I know you mentioned there would be a command line version, and so here it is. I have however put it in a shell script, which keeps it in a file you can then put into your project or a local bin directory and run again when needed. This worked on a couple of examples I threw together and without any un escaped character errors. As mentioned by previous comments, your code is fine with the noted changes, but I still thought you might be interested in a smaller command line solution as well. 
#!/bin/sh
for file in `find ./ -name '*.html'`; do 
perl -i.bak -ane "s/<!--#include virtual=\"(.*)\" *-->/<?php include(\
+\$\_SERVER['DOCUMENT_ROOT'].'\$1');?>/g; print;" $file
done

[download]

---
echo S 1 [ Y V U | perl -ane 'print reverse map { $_ = chr(ord($_)-1) } @F;'

In reply to Re: modify file in place in script? Regex for changing includes from SSI to PHP by tuxz0r
in thread modify file in place in script? Regex for changing includes from SSI to PHP by hmbscully

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.