Not a permissions problem two different entrypoints read config from two different places

clickhouse start is the installer wrapper It builds the server command line itself

command = fmt::format("{} --config-file {} --pid-file {} --daemon", executable, config, pid_file);

with config hardcoded from --config-path defaulting to etc/clickhouse-server/config.xml under the install prefix That is why edits under /etc/clickhouse-server show up there

clickhouse server runs the binary directly With no --config-file given it falls back to

std::string BaseDaemon::getDefaultConfigFileName() const { return "config.xml"; }

a bare relative name resolved against whatever directory you happened to launch from not /etc

And it fails silently instead of erroring Server.cpp registers an embedded copy of config.xml and ConfigProcessor falls back to that embedded config whenever the real file is not found at the resolved path So the server boots fine on built in defaults and every edit you made is quietly ignored no error no warning

Fix is one flag

clickhouse server --config-file /etc/clickhouse-server/config.xml

or cd /etc/clickhouse-server first or just keep using clickhouse start

Side note the trailing start in clickhouse server start is not a subcommand of server server and start are two separate top level clickhouse commands you are not chaining them