How to allow .markdown and .md (at the same time) as valid extensions for source files? The default is .mdwn.

Add md to your add_plugins, set libdir if not already set, put the following in ${libdir}/IkiWiki/Plugin/, and rebuild:

package IkiWiki::Plugin::md;

use warnings;
use strict;
use IkiWiki 3.00;

my @ADDITIONAL_EXTENSIONS = qw(md markdown);

sub import {
    foreach my $ext (@ADDITIONAL_EXTENSIONS) {
        hook(type => "htmlize", id => $ext, call => \&IkiWiki::Plugin::mdwn::htmlize, longname => "Markdown (.$ext)");