doxyassist file for StepClassLibrary - subprojects don't show up in main project

doxyassist.xml

<?xml version="1.0" encoding="utf-8"?>
<!-- run doxyassist from scl root dir:
    ../doxyassist/doxyassist.py doc/doxyassist.xml -->

<!-- The main tag provides the version (1.0 only for now). The type attribute
     is not required, and defaults to "generic". To use a different project handler,
     change its type. The "name" attribute defines the name of your configuration.
     Note: you must define and use the "http://simply-life.net/doxyassist/project.xsd"
     namespace for the XML file to be processed properly.  -->
<DoxyAssist xmlns="http://simply-life.net/doxyassist/doxyassist.xsd"
            xmlns:da="http://simply-life.net/doxyassist/doxyassist.xsd"
            version="1.0" type="generic" name="My DoxyAssist Project">
  <!-- You can set global settings here. The doxyfile attribute defines the
       Doxyfile to load by default. If none is given, or the template cannot be
       loaded, the default Doxygen settings are used as base.

       You can include any setting here, and it will be passed to Doxygen
       (even if it is not a recognized setting). You can add as many as you like,
       overriding the template or default Doxyfile.

       The given template file will never be overwritten by Doxygen Assistant.
       Instead the project specific version will be kept in memory and written
       to Doxygen over a pipe.

       Note that some settings are always overridden due to project definitions.
       See the information near the projects for more information. Changing these
       settings here will have no effect when using the Doxygen Assistant to
       run Doxygen. -->
  <doxygen doxyfile="./doc/Doxyfile">
    <!-- A boolean setting is defined like this. This will write "YES" or "NO" for
         the specific setting in the Doxyfile passed to Doxygen. -->
    <bool name="CREATE_SUBDIRS">false</bool>
    <!-- A numeric setting is written like this. It will be written to the Doxyfile
         without quotes. -->
    <int name="TAB_SIZE">8</int>
    <!-- This is a single string setting. When writing this out to the doxyfile,
         it will be quoted and treated as a whole. -->
    <string name="OUTPUT_LANGUAGE">English</string>
    <!-- A list setting contains multiple elements, seperated by whitespace. Each
         individual item will be quoted and treated as a whole for Doxygen. By
         default a list replaces the existing setting. If the append attribute is
         set to true, then the items will be added to the existing set. -->
    <list name="FILE_PATTERNS" append="false">
      <item>*.h</item>
      <item>*.c</item>
      <item>*.hh</item>
      <item>*.cc</item>
      <item>README</item>
  </list>
  </doxygen>

  <!-- Settings for the Qt Help Collection to create. If not present, no
       help collection will be created. See
       http://doc.trolltech.com/assistant-custom-help-viewer.html for a
       description of all settings; the inner configuration is copied directly
       into the <assistant> section of the project file.

       The collectionFile attribute contains the path to the collection file to
       create (this file must be writable). Additionally provide the name for the
       project file in the projectFile attribute. By default this is the same
       as the collection file, with an extension of "qhcp" instead of "qhc"

       The storage attribute defines the subdirectory to place copies of Qt
       Compressed Help files in. The copyAction attribute defaults to making
       actual copies; this attribute can be set to "copy", "move" and "symlink".
  -->
  <qtHelp collectionFile="./doc/helpcollection.qhc"
          projectFile="./doc/helpcollection.qhcp"
          storage="./doc/qch" copyAction="copy">
    <title>StepClassLibrary</title>
    <startPage>qthelp://com.github.mpictor/doc/index.html</startPage>
    <!-- See http://doc.trolltech.com/assistant-custom-help-viewer.html for more
         settings in the <assistant> section. -->
  </qtHelp>
  <!-- Start a list of projects -->
  <projects>
    <!-- A project contains information about one Doxygen run, as well as
         as well as subprojects. It can have its completely own Doxygen
         configuration.

         Various settings are determined by the Doxygen Assistant; they will
         always override the Doxyfile settings. All values are by default inherited
         from the parent project, or empty if there is nothing to inherit from,
         unless noted otherwise. Note that even if a value is empty, this will
         override the Doxyfile settings. The following Doxyfile settings are
         overridden:
         - PROJECT_NAME
         - PROJECT_VERSION
         - INPUT
         - EXCLUDE
         - OUTPUT_DIRECTORY
         - WARN_LOGFILE
         - DOCSET_BUNDLE_ID
         - QCH_FILE
         - QHP_NAMESPACE
         - QHP_CUST_FILTER_NAME
         - QHP_CUST_FILTER_ATTRS
         - QHP_SECT_FILTER_ATTRS
    -->
    <project>
      <!-- The name of the project -->
      <name>StepClassLibrary</name>
      <!-- The version number of the documentation -->
      <version>0.2</version>
      <!-- Whether to build version specific documentation for the projects or not.
         Note that if this is set, Qt Help filters may become invalid when newer
         versions of the documentation are built. Due to user-specific settings,
         it may be necessary to remove the user specific cache files to reset
         the filters. It does however allow you to keep documentation of multiple
         versions next to each other. Default value is false.

