Add -cli, -alias, and -noalias setup flags to help

The `-cli`/`-alias` flags are useful when you don't want lime to mess with
libraries that might be intentionally set to specific versions.

tools/CommandLineTools.hx

@@ -952,6 +952,12 @@ class CommandLineTools
 		Log.println(" " + Log.accentColor + "Options:" + Log.resetColor);
 		Log.println("");
 
+		if (command == "setup")
+		{
+			Log.println("  \x1b[1m-cli\x1b[0;3m/\x1b[0m\x1b[1m-alias\x1b[0m -- Set up " + defaultLibraryName + " alias only, skipping haxelib installs");
+			Log.println("  \x1b[1m-noalias\x1b[0m -- Do not set up " + defaultLibraryName + " alias");
+		}
+
 		if (isBuildCommand)
 		{
 			Log.println("  \x1b[1m-D\x1b[0;3mvalue\x1b[0m -- Specify a define to use when processing other commands");