cmd/utils: fix command line flag resolve (#20167)

In Geth, we have two sources for configuration:
(1) Config file
(2) Command line flag

Basically geth will first resolve config file and then overwrite
configs with command line flags.

This issue is: geth should only overwrite configs if flags are truly
set. So before we apply any flag to configs, `GlobalIsSet` check
is necessary.

cmd/utils/flags.go

@@ -1453,9 +1453,12 @@ func SetEthConfig(ctx *cli.Context, stack *node.Node, cfg *eth.Config) {
 	if gcmode := ctx.GlobalString(GCModeFlag.Name); gcmode != "full" && gcmode != "archive" {
 		Fatalf("--%s must be either 'full' or 'archive'", GCModeFlag.Name)
 	}
-	cfg.NoPruning = ctx.GlobalString(GCModeFlag.Name) == "archive"
+	if ctx.GlobalIsSet(GCModeFlag.Name) {
-	cfg.NoPrefetch = ctx.GlobalBool(CacheNoPrefetchFlag.Name)
+		cfg.NoPruning = ctx.GlobalString(GCModeFlag.Name) == "archive"
-
+	}
+	if ctx.GlobalIsSet(CacheNoPrefetchFlag.Name) {
+		cfg.NoPrefetch = ctx.GlobalBool(CacheNoPrefetchFlag.Name)
+	}
 	if ctx.GlobalIsSet(CacheFlag.Name) || ctx.GlobalIsSet(CacheTrieFlag.Name) {
 		cfg.TrieCleanCache = ctx.GlobalInt(CacheFlag.Name) * ctx.GlobalInt(CacheTrieFlag.Name) / 100
 	}