diff --git a/daffodil-cli/src/main/scala/org/apache/daffodil/cli/Main.scala b/daffodil-cli/src/main/scala/org/apache/daffodil/cli/Main.scala
index 8aec2dcb71..ba35a43064 100644
--- a/daffodil-cli/src/main/scala/org/apache/daffodil/cli/Main.scala
+++ b/daffodil-cli/src/main/scala/org/apache/daffodil/cli/Main.scala
@@ -323,24 +323,17 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
   shortSubcommandsHelp()
 
   // Global Options
-  val debug = opt[Option[String]](
-    argName = "file",
-    descr =
-      "Enable the interactive debugger. Optionally, read initial debugger commands from [file] if provided."
-  )(optionalValueConverter[String](a => a))
-  val trace = opt[Boolean](descr = "Run this program with verbose trace output")
   val verbose = tally(descr = "Increment verbosity level, one level for each -v")
   val version = opt[Boolean](descr = "Show Daffodil's version")
 
   // Parse Subcommand Options
   object parse extends scallop.Subcommand("parse") {
-    banner("""|Usage: daffodil parse (-s <schema> [-r <root>] | -P <parser>)
-              |                      [-c <file>] [-D<variable>=<value>...] [-I <infoset_type>]
-              |                      [-o <output>] [--stream] [-T<tunable>=<value>...] [-V <mode>]
-              |                      [infile]
+    banner("""|Usage: daffodil parse (-s <schema> | -P <parser>) [PARSE_OPTS] [--] [infile]
               |
               |Parse a file, using either a DFDL schema or a saved parser
               |
+              |-- can be used to separate command-line options from trailing arguments
+              |
               |Parse Options:""".stripMargin)
 
     descr("Parse data to a DFDL infoset")
@@ -380,8 +373,9 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
     val rootNS = opt[RefQName](
       "root",
       argName = "node",
-      descr =
-        "Root element to use. Can be prefixed with {namespace}. Must be a top-level element. Defaults to first top-level element of DFDL schema."
+      descr = "Root element to use. Can be prefixed with {namespace}. " +
+        "Must be a top-level element. Defaults to first top-level element of DFDL schema. " +
+        "Only valid with the --schema option."
     )
     val schema =
       opt[URISchemaSource](
@@ -402,7 +396,8 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
       name = 'T',
       keyName = "tunable",
       valueName = "value",
-      descr = "Tunable configuration options to change Daffodil's behavior"
+      descr = "Tunable configuration options to change Daffodil's behavior. " +
+        "Only valid with the --schema option."
     )
     val validate: ScallopOption[ValidationMode.Type] = opt[ValidationMode.Type](
       short = 'V',
@@ -410,6 +405,16 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
       argName = "mode",
       descr = "Validation mode. Use 'on', 'limited', 'off', or a validator plugin name."
     )
+    val debug = opt[Option[String]](
+      argName = "file",
+      descr =
+        "Enable the interactive debugger. Optionally, read initial debugger commands from [file] if provided. " +
+          "Cannot be used with --trace option."
+    )(optionalValueConverter[String](a => a))
+    val trace = opt[Boolean](
+      descr = "Run this program with verbose trace output. " +
+        "Cannot be used with the --debug option."
+    )
 
     val infile = trailArg[String](
       required = false,
@@ -419,6 +424,8 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
     // must have one of --schema or --parser
     requireOne(schema, parser)
 
+    mutuallyExclusive(trace, debug) // cannot provide both --trace and --debug
+
     // if --parser is provided, cannot also provide --root or -T
     conflicts(parser, List(rootNS, tunables))
 
