WarningLevel>
+  </PropertyGroup>
+  <ItemGroup>
+    <Reference Include="System" />
+    <Reference Include="System.Core" />
+    <Reference Include="System.Xml.Linq" />
+    <Reference Include="System.Data.DataSetExtensions" />
+    <Reference Include="Microsoft.CSharp" />
+    <Reference Include="System.Data" />
+    <Reference Include="System.Xml" />
+  </ItemGroup>
+  <ItemGroup>
+    <Compile Include="Program.cs" />
+    <Compile Include="Properties\AssemblyInfo.cs" />
+  </ItemGroup>
+  <ItemGroup>
+    <None Include="App.config" />
+  </ItemGroup>
+  <ItemGroup>
+    <ProjectReference Include="..\LibCombine\LibCombine.csproj">
+      <Project>{fa52a855-38b5-4110-9c69-d62fc7d9ef7b}</Project>
+      <Name>LibCombine</Name>
+    </ProjectReference>
+  </ItemGroup>
+  <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
+  <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
+       Other similar extension points exist, see Microsoft.Common.targets.
+  <Target Name="BeforeBuild">
+  </Target>
+  <Target Name="AfterBuild">
+  </Target>
+  -->
+</Project>

CombineCLI/Program.cs

@@ -0,0 +1,66 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using LibCombine;
+
+namespace CombineCLI
+{
+    class Program
+    {
+        static void Main(string[] args)
+        {
+
+             var archive = 
+                 CombineArchive.FromFile(@"C:\Users\fbergmann\Desktop\isola_oscillations_sed.sed.omex");
+
+             Console.WriteLine("Num SEDML files: {0}", archive.GetNumFilesWithFormat("SEDML"));
+             Console.WriteLine("Num SBML files: {0}", archive.GetNumFilesWithFormat("sbml"));
+             Console.WriteLine("Num SBML files: {0}", archive.GetNumFilesWithFormat("sbml"));
+
+             archive.SaveTo(@"C:\Users\fbergmann\Desktop\isola.omex");
+
+
+             var newArchive = new CombineArchive
+             {
+                 BaseDir = @"C:\Users\fbergmann\Documents\SBML Models\",
+                 Descriptions = new List<OmexDescription> { 
+                     new OmexDescription
+                {
+                    About = "./BorisEJB.xml",
+                    Description = "original JDesigner model for Kholodenko2000 - MAPK feedback",
+                    Creators =
+                        new List<VCard> 
+                        { 
+                            new VCard 
+                            { 
+                                FamilyName = "Bergmann", 
+                                GivenName = "Frank", 
+                                Email = "[email protected]", 
+                                Organization = "California Institute of Technology" 
+                            } 
+                        },
+                    Created = DateTime.Parse("2013-04-04 16:00+1")
+                }
+                 },
+                 Entries = new List<Entry> { 
+                     new Entry { Location = "./BorisEJB.xml", Format = Entry.KnownFormats["sbml"] }, 
+                     new Entry { Location = "./paper/Kholodenko2000.pdf", Format = Entry.KnownFormats["pdf"] }, 
+                     new Entry { Location = "http://www.ebi.ac.uk/biomodels-main/BIOMD0000000010", Format = Entry.KnownFormats["sbml"] }, 
+                 }
+             };
+
+             newArchive.SaveTo(@"C:\Users\fbergmann\Desktop\Boris.omex");
+
+             var omex = CombineArchive.FromFile(@"C:\Users\fbergmann\Desktop\Boris.omex");
+
+             if (omex.HasEntriesWithFormat("pdf"))
+                 omex.GetEntriesWithFormat("PDF").First().OpenLocation();
+
+
+            Console.ReadKey();
+        }
+    }
+}
+

CombineCLI/Properties/AssemblyInfo.cs

@@ -0,0 +1,36 @@
+using System.Reflection;
+using System.Runtime.CompilerServices;
+using System.Runtime.InteropServices;
+
+// General Information about an assembly is controlled through the following 
+// set of attributes. Change these attribute values to modify the information
+// associated with an assembly.
+[assembly: AssemblyTitle("CombineCLI")]
+[assembly: AssemblyDescription("")]
+[assembly: AssemblyConfiguration("")]
+[assembly: AssemblyCompany("")]
+[assembly: AssemblyProduct("CombineCLI")]
+[assembly: AssemblyCopyright("Copyright ©  2013")]
+[assembly: AssemblyTrademark("")]
+[assembly: AssemblyCulture("")]
+
+// Setting ComVisible to false makes the types in this assembly not visible 
+// to COM components.  If you need to access a type in this assembly from 
+// COM, set the ComVisible attribute to true on that type.
+[assembly: ComVisible(false)]
+
+// The following GUID is for the ID of the typelib if this project is exposed to COM
+[assembly: Guid("3b02161b-f2ef-4781-8775-8f83d6f29c9d")]
+
+// Version information for an assembly consists of the following four values:
+//
+//      Major Version
+//      Minor Version 
+//      Build Number
+//      Revision
+//
+// You can specify all the values or you can default the Build and Revision Numbers 
+// by using the '*' as shown below:
+// [assembly: AssemblyVersion("1.0.*")]
+[assembly: AssemblyVersion("1.0.0.0")]
+[assembly: AssemblyFileVersion("1.0.0.0")]