The [[plugins/map]] plugin has inconsistent behaviour.  In particular, I have in my wiki some directory structures holding files without wikitext pointers (I point directly to the files from elsewhere).  For example, imagine the following file structure in the source dir:

    ; ls -R dirA dirB
    dirA:
    subA	subB
    
    dirA/subA:
    filea.mdwn	fileb.mdwn
    
    dirA/subB:
    filec.mdwn	filed.mdwn
    
    dirB:
    subA	subC
    
    dirB/subA:
    filea.mdwn
    
    dirB/subC:
    fileb.mdwn	filec.mdwn

When I use map to make a map of this, the result looks more like this:

<ul>
<li><span class="createlink">? dirA</span>
<ul>
<li><span class="createlink">? subA</span>
<ul>
<li>filea
</li>
</ul>
<ul>
<li>fileb
</li>
</ul>
<ul>
<li>filec
</li>
<li>filed
</li>
</ul>
</li>
</ul>
</li>
<li><span class="createlink">? dirB</span>
<ul>
<li><span class="createlink">? subA</span>
<ul>
<li>filea
</li>
</ul>
</li>
</ul>
<ul>
<li><span class="createlink">? subC</span>
<ul>
<li>fileb
</li>
</ul>
<ul>
<li>filec
</li>
</ul>
</li>
</ul>
</li>
</ul>

Note that while the dirA/subA directory exists with a create link, the dirA/subB directory is missing from the map.  Interstingly, dirB/subC is shown in the map.  If you add a second file to dirB/subA then dirB/subC disappears as well.

I could imagine including all 'bare' directories in the map, and I could imagine including no 'bare' directories in the map.  Just including the first bare directory seems a strange intermediate point.