@@ -450,13 +457,12 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
 
   // Unparse Subcommand Options
   object unparse extends scallop.Subcommand("unparse") {
-    banner("""|Usage: daffodil unparse (-s <schema> [-r <root>] | -P <parser>)
-              |                        [-c <file>] [-D<variable>=<value>...] [-I <infoset_type>]
-              |                        [-o <output>] [--stream] [-T<tunable>=<value>...] [-V <mode>]
-              |                        [infile]
+    banner("""|Usage: daffodil unparse (-s <schema> | -P <parser>) [--] [infile]
               |
               |Unparse an infoset file, using either a DFDL schema or a saved parser
               |
+              |-- can be used to separate command-line options from trailing arguments
+              |
               |Unparse Options:""".stripMargin)
 
     descr("Unparse a DFDL infoset")
@@ -495,8 +501,9 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
     val rootNS = opt[RefQName](
       "root",
       argName = "node",
-      descr =
-        "Root element to use. Can be prefixed with {namespace}. Must be a top-level element. Defaults to first top-level element of DFDL schema."
+      descr = "Root element to use. Can be prefixed with {namespace}. " +
+        "Must be a top-level element. Defaults to first top-level element of DFDL schema. " +
+        "Only valid with the --schema option."
     )
     val schema =
       opt[URISchemaSource](
@@ -516,7 +523,8 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
       name = 'T',
       keyName = "tunable",
       valueName = "value",
-      descr = "Tunable configuration options to change Daffodil's behavior"
+      descr = "Tunable configuration options to change Daffodil's behavior. " +
+        "Only valid with the --schema option."
     )
     val validate: ScallopOption[ValidationMode.Type] = opt[ValidationMode.Type](
       short = 'V',
@@ -524,7 +532,16 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
       argName = "mode",
       descr = "Validation mode. Use 'on', 'limited', 'off', or a validator plugin name."
     )
-
+    val debug = opt[Option[String]](
+      argName = "file",
+      descr =
+        "Enable the interactive debugger. Optionally, read initial debugger commands from [file] if provided. " +
+          "Cannot be used with --trace option."
+    )(optionalValueConverter[String](a => a))
+    val trace = opt[Boolean](
+      descr = "Run this program with verbose trace output. " +
+        "Cannot be used with the --debug option."
+    )
     val infile = trailArg[String](
       required = false,
       descr = "Input file to unparse. If not specified, or a value of -, reads from stdin."
@@ -533,6 +550,8 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
     // must have one of --schema or --parser
     requireOne(schema, parser)
 
+    mutuallyExclusive(trace, debug) // cannot provide both --trace and --debug
+
     // if --parser is provided, cannot also provide --root or -T
     conflicts(parser, List(rootNS, tunables))
 
@@ -558,12 +577,12 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
 
   // Save Parser Subcommand Options
   object save extends scallop.Subcommand("save-parser") {
-    banner("""|Usage: daffodil save-parser -s <schema> [-r <root>]
-              |                            [-c <file>] [-D<variable>=<value>...] [-T<tunable>=<value>...]
-              |                            [outfile]
+    banner("""|Usage: daffodil save-parser -s <schema> [SAVE_PARSER_OPTIONS] [--] [outfile]
               |
               |Create and save a parser using a DFDL schema
               |
+              |-- can be used to separate command-line options from trailing arguments
+              |
               |Save Parser Options:""".stripMargin)
 
     descr("Save a Daffodil parser for reuse")
@@ -617,11 +636,13 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
   // Test Subcommand Options
   object test extends scallop.Subcommand("test") {
     banner(
-      """|Usage: daffodil test [-I <implementation>] [-l] [-r] [-i] <tdmlfile> [testnames...]
-              |
-              |List or execute tests in a TDML file
-              |
-              |Test Options:""".stripMargin
+      """|Usage: daffodil test [TEST_OPTIONS] [--] <tdmlfile> [testnames...]
+         |
+         |List or execute tests in a TDML file
+         |
+         |-- can be used to separate command-line options from trailing arguments
+         |
+         |Test Options:""".stripMargin
     )
 
