@iJoel You can do this by simply concatenating the intermediate and CA cert files into a single cert file.
So, in the '.crt' file which you upload to Cloudron, it will have:
-----BEGIN CERTIFICATE-----
the *.foo.com certificate
-----END CERTIFICATE-----
-----BEGIN CERTIFICATE-----
intermediate cert
-----END CERTIFICATE-----
-----BEGIN CERTIFICATE-----
root cert if any
-----END CERTIFICATE-----
The ordering of the certs is important above.