Shallow Numbering for Chapters Only
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The default numbering system is to only number the chapters in the TOC and in the content (shallow numbering).
Note: For a plain DITA map, the chapters are the <topicref> elements that are placed on the first level. For bookmaps, the chapters are the topics referenced by a <chapter> element.

Shallow Numbering - Input XML Fragments
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The numbering affects three parts of your publication, the table of contents, headers/footers, and chapter titles:

The Table of Contents

The table of contents is a tree of <topicref> elements. 

<map xmlns:ditaarch="http://dita.oasis-open.org/architecture/2005/" ...>
  <oxy:front-page xmlns:oxy="http://www.oxygenxml.com/extensions/author" 
        class=" front-page/front-page ">
        ...
  </oxy:front-page>
  <opentopic:map xmlns:opentopic="http://www.idiominc.com/opentopic" class=" toc/toc ">
    <title class="- topic/title ">Publication Title</title>

    <topicref is-chapter="true" class="- map/topicref " ... >
      <topicmeta class="- map/topicmeta " ... >
        <navtitle href="#unique_1" class="- topic/navtitle ">Overview</navtitle>
            ...
      </topicmeta>
      <topicref class="- map/topicref " ...>
        <topicmeta class="- map/topicmeta " data-topic-id="dcpp_resources">
          <navtitle href="#unique_2" class="- topic/navtitle ">Resources</navtitle>
            ...
        </topicmeta>
      </topicref>
        ...
  </opentopic:map>
...
</map>
Note: The <opentopic:map> element contains the effective table of contents structure.
Note: The TOC items are the elements with the class: - map/topicref.
Note: The ones identified as chapters have the @is-chapter attribute set.

For the DITA Map PDF - based on HTML5 & CSS transformation type, the merged map is further processed resulting in a collection of HTML5 <div> elements. These elements preserve the original DITA @class attribute values and add a new value derived from the DITA element name.

<div class="- map/map map" ...>
  <div 
        class=" front-page/front-page front-page">
        ...
  </div>
  <div class=" toc/toc toc">
    <div class="- topic/title title">Publication Title</title>

    <div is-chapter="true" class="- map/topicref topicref" ... >
      <div class="- map/topicmeta topicmeta" ... >
        <div href="#unique_1" class="- topic/navtitle navtitle">Overview</div>
            ...
      </div>
      <div class="- map/topicref " ...>
        <div class="- map/topicmeta " data-topic-id="dcpp_resources">
          <div href="#unique_2" class="- topic/navtitle ">Resources</div>
            ...
        </div>
      </div>
        ...
  </div>
...
</div>

The Header and Footers

These are based on string sets generated for the titles. The complete set of strings is defined in: [INSTALLATION_DIR]/css/print/p-pages-and-headers.css.

The CSS rules that build the string sets are matching the map title from the front page and the titles from the content.
<oxy:front-page xmlns:oxy="http://www.oxygenxml.com/extensions/author">
        <oxy:front-page-title>
            <title class="- topic/title ">Publication Title</title>
        </oxy:front-page-title>
</oxy:front-page>
For the DITA Map PDF - based on HTML5 & CSS transformations:
<div class=" front-page/front-page front-page">
        <div class=" front-page-title/front-page-title front-page-title">
            <div class="- topic/title title ">Publication Title</div>
        </div>
</div>
The main content is organized as follows:
<map xmlns:ditaarch="http://dita.oasis-open.org/architecture/2005/" ...>
    ...
    <opentopic:map xmlns:opentopic="http://www.idiominc.com/opentopic">
      ...
    </opentopic:map>

    <topic is-chapter="true" oid="dcpp_overview">
        <title class="- topic/title ">Overview</title>
        <body class="- topic/body ">
            ...
        </body>
        <topic class="- topic/topic " id="unique_2" oid="dcpp_resources">
            <title class="- topic/title ">Resources</title>
            ...
        </topic>
        <topic class="- topic/topic " id="unique_2" oid="dcpp_parameters">
            <title class="- topic/title ">Parameters</title>
            ...
        </topic>
    </topic>
For the DITA Map PDF - based on HTML5 & CSS transformations:
<div class=" map/map map" ...>
    ...
   <div class=" toc/toc toc">
      ...
    </div>

    <div is-chapter="true" oid="dcpp_overview" class="- topic/topic topic">
        <div class="- topic/title title">Overview</title>
        <div class="- topic/body body">
            ...
        </div>
        <div class="- topic/topic topic" id="unique_2" oid="dcpp_resources">
            <div class="- topic/title title">Resources</div>
            ...
        </div>
        <div class="- topic/topic topic" id="unique_2" oid="dcpp_parameters">
            <div class="- topic/title title">Parameters</div>
            ...
        </div>
    </div>
Note: The topic content comes after the <opentopic:map> element.
Note: The child topics are the elements that have the class - topic/topic included in the parents.
Note: The ones identified as chapters have the @is-chapter attribute set.

The Titles of Chapters

The titles from the content are children of the topics:
<topic class="- topic/topic " id="unique_2" oid="dcpp_parameters">
        <title class="- topic/title ">Parameters</title>
            ...
</topic>
For the DITA Map PDF - based on HTML5 & CSS transformations:
<div class="- topic/topic topic" id="unique_2" oid="dcpp_parameters">
        <div class="- topic/title title ">Parameters</div>
            ...
</div>
Note: The title elements have the class: - topic/title. The actual element name can be different.

Shallow Numbering - Built-in CSS
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There is a file located in [PLUGIN_DIR]/css/print/p-numbering-shallow. This contains all the rules for numbering only the topics on the first level (the chapters).