     descr("List or execute TDML tests")
@@ -638,25 +659,37 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
       tally(descr = "Increment test result information output level, one level for each -i")
     val list = opt[Boolean](descr = "Show names and descriptions instead of running test cases")
     val regex = opt[Boolean](descr = "Treat <testnames...> as regular expressions")
+    val debug = opt[Option[String]](
+      argName = "file",
+      descr =
+        "Enable the interactive debugger. Optionally, read initial debugger commands from [file] if provided. " +
+          "Cannot be used with --trace option."
+    )(optionalValueConverter[String](a => a))
+    val trace = opt[Boolean](
+      descr = "Run this program with verbose trace output. " +
+        "Cannot be used with the --debug option."
+    )
     val tdmlfile =
       trailArg[String](required = true, descr = "Test Data Markup Language (TDML) file")
     val testnames = trailArg[List[String]](
       required = false,
       descr = "Name(s) of test cases in tdmlfile. If not given, all tests in tdmlfile are run."
     )
+
+    mutuallyExclusive(trace, debug) // cannot provide both --trace and --debug
   }
 
   // Performance Subcommand Options
   object performance extends scallop.Subcommand("performance") {
-    banner("""|Usage: daffodil performance (-s <schema> [-r <root>] | -P <parser>)
-              |                            [-c <file>] [-D<variable>=<value>...] [-I <infoset_type>]
-              |                            [-N <number>] [-t <threads>] [-T<tunable>=<value>...]
-              |                            [-u] [-V <mode>]
-              |                            <infile>
+    banner(
+      """|Usage: daffodil performance (-s <schema> | -P <parser>) [PERFORMANCE_OPTIONS] [--] <infile>
               |
               |Run a performance test, using either a DFDL schema or a saved parser
               |
-              |Performance Options:""".stripMargin)
+              |-- can be used to separate command-line options from trailing arguments
+              |
+              |Performance Options:""".stripMargin
+    )
 
     descr("Run performance test")
     helpWidth(width)
@@ -696,8 +729,9 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
     val rootNS = opt[RefQName](
       "root",
       argName = "node",
-      descr =
-        "Root element to use. Can be prefixed with {namespace}. Must be a top-level element. Defaults to first top-level element of DFDL schema."
+      descr = "Root element to use. Can be prefixed with {namespace}. " +
+        "Must be a top-level element. Defaults to first top-level element of DFDL schema. " +
+        "Only valid with the --schema option."
     )
     val schema =
       opt[URISchemaSource](
@@ -717,7 +751,8 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
       name = 'T',
       keyName = "tunable",
       valueName = "value",
-      descr = "Tunable configuration options to change Daffodil's behavior"
+      descr = "Tunable configuration options to change Daffodil's behavior. " +
+        "Only valid with the --schema option."
     )
     val unparse = opt[Boolean](
       default = Some(false),
@@ -772,13 +807,15 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
       extends scallop.Subcommand(languageArg) {
 
       val language = languageArg
-      banner(s"""|Usage: daffodil generate $language -s <schema> [-r <root>]
-                 |                              [-c <file>] [-T<tunable>=<value>...]
-                 |                              [outdir]
+      banner(
+        s"""|Usage: daffodil generate $language -s <schema> [GENERATE_OPTIONS] [--] [outdir]
                  |
                  |Generate $languageName code from a DFDL schema to parse or unparse data
                  |
-                 |Generate Options:""".stripMargin)
+                 |-- can be used to separate command-line options from trailing arguments
+                 |
+                 |Generate Options:""".stripMargin
+      )
       descr(s"Generate $languageName code from a DFDL schema")
       helpWidth(width)
 
