tools: customize mk-ca-bundle.pl

Remove unneeded functionality and tweak the generated output so we
can #include it in C++ source code.

This commit essentially reapplies the changes from commit e159073d
("tools: customize mk-ca-bundle.pl") to the updated script.

PR-URL: https://github.com/nodejs/io.js/pull/1833


Reviewed-By: Shigeki Ohtsu <ohtsu@iij.ad.jp>