This pipeline copies a ZIP file, renaming "README.md" to "README.txt". It requires XML Calabash 1.0.16 or later (because there are a couple of bugs in earlier versions of the zip/unzip implementations).

renamezip.xpl

<p:declare-step xmlns:p="http://www.w3.org/ns/xproc"
                xmlns:cx="http://xmlcalabash.com/ns/extensions"
                xmlns:c="http://www.w3.org/ns/xproc-step"
                xmlns:pxp="http://exproc.org/proposed/steps"
                name="main" version="1.0">
  <p:input port="parameters" kind="parameter"/>
  <p:output port="result">
    <p:pipe step="zip" port="result"/>
  </p:output>
  <p:serialization port="result" indent="true"/>
  <p:import href="http://xmlcalabash.com/extension/steps/library-1.0.xpl"/>

  <pxp:unzip href="testzip.zip"/>

  <p:for-each name="loop">
    <p:iteration-source select="/c:zipfile/c:file"/>
    <p:output port="docs">
      <p:pipe step="unzip" port="result"/>
    </p:output>
    <p:output port="entries">
      <p:pipe step="entry" port="result"/>
    </p:output>

    <pxp:unzip name="unzip" href="testzip.zip" content-type="application/octet-stream">
      <p:with-option name="file" select="/c:file/@name"/>
    </pxp:unzip>

    <p:choose>
      <p:xpath-context>
        <p:pipe step="loop" port="current"/>
      </p:xpath-context>
      <p:when test="/c:file/@name = 'README.md'">
        <p:identity>
          <p:input port="source">
            <p:inline><c:entry name="README.txt"/></p:inline>
          </p:input>
        </p:identity>
      </p:when>
      <p:otherwise>
        <p:add-attribute attribute-name="name" match="/c:entry">
          <p:input port="source">
            <p:inline><c:entry/></p:inline>
          </p:input>
          <p:with-option name="attribute-value" select="/c:file/@name">
            <p:pipe step="loop" port="current"/>
          </p:with-option>
        </p:add-attribute>
      </p:otherwise>
    </p:choose>

    <p:add-attribute name="entry" attribute-name="href" match="/c:entry">
      <p:with-option name="attribute-value" select="base-uri(/c:data)">
        <p:pipe step="unzip" port="result"/>
      </p:with-option>
    </p:add-attribute>
  </p:for-each>

  <p:wrap-sequence name="manifest" wrapper="c:zip-manifest">
    <p:input port="source">
      <p:pipe step="loop" port="entries"/>
    </p:input>
  </p:wrap-sequence>

  <pxp:zip name="zip" href="/tmp/newzip.zip">
    <p:input port="source">
      <p:pipe step="loop" port="docs"/>
    </p:input>
    <p:input port="manifest">
      <p:pipe step="manifest" port="result"/>
    </p:input>
  </pxp:zip>

</p:declare-step>

Adding a <p:with-option name="href" select="resolve-uri('newzip.zip', document-uri())"/> seems to work.