@@ -825,10 +862,12 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
 
   // Encode or decode EXI Subcommand Options
   object exi extends scallop.Subcommand("exi") {
-    banner("""|Usage: daffodil exi [-d] [-s <schema>] [-o <output>] [infile]
+    banner("""|Usage: daffodil exi [EXI_OPTIONS] [--] [infile]
               |
               |Encode/decode an XML file with EXI. If a schema is specified, it will use schema aware encoding/decoding.
               |
+              |-- can be used to separate command-line options from trailing arguments
+              |
               |EncodeEXI Options:""".stripMargin)
 
     descr("Encode an XML file with EXI")
@@ -860,7 +899,6 @@ class CLIConf(arguments: Array[String], stdout: PrintStream, stderr: PrintStream
   addSubcommand(generate)
   addSubcommand(exi)
 
-  mutuallyExclusive(trace, debug) // cannot provide both --trace and --debug
   requireSubcommand()
 
   verify()
@@ -1012,23 +1050,15 @@ class Main(
     }
   }
 
-  def withDebugOrTrace(proc: DFDL.DataProcessor, conf: CLIConf): DFDL.DataProcessor = {
-    (conf.trace() || conf.debug.isDefined) match {
+  def withDebugOrTrace(
+    proc: DFDL.DataProcessor,
+    traceArg: ScallopOption[Boolean],
+    debugArg: ScallopOption[Option[String]]
+  ): DFDL.DataProcessor = {
+    (traceArg() || debugArg.isDefined) match {
       case true => {
         val runner =
-          if (conf.trace()) {
-            new TraceDebuggerRunner(STDOUT)
-          } else {
-            if (System.console == null) {
-              Logger.log.warn(
-                s"Using --debug on a non-interactive console may result in display issues"
-              )
-            }
-            conf.debug() match {
-              case Some(f) => new CLIDebuggerRunner(new File(f), STDIN, STDOUT)
-              case None => new CLIDebuggerRunner(STDIN, STDOUT)
-            }
-          }
+          getTraceOrCLIDebuggerRunner(traceArg, debugArg)
         val id = new InteractiveDebugger(runner, ExpressionCompilers)
         proc.withDebugger(id).withDebugging(true)
       }
@@ -1036,6 +1066,25 @@ class Main(
     }
   }
 
+  private def getTraceOrCLIDebuggerRunner(
+    trace: ScallopOption[Boolean],
+    debug: ScallopOption[Option[String]]
+  ) = {
+    if (trace()) {
+      new TraceDebuggerRunner(STDOUT)
+    } else {
+      if (System.console == null) {
+        Logger.log.warn(
+          s"Using --debug on a non-interactive console may result in display issues"
+        )
+      }
+      debug() match {
+        case Some(f) => new CLIDebuggerRunner(new File(f), STDIN, STDOUT)
+        case None => new CLIDebuggerRunner(STDIN, STDOUT)
+      }
+    }
+  }
+
   def createProcessorFromSchema(
     schemaSource: URISchemaSource,
     rootNS: Option[RefQName],
@@ -1161,7 +1210,7 @@ class Main(
         }.map {
           _.withExternalVariables(combineExternalVariables(parseOpts.vars, optDafConfig))
         }.map { _.withValidationMode(validate) }
-          .map { withDebugOrTrace(_, conf) }
+          .map { withDebugOrTrace(_, parseOpts.trace, parseOpts.debug) }
 
         val rc = processor match {
           case None => ExitCode.UnableToCreateProcessor
@@ -1499,7 +1548,7 @@ class Main(
         }.map {
           _.withExternalVariables(combineExternalVariables(unparseOpts.vars, optDafConfig))
         }.map { _.withValidationMode(validate) }
-          .map { withDebugOrTrace(_, conf) }
+          .map { withDebugOrTrace(_, unparseOpts.trace, unparseOpts.debug) }
 
         val output = unparseOpts.output.toOption match {
           case Some("-") | None => STDOUT
@@ -1619,20 +1668,8 @@ class Main(
         val optTDMLImplementation = testOpts.implementation.toOption
         val tdmlRunnerInit = Runner(tdmlFile, optTDMLImplementation)
 
