makepages.py

#!/usr/bin/env python

import os

import markdown2

with open('head.html') as f:
    head = f.read()
with open('foot.html') as f:
    foot = f.read()

for root, __, files in os.walk('.'):
    for name in files:
        filename = os.path.splitext(name)
        if not len(filename) == 2:
            continue
        if not filename[1] == '.md':
            continue
        html = markdown2.markdown_path(os.path.join(root, name))
        with open(os.path.join(root, os.path.splitext(name)[0] + '.html'), 'w') as f:
            f.write(head)
            f.write(html)
            f.write(foot)

This needs the python module markdown2 (pip install markdown2)