The description of system-files in The system-files interface appears to indicate you can access files from the host system directly - but clearly this is not the case - so are you saying that only certain paths get added to a snap’s mount namespace (and so I am guessing /usr/include etc is not part of this - although clearly /usr/include/sudo_plugin.h is…?)
Is it possible to have the entire host file-system appear in the snap’s mount namespace at / without having to go via /var/lib/snapd/hostfs (since I don’t think it is feasible for applications to have to handle this in some transparent manner - ie. the ccls application would have to be snap-aware to translate /usr/include/foo -> /var/lib/snapd/hostfs/usr/lib/foo).
IMO it would be great if the system-files implementation be changed to ensure that anything listed via system-files gets added to the snaps mount namespace automatically as I suspect this is how most snap developers would expect it to operate. @jdstrand @pedronis can you comment?