-        val tdmlRunner = if (conf.trace() || conf.debug.isDefined) {
-          val db = if (conf.trace()) {
-            new TraceDebuggerRunner(STDOUT)
-          } else {
-            if (System.console == null) {
-              Logger.log.warn(
-                s"Using --debug on a non-interactive console may result in display issues"
-              )
-            }
-            conf.debug() match {
-              case Some(f) => new CLIDebuggerRunner(new File(f), STDIN, STDOUT)
-              case None => new CLIDebuggerRunner(STDIN, STDOUT)
-            }
-          }
+        val tdmlRunner = if (testOpts.trace() || testOpts.debug.isDefined) {
+          val db = getTraceOrCLIDebuggerRunner(testOpts.trace, testOpts.debug)
           val id = new InteractiveDebugger(db, ExpressionCompilers)
           tdmlRunnerInit.setDebugger(id)
           tdmlRunnerInit
diff --git a/daffodil-cli/src/test/scala/org/apache/daffodil/cli/cliTest/TestCLIParsing.scala b/daffodil-cli/src/test/scala/org/apache/daffodil/cli/cliTest/TestCLIParsing.scala
index ae0deafc8e..1df8726f25 100644
--- a/daffodil-cli/src/test/scala/org/apache/daffodil/cli/cliTest/TestCLIParsing.scala
+++ b/daffodil-cli/src/test/scala/org/apache/daffodil/cli/cliTest/TestCLIParsing.scala
@@ -536,7 +536,7 @@ class TestCLIParsing {
       "daffodil-test/src/test/resources/org/apache/daffodil/section06/namespaces/multi_base_15.dfdl.xsd"
     )
 
-    runCLI(args"-t parse -s $schema") { cli =>
+    runCLI(args"parse -t -s $schema") { cli =>
       cli.sendLine("test", inputDone = true)
       cli.expect("parser: <Element name='rabbitHole'>")
     }(ExitCode.Success)
@@ -547,7 +547,7 @@ class TestCLIParsing {
       "daffodil-test/src/test/resources/org/apache/daffodil/section06/entities/charClassEntities.dfdl.xsd"
     )
 
-    runCLI(args"-t parse -s $schema") { cli =>
+    runCLI(args"parse -t -s $schema") { cli =>
       cli.sendLine("0,1,2,3,,,,", inputDone = true)
       cli.expectErr("Left over data. Consumed 56 bit(s) with at least")
       cli.expectErr("Left over data (Hex) starting at byte 8 is: (")
@@ -775,7 +775,7 @@ class TestCLIParsing {
       "daffodil-cli/src/test/resources/org/apache/daffodil/cli/cli_schema_02.dfdl.xsd"
     )
 
-    runCLI(args"--trace parse --stream -s $schema") { cli =>
+    runCLI(args"parse --trace --stream -s $schema") { cli =>
       cli.send("123", inputDone = true)
       cli.expect("<a>1</a>")
       cli.expect("bitPosition: 8")
diff --git a/daffodil-cli/src/test/scala/org/apache/daffodil/cli/cliTest/TestCLISaveParser.scala b/daffodil-cli/src/test/scala/org/apache/daffodil/cli/cliTest/TestCLISaveParser.scala
index 973aa09aa1..a802adb91b 100644
--- a/daffodil-cli/src/test/scala/org/apache/daffodil/cli/cliTest/TestCLISaveParser.scala
+++ b/daffodil-cli/src/test/scala/org/apache/daffodil/cli/cliTest/TestCLISaveParser.scala
@@ -235,30 +235,28 @@ class TestCLISaveParser {
     }
   }
 
-  // DAFFODIL-1141
-  /*@Test*/
+  @Test
   def test_CLI_Saving_SaveParser_debug(): Unit = {
     val schema = path(
       "daffodil-test/src/test/resources/org/apache/daffodil/section06/entities/charClassEntities.dfdl.xsd"
     )
 
     withTempFile { parser =>
-      runCLI(args"-d save-parser -s $schema -r matrix $parser") { cli =>
-        cli.expectErr("Some error about -d not being valid with save-parser")
+      runCLI(args"save-parser -d -s $schema -r matrix $parser") { cli =>
+        cli.expectErr("Unknown option 'd'")
       }(ExitCode.Usage)
     }
   }
 
