Per the howto in the v3 helpfile, I've been first defining the folder
structure of a project then adding the files via DirectoryRef's.  

Now that I am adding more functionality to my projects, I find it much
easier to work with if I separate the file into logical chunks, such as IIS
configuration or XML file changes. However from the example below, you will
notice that there is a bit of redundancy happening with the multiple
DirectoryRef's. 

<!-- Directories -->
<Directory Id="TARGETDIR" Name="SourceDir">
    <Directory Id="ProgramFilesFolder">
        <Directory Id="APPLICATIONROOTDIRECTORY" Name="My Application
Name"/>
        <Directory Id="ANOTHERDIRECTORY" Name="Another Directory Name"/>
    </Directory>
</Directory>

<!-- File System -->
<DirectoryRef Id="APPLICATIONROOTDIRECTORY">
    <Component Id="myapplication.exe" Guid="PUT-GUID-HERE">
        <File Id="myapplication.exe"
Source="MySourceFiles\MyApplication.exe" KeyPath="yes" Checksum="yes"/>
    </Component>
    <Component Id="documentation.html" Guid="PUT-GUID-HERE">
        <File Id="documentation.html"
Source="MySourceFiles\documentation.html" KeyPath="yes"/>
    </Component>
</DirectoryRef>

<!-- IIS -->
<DirectoryRef Id="APPLICATIONROOTDIRECTORY">
  <Component Id="MyVirtualDirComponent" Guid="PUT-GUID-HERE" KeyPath="yes">
    <iis:WebVirtualDir Id="MyVDir" Alias="VirtualDir"
Directory="APPLICATIONROOTDIRECTORY" etc etc>
  </Component>
</DirectoryRef>

<!-- XML -->
<DirectoryRef Id="APPLICATIONROOTDIRECTORY">
  <Component Id="XmlConfigFile" Guid="PUT-GUID-HERE" KeyPath="yes">
    <File Id="xmlfile.xml" Name="xml.xml"
File="[APPLICATIONROOTDIRECTORY]xmlfile.xml" etc etc />
      <util:XmlFile Id="xmlfile.xml" etc etc />
  </Component>
</DirectoryRef>

I like this layout because its easier for me to read and also I can get to a
specific piece of functionality pretty quickly.  But I'm wondering if this
method is really the right way I should be doing it.  Both from a
performance standpoint (ie compile-link-generate times) and from a
maintainability standpoint.

Am I better off having one DirectoryRef element for any given folder and
putting all the IIS, XML, SQL, etc stuff underneath that, rather than
spreading it all out like I am doing now?

Thanks in advance. 
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