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Hi Hugo,

After about 3 weeks, I have finally managed to get my wordpress 4.2.2 multisite installation using subdirectories (rather than subdomains) to work.
Here is the urltollkit that I had to use:

UrlToolkit {
    ToolkitID = wp-multi-subdir
    Match ^/index\.php$ Return
    Match ^/([_0-9a-zA-Z-]+/)?wp-admin$ Redirect /$1wp-admin/
    RequestURI exists Return
    Match ^/([_0-9a-zA-Z-]+/)?(wp-(content|admin|includes).*) Rewrite /$2
    Match ^/([_0-9a-zA-Z-]+/)?(.*\.php)$ Rewrite /$2
    Match ^/[_0-9a-zA-Z-]+(/wp-.*) Rewrite /$1    # if not present 404 - error is displayed
   # Match ^/[_0-9a-zA-Z-]+(/.*\.php)$ Rewrite /$1 #test
    Match .* Rewrite /index.php?$1
}

I have tested it extensively and I really feel that it should go on your "HOWTO: URL rewrite rules" page as I believe other people is struggling in figuring this out

Thank you for all you patience, help and support so far
Hiawatha version: 9.12
Operating System: FreeBSD 10.1

Thanks! I've added it to the HOWTO page.