-  // DAFFODIL-1141
-  /*@Test*/
+  @Test
   def test_CLI_Saving_SaveParser_trace(): Unit = {
     val schema = path(
       "daffodil-test/src/test/resources/org/apache/daffodil/section06/entities/charClassEntities.dfdl.xsd"
     )
 
     withTempFile { parser =>
-      runCLI(args"-t save-parser -s $schema -r matrix $parser") { cli =>
-        cli.expectErr("Some error about -t not being valid with save-parser")
+      runCLI(args"save-parser -t -s $schema -r matrix $parser") { cli =>
+        cli.expectErr("Unknown option 't'")
       }(ExitCode.Usage)
     }
   }
@@ -272,7 +270,7 @@ class TestCLISaveParser {
     )
 
     withTempFile { parser =>
-      runCLI(args"-t save-parser -s $schema -r matrix $parser") { _ => }(ExitCode.Success)
+      runCLI(args"save-parser -s $schema -r matrix $parser") { _ => }(ExitCode.Success)
 
       runCLI(args"unparse --parser $parser $input") { cli =>
         cli.expect("0,1,2")
diff --git a/daffodil-cli/src/test/scala/org/apache/daffodil/cli/cliTest/TestCLItdml.scala b/daffodil-cli/src/test/scala/org/apache/daffodil/cli/cliTest/TestCLItdml.scala
index 900fe98097..a1df130422 100644
--- a/daffodil-cli/src/test/scala/org/apache/daffodil/cli/cliTest/TestCLItdml.scala
+++ b/daffodil-cli/src/test/scala/org/apache/daffodil/cli/cliTest/TestCLItdml.scala
@@ -115,7 +115,7 @@ class TestCLItdml {
       "daffodil-test/src/test/resources/org/apache/daffodil/section06/entities/Entities.tdml"
     )
 
-    runCLI(args"-t test $tdml byte_entities_6_08") { cli =>
+    runCLI(args"test -t $tdml byte_entities_6_08") { cli =>
       cli.expect("parser:")
       cli.expect("bitPosition:")
       cli.expect("data:")
@@ -131,7 +131,7 @@ class TestCLItdml {
       "daffodil-cli/src/test/resources/org/apache/daffodil/cli/debug.txt"
     )
 
-    runCLI(args"-d $debugFile test $tdml byte_entities_6_08") { cli =>
+    runCLI(args"test -d $debugFile $tdml byte_entities_6_08") { cli =>
       cli.expect("(debug)")
       cli.expect("Usage:")
       cli.expect("[Pass] byte_entities_6_08")
diff --git a/daffodil-test-integration/src/test/scala/org/apache/daffodil/cliTest/TestCLIDebugger.scala b/daffodil-test-integration/src/test/scala/org/apache/daffodil/cliTest/TestCLIDebugger.scala
index 1f36e4edc1..b3cd2c7703 100644
--- a/daffodil-test-integration/src/test/scala/org/apache/daffodil/cliTest/TestCLIDebugger.scala
+++ b/daffodil-test-integration/src/test/scala/org/apache/daffodil/cliTest/TestCLIDebugger.scala
@@ -89,7 +89,7 @@ class TestCLIDebugger {
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input1.txt")
 
     intercept[Exception] {
-      runCLI(args"-d parse -s $schema -r matrix $input", fork = false) { cli =>
+      runCLI(args"parse -d -s $schema -r matrix $input", fork = false) { cli =>
         cli.expect("(debug)")
         cli.sendLine("continue")
       }(ExitCode.Success)
@@ -102,7 +102,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input1.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("eval (/invalid)")
@@ -137,7 +137,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input1.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
       cli.sendLine("garbage")
       cli.expect("error: undefined command: garbage")
@@ -151,7 +151,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input2.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("debug")
 
       cli.sendLine("info data")
@@ -172,7 +172,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input1.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
       cli.sendLine("continue")
 
