Cleanup hack to process flags in add command

Rather than have the add command hack in support for optional values to
flags make it a core feature of `ELCLI`. That seems like the proper
place to handle this situation and also doesn't break existing
functionality/assumptions in all the other uses/tests.

Author: dmiedema

Modules/ELCLI/ELCLI/CLI.swift

@@ -154,7 +154,20 @@ open class CLI {
                             // it's a "--flag value" type argument.
                             if index < arguments.count - 1 {
                                 value = arguments[index + 1]
-                                skipNext = true
+                                // If we're assuming `--flag value` make sure
+                                // our `value` isn't a stop marker or flag. If it is
+                                // our value should instead be `nil`'d out so our
+                                // command does not get a value where it is our next
+                                // argument.
+                                if let argValue = value,
+                                    isStopMarker(argValue) || isFlag(argValue) {
+                                    value = nil
+                                } else {
+                                    // However if that's not the case we should skip
+                                    // the next command because we really did get
+                                    // `--flag value`
+                                    skipNext = true
+                                }
                             }
                         }
                     }

ModuloKit/Commands/AddCommand.swift

@@ -44,21 +44,7 @@ open class AddCommand: NSObject, Command {
 
         addOptionValue(["--unmanaged"], usage: "specifies that this module will be unmanaged", valueSignature: "<[hash|branch|nothing]>") { (option, value) -> Void in
             self.unmanaged = true
-            if let value = value {
-                if !value.hasPrefix("-") {
-                    self.unmanagedValue = value
-                }  else {
-                    if self.verbose {
-                        writeln(.stderr, "Assuming '\(value)' is a flag and not a branch/commit hash since it begins with '-' and will not track it.")
-                    }
-                    // TODO: Somehow reprocess this `value` as a flag
-                    self.options.filter({ (option) -> Bool in
-                        option.flags?.contains(value) ??  false
-                    }).forEach({ (option) in
-                        option.closure(value, nil)
-                    })
-                }
-            }
+            self.unmanagedValue = value
         }
 
         addOption(["-u", "--update"], usage: "performs the update command after adding a module") { (option, value) in