mono: Don't clean mono's runtime directories.

xbuild requires the various .exe files in the runtime directories to
be executable.

Closes #31457.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
mono: update 3.4.0_1 bottle.
nexus 2.9.0-04

Closes #31520.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
mongodb 2.6.4
mongodb: update 2.6.4 bottle.