@@ -185,7 +185,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input1.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("display eval (.)")
@@ -222,7 +222,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input6.txt")
 
-    runCLI(args"-d parse -s $schema -r e $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r e $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
       cli.sendLine("set removeHidden false")
       cli.sendLine("display info infoset")
@@ -244,7 +244,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input6.txt")
 
-    runCLI(args"-d parse -s $schema -r e $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r e $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
       cli.sendLine("set removeHidden false")
       cli.sendLine("display info infoset")
@@ -264,7 +264,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input3.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("break cell")
@@ -315,7 +315,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input3.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("set breakOnlyOnCreation false")
@@ -367,7 +367,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input5.txt")
 
-    runCLI(args"-d parse -s $schema -r Item2 $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r Item2 $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("display info pointsOfUncertainty")
@@ -394,7 +394,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input1.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("display info infoset")
@@ -430,7 +430,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input2.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("display info infoset")
@@ -461,7 +461,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input2.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("display info infoset")
@@ -484,7 +484,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input2.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("display info occursIndex")
@@ -519,7 +519,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input3.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("display info infoset")
@@ -557,7 +557,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input1.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("display info bitPosition")
@@ -584,7 +584,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input4.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("break cell")
@@ -612,7 +612,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input1.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("break cell")
@@ -637,7 +637,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input2.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("break cell")
@@ -661,7 +661,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input9.txt")
 
-    runCLI(args"-d parse -r list -s $schema $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -r list -s $schema $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("display info groupIndex")
@@ -689,7 +689,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input9.txt")
 
-    runCLI(args"-d parse -r list -s $schema $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -r list -s $schema $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("display info dne1")
@@ -708,7 +708,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input2.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("display info data")
@@ -737,7 +737,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input2.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("display data")
@@ -757,7 +757,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input2.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("break row")
@@ -792,7 +792,7 @@ class TestCLIDebugger {
       "daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/hextest.txt"
     )
 
-    runCLI(args"-d parse -s $schema -r e2 $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r e2 $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("info data")
@@ -808,7 +808,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input1.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("info infoset")
@@ -830,7 +830,7 @@ class TestCLIDebugger {
     withTempFile { input =>
       Files.write(input, "2~3".getBytes(UTF_8))
 
-      runCLI(args"-d parse -s $schema -r e5 $input", fork = true, envs = envs) { cli =>
+      runCLI(args"parse -d -s $schema -r e5 $input", fork = true, envs = envs) { cli =>
         cli.expect("(debug)")
 
         cli.sendLine("break f")
@@ -863,7 +863,7 @@ class TestCLIDebugger {
     withTempFile { input =>
       Files.write(input, "2~3".getBytes(UTF_8))
 
-      runCLI(args"-d parse -s $schema -r e4 $input", fork = true, envs = envs) { cli =>
+      runCLI(args"parse -d -s $schema -r e4 $input", fork = true, envs = envs) { cli =>
         cli.expect("(debug)")
 
         cli.sendLine("break f")
@@ -896,7 +896,7 @@ class TestCLIDebugger {
     withTempFile { input =>
       Files.write(input, "2,3".getBytes(UTF_8))
 
-      runCLI(args"-d parse -s $schema -r e8 $input", fork = true, envs = envs) { cli =>
+      runCLI(args"parse -d -s $schema -r e8 $input", fork = true, envs = envs) { cli =>
         cli.expect("(debug)")
 
         cli.sendLine("break a")
@@ -936,7 +936,7 @@ class TestCLIDebugger {
     withTempFile { input =>
       Files.write(input, "[6~]9".getBytes(UTF_8))
 
