Some examples of integration points in a MS Deploy

filesystem.pubxml

<?xml version="1.0" encoding="utf-8"?>
<!--
This file is used by the publish/package process of your Web project. You can customize the behavior of this process
by editing this MSBuild file. In order to learn more about this please visit http://go.microsoft.com/fwlink/?LinkID=208121. 
-->
<Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
      <PropertyGroup>
        <PipelineCollectFilesPhaseDependsOn>
          CustomCollectFiles;
          $(PipelineCollectFilesPhaseDependsOn);
        </PipelineCollectFilesPhaseDependsOn>
      </PropertyGroup>

      <PropertyGroup>
        <OnAfterCopyAllFilesToSingleFolderForPackage>
            CreateEmptyFolders;
            $(OnAfterCopyAllFilesToSingleFolderForPackage)
        </OnAfterCopyAllFilesToSingleFolderForPackage>
      </PropertyGroup>

    <PropertyGroup>
        <AfterAddIisSettingAndFileContentsToSourceManifest Condition="'$(AfterAddIisSettingAndFileContentsToSourceManifest)'==''">
              $(AfterAddIisSettingAndFileContentsToSourceManifest);
              AddCustomSkipRules;
        </AfterAddIisSettingAndFileContentsToSourceManifest>    
        <WebPublishMethod>FileSystem</WebPublishMethod>
        <LastUsedBuildConfiguration>Release</LastUsedBuildConfiguration>
        <LastUsedPlatform>Any CPU</LastUsedPlatform>
        <SiteUrlToLaunchAfterPublish/>
        <LaunchSiteAfterPublish>True</LaunchSiteAfterPublish>
        <ExcludeApp_Data>False</ExcludeApp_Data>
        <publishUrl>c:\temp\ApplicationCataloguePackage</publishUrl>
        <DeleteExistingFiles>False</DeleteExistingFiles>        
    </PropertyGroup>

    <Target Name="CreateEmptyFolders">
        <Message Text="Custom task to create required empty folders  $(_MSDeployDirPath) and $(_MSDeployDirPath_FullPath)" />
        <MakeDir Directories="$(PublishUrl)\App_Data" />
    </Target>

    <Target Name="AddCustomSkipRules" DependsOnTargets="CreateEmptyFolders">
        <Message Text="Custom task running to skip folders created on a previous deployment.  $(_MSDeployDirPath) and $(_MSDeployDirPath_FullPath)" Importance="High"/>
    </Target>

    <Target Name="CustomCollectFiles">
        <Message Text="Please, please, please let this work  $(_MSDeployDirPath) and $(_MSDeployDirPath_FullPath)" Importance="High" />
    </Target>

    <Target Name="CustomAction" AfterTargets="CopyAllFilesToSingleFolderForPackage">
        <Message Text="Fingers crossed since this might be better $(_MSDeployDirPath) and $(_MSDeployDirPath_FullPath)" Importance="High" />
        <MakeDir Directories="$(PublishUrl)\App_Data" />
    </Target>

<Target Name="AfterPublish" AfterTargets="MSDeployPublish" >
    <Message Importance="High" Text="Project Published, Forrest" ></Message>
  </Target>

     <ItemGroup>
        <MsDeploySourceManifest Include="setAcl">
            <Path>$(PublishUrl)\App_Data</Path>
            <setAclUser>DefaultAppPool</setAclUser>
            <setAclAccess>Read</setAclAccess>
            <setAclResourceType>Directory</setAclResourceType>
            <AdditionalProviderSettings>setAclUser;setAclResourceType;setAclAccess</AdditionalProviderSettings>
        </MsDeploySourceManifest>
    </ItemGroup>
</Project>