go-cobra-dead-persistent-flag

Answer

Root cause. Cobra binds persistent flags to variables only during ParseFlags, which runs inside ExecuteContext — after main.go's run() builds the registry. Reading the flag-bound variable before execution always yields "", so --data-dir was a dead flag and the registry silently fell back to config/default. Independently, the dashboard server derived paths from the hardcoded app.DefaultDataDir() instead of the registry, so even a config data_dir pointing elsewhere was ignored by everything the server touched.

Fix 1 — pre-parse os.Args before building the registry (flagparse.go):

// parseDataDirFlag pre-parses os.Args for the root persistent flag
// --data-dir. Cobra only parses flags during ExecuteContext, which runs
// AFTER registry construction, so reading the bound variable early is
// always empty (dead flag). This recovers the value before that point.
func parseDataDirFlag(args []string) string {
    dataDir := ""
    for i := 0; i < len(args); i++ {
        arg := args[i]
        switch {
        case arg == "--":
            return dataDir // everything after "--" is positional
        case arg == "--data-dir":
            if i+1 < len(args) {
                dataDir = args[i+1]
                i++ // consume the value
            }
        case strings.HasPrefix(arg, "--data-dir="):
            dataDir = strings.TrimPrefix(arg, "--data-dir=")
        }
    }
    return dataDir
}

Wire it into run() (precedence: flag > config > default):

func run(cfgPath string, args []string) (*Registry, error) {
    cfg := loadConfig(cfgPath)
    dataDir := parseDataDirFlag(args) // pre-parse, NOT dataDirFlag
    if dataDir == "" {
        dataDir = cfg.DataDir
    }
    return NewRegistry(dataDir), nil
}

func main() {
    registry, err := run(defaultConfigPath, os.Args[1:]) // registry built first
    if err != nil { /* exit */ }
    if err := newRootCmd(registry).ExecuteContext(context.Background()); err != nil { /* exit */ }
}

Keep the persistent flag declared — cobra still parses it during ExecuteContext and --help shows it; pre-execution consumers just don't read the bound variable:

root.PersistentFlags().StringVar(&dataDirFlag, "data-dir", "", "override configured data dir")

Fix 2 — dashboard derives paths from the registry (dashboard.go):

func (d *Dashboard) DataDir() string { return d.registry.DataDir() } // was: DefaultDataDir