-      runCLI(args"-d parse -s $schema -r e9 $input", fork = true, envs = envs) { cli =>
+      runCLI(args"parse -d -s $schema -r e9 $input", fork = true, envs = envs) { cli =>
         cli.expect("(debug)")
 
         cli.sendLine("break e")
@@ -1004,7 +1004,7 @@ class TestCLIDebugger {
       "daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input12.txt"
     )
 
-    runCLI(args"-d unparse -s $schema -r e1 $input", fork = true, envs = envs) { cli =>
+    runCLI(args"unparse -d -s $schema -r e1 $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
       cli.sendLine("break e1")
       cli.expect("1: e1")
@@ -1022,7 +1022,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/prefix.txt")
 
-    runCLI(args"-d parse -s $schema $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
       cli.sendLine("display info infoset")
       cli.expect("(debug)")
@@ -1046,7 +1046,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input1.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
       cli.sendLine("info variables byteOrder")
       cli.expect("byteOrder: bigEndian (default)")
@@ -1060,7 +1060,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input1.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
       cli.sendLine("display info data text")
       cli.expect("(debug)")
@@ -1076,7 +1076,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input1.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
       cli.sendLine("display info data binary")
       cli.expect("(debug)")
@@ -1092,7 +1092,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input1.txt")
 
-    runCLI(args"-d parse -s $schema -r c $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r c $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
       cli.sendLine("display info diff")
       cli.expect("(debug)")
@@ -1120,7 +1120,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input1.txt")
 
-    runCLI(args"-d parse -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r matrix $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
       cli.sendLine("display info diff")
       cli.expect("(debug)")
@@ -1154,7 +1154,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input6.txt")
 
-    runCLI(args"-d parse -s $schema -r e $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema -r e $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
       cli.sendLine("display info diff")
       cli.expect("(debug)")
@@ -1184,7 +1184,7 @@ class TestCLIDebugger {
       "daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input1.txt.xml"
     )
 
-    runCLI(args"-d unparse -s $schema -r matrix -o $devNull $input", fork = true, envs = envs) {
+    runCLI(args"unparse -d -s $schema -r matrix -o $devNull $input", fork = true, envs = envs) {
       cli =>
         cli.expect("(debug)")
         cli.sendLine("display info diff")
@@ -1224,7 +1224,7 @@ class TestCLIDebugger {
       "daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input9.txt.xml"
     )
 
-    runCLI(args"-d unparse -r list -s $schema -o $devNull $input", fork = true, envs = envs) {
+    runCLI(args"unparse -d -r list -s $schema -o $devNull $input", fork = true, envs = envs) {
       cli =>
         cli.expect("(debug)")
         cli.sendLine("set diffExcludes doesNotExist1 bitLimit doesNotExist2")
@@ -1259,7 +1259,7 @@ class TestCLIDebugger {
     )
     val input = path("daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input3.txt")
 
-    runCLI(args"-d parse -s $schema $input", fork = true, envs = envs) { cli =>
+    runCLI(args"parse -d -s $schema $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("info parser")
@@ -1283,7 +1283,7 @@ class TestCLIDebugger {
       "daffodil-cli/src/test/resources/org/apache/daffodil/cli/input/input1.txt.xml"
     )
 
-    runCLI(args"-d unparse -s $schema $input", fork = true, envs = envs) { cli =>
+    runCLI(args"unparse -d -s $schema $input", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
 
       cli.sendLine("info unparser")
@@ -1302,7 +1302,7 @@ class TestCLIDebugger {
       "daffodil-test/src/test/resources/org/apache/daffodil/section06/entities/Entities.tdml"
     )
 
-    runCLI(args"-d test $tdml byte_entities_6_08", fork = true, envs = envs) { cli =>
+    runCLI(args"test -d -- $tdml byte_entities_6_08", fork = true, envs = envs) { cli =>
       cli.expect("(debug)")
       cli.sendLine("continue")
       cli.expect("[Pass] byte_entities_6_08")