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/test/kotlin/org/pkl/doc/CliMainTest.kt

@@ -23,7 +23,8 @@ import org.pkl.commons.cli.CliException
 class CliMainTest {
   @Test
   fun `CLI run test`() {
-    val e = assertThrows<CliException> { DocCommand.parse(arrayOf("foo", "--output-dir", "/tmp")) }
+    val e =
+      assertThrows<CliException> { DocCommand().parse(arrayOf("foo", "--output-dir", "/tmp")) }
     assertThat(e)
       .hasMessageContaining("must contain at least one module named `doc-package-info.pkl`")
   }