         Note that regardless of this setting, the version is still used in the
         PROJECT_NUMBER setting, as well as the PROJECT_NAME of subprojects -->
      <versionSpecific>false</versionSpecific>
      <!-- Full path to the directory with documented source code. You can add
           multiple input lines if you need to add multiple locations.

           If you want documentation of subprojects to be explicitly included as well,
           you must list the EXACT same input directories in the parent; this
           will prevent the directories from being excluded. -->
      <input>./src</input>
      <input>./include</input>
      <!-- A list of files/paths to exclude. Add one <exclude> tag per path to
           exclude. This will automatically be expanded to exclude input directories
           of subprojects, and prevent mangled documentation. -->
<!--       <exclude>/path/to/my-application/src/excluded</exclude> -->
      <!-- Directory to store Doxygen output for this project. Note that within
           this directory, a subdirectory is created based on the project name.
           Additionally, if the <versionspecific> setting has a value of true,
           another subdirectory based on the version number will be created (e.g.
           "/path/to/my-application/out/my-application/1.0". -->
      <output>./doc/doxygen</output>
      <!-- The directory where error and log files will be stored. Log and error
           files will be named "my-application.1-0.log" and
           "my-application.1-0-error.log" respectively. -->
      <logDirectory>./doc/doxygen/log</logDirectory>
      <!-- Optional base namespace for this application. This is prefixed to the
           normalized project name and version number (if version specific is set).
           The full namespace would now become "com.mycompany.my-application.1-0"
           in this example. -->
      <namespace>github.mpictor</namespace>
      <!-- You can define a <doxygen> block, in which you set project specific
           settings. This will hold for this and all subprojects. See also the
           <doxygen> block above. If you provide a doxyfile attribute, that
           file will be used as template instead; this also implies all settings
           in parent projects including the main doxygen settings will be
           discarded. -->
<!--      <doxygen>
        <list name="FILE_PATTERNS" append="true">
          <item>*.module</item>
          <item>*.inc</item>
          <item>*.html</item>
        </list>
      </doxygen>-->

      <!-- You can define subprojects here. Input directories of subprojects are
           automatically excluded from parent projects. As such, documentation will
           not be mixed.

           Note that by default _all_ settings will be inherited from the parent.
      -->
      <project>
        <!-- The name of the subproject -->
        <name>CLStepCore</name>
        <!-- And its version -->
<!--         <version>1.1</version> -->
        <!-- Whether to build version specific documentation for this subproject.
             If the parent is version specific, that setting will still be
             adhered to. If this is left out, the parent setting is inherited. -->
        <versionSpecific>false</versionSpecific>
        <!-- Full path to the directory with documented source code -->
        <input>./src/clstepcore</input>
        <!-- Subproject excluded directories -->
<!--         <exclude>/path/to/my-application/src/mymodule/excluded</exclude> -->
        <!-- Optional output directory. If omitted, the parent project's output
             directory is inherited. The actual output is written to the same
             subdirectory of the parent project, in an extra subdirectory with a
             name based on the project name and optionally version. -->
<!--         <output>/path/to/my-application/out</output> -->
        <!-- The optional log directory. If omitted, the parent project's log
             directory is inherited. Files will be named using project name and
             version number (if versionSpecific is true), including the parent
             project's information. Log and error files will, in this example,
             be named "my-application.1-0.my-module.log" and
             "my-application.1-0.my-module.err" respectively. -->
<!--         <logDirectory>/path/to/my-application/doc/log</logDirectory> -->
        <!-- Additional part to prefix the project's subnamespace with. In this
             example, the namespace would become
             "com.mycompany.my-application.1-0.modules.my-module". -->
<!--         <namespace>modules</namespace> -->
        <!-- You can add subprojects to subprojects as well, if you like -->
      </project>
        <project>
            <name>CLDAI</name>
            <versionSpecific>false</versionSpecific>
            <input>./src/cldai</input>
            <input>./include</input>
        </project>
        <project>
            <name>CLEditor</name>
            <versionSpecific>false</versionSpecific>
            <input>./src/cleditor</input>
            <input>./include</input>
        </project>
        <project>
            <name>CLProbe-ui</name>
            <versionSpecific>false</versionSpecific>
            <input>./src/clprobe-ui</input>
            <input>./include</input>
        </project>
        <project>
            <name>CLUtils</name>
            <versionSpecific>false</versionSpecific>
            <input>./src/clutils</input>
            <input>./include</input>
        </project>
        <project>
            <name>ExPPP</name>
            <versionSpecific>false</versionSpecific>
            <input>./src/exppp</input>
            <input>./include</input>
            <input>./include/exppp</input>
        </project>
        <project>
            <name>Express</name>
            <versionSpecific>false</versionSpecific>
            <input>./src/express</input>
            <input>./include</input>
            <input>./include/express</input>
        </project>
        <project>
            <name>Fedex Plus</name>
            <versionSpecific>false</versionSpecific>
            <input>./src/fedex_plus</input>
            <input>./include</input>
        </project>
        <project>
            <name>Tests</name>
            <versionSpecific>false</versionSpecific>
            <input>./src/test</input>
            <input>./include</input>
        </project>
    </project>
    <!-- And you can even add more top level projects to collect. -->
  </projects>
</DoxyAssist>