Make commands classes instead of objects (#946)

Making these classes caused native-image to statically initialize
them at build time, which included CLI argument default values
(like working dir).

This turns them back into classes.

Co-authored-by: Islon Scherer <islonscherer@gmail.com>

pkl-doc/src/main/kotlin/org/pkl/doc/Main.kt

@@ -34,10 +34,10 @@ import org.pkl.core.Release
 
 /** Main method for the Pkldoc CLI. */
 internal fun main(args: Array<String>) {
-  cliMain { DocCommand.main(args) }
+  cliMain { DocCommand().main(args) }
 }
 
-object DocCommand :
+class DocCommand :
   BaseCommand(name = "pkldoc", helpLink = Release.current().documentation().homepage()) {
 
   private val modules: List<URI> by