CIS Benchmark Compliance
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This is the out of the box results on a fully patched/updated Cloudron per Wazuh (as of about 90 seconds ago).

I will be deploying a test instance of Cloudron on a VM with a set of CIS/NIST ansible playbooks to get the node to 100% compliance and see if anything breaks.
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I have uploaded it here: https://staticbits.reachableceo.com/CloudronWazuhReport-2025-30-12.csv
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From a quick read it seems most (all?) are just general linux things. Have you tried this on a fresh Ubuntu 24.04 system without Cloudron? Because I suspect most of these "issues" are in that as well. Most of them are not really issues in my eyes atleast.
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As I mentioned, I'll be applying Ansible playbooks to bring the base system to 100% compliance.
I never said these were Cloudron issues. I said that I would be testing Cloudron on a 100% compliant base system and fixing anything that is broken. I don't expect any issues. Because, as you mentioned, these are all base system config tweaks.
Cloudron runs everything 100% in Docker images.
Where I suspect change may be needed, is at the Cloudron container level when I start scanning everything with Trivy.
Do you use hardened Docker base images?
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As I have said, I'm deploying a FLO stack (with Cloudron at the core) into a startup that I'm building (as CIO/CTO). We have to be CMMC compliant. Making sure Cloudron works on a 100% compliant base system is the first milestone. While you may not consider them issues, they do need to be addressed to be compliant. That's "my problem". If a fully compliant base system causes an issue in Cloudron , that's "our problem".

While you, and many Cloudron users may not care about CMMC/HIPPA/SOC/PCI compliance, I (and my board) do. I'm also building a small side business which will sell Cloudron as a service (pre setup/configured, all applications have admin password changed, admin passwords stored in Bitwarden) (the new Bitwarden SSO makes that possible without bootstrapping issues) and it will have CMMC/SOC/PCI/HIPPA compliance (at the higher tier).