Use WarningMsg rather than ErrorMsg for deprecation warnings.

common/content/dactyl.js

@@ -303,7 +303,6 @@ var Dactyl = Module("dactyl", XPCOM(Ci.nsISupportsWeakReference, ModuleBase), {
         commandline.echo(str, commandline.HL_NORMAL, flags);
     },
 
-    // TODO: Vim replaces unprintable characters in echoerr/echomsg
     /**
      * Outputs an error message to the command line.
      *
@@ -327,6 +326,17 @@ var Dactyl = Module("dactyl", XPCOM(Ci.nsISupportsWeakReference, ModuleBase), {
         commandline.echo(str, commandline.HL_ERRORMSG, flags);
     },
 
+    /**
+     * Outputs a warning message to the command line.
+     *
+     * @param {string} str The message to output.
+     * @param {number} flags These control the multi-line message behavior.
+     *     See {@link CommandLine#echo}.
+     */
+    warn: function warn(str, flags) {
+        commandline.echo(str, "WarningMsg", flags | commandline.APPEND_TO_MESSAGES);
+    },
+
     // TODO: add proper level constants
     /**
      * Outputs an information message to the command line.

common/modules/base.jsm

@@ -274,7 +274,7 @@ function deprecated(alternative, fn) {
                       "";
         let filename = (frame.filename || "unknown").replace(/.* -> /, "");
         if (!set.add(deprecatedMethod.seen, filename))
-            util.dactyl(fn).echoerr(
+            util.dactyl(fn).warn(
                 util.urlPath(filename) + ":" + frame.lineNumber + ": " +
                 obj + (fn.name || name) + " is deprecated: Please use " + alternative + " instead");
         return func.apply(this, arguments);

common/modules/prefs.jsm

@@ -174,7 +174,7 @@ var Prefs = Module("prefs", XPCOM([Ci.nsIObserver, Ci.nsISupportsWeakReference])
             let msg = "Warning: setting preference " + name + ", but it's changed from its default value.";
             if (message)
                 msg = template.linkifyHelp(msg + " " + message);
-            util.dactyl.echomsg(msg);
+            util.dactyl.warn(msg);
         }
     },