Be somewhat less insistent/more informative in deprecation complaints.

common/content/commands.js

@@ -131,9 +131,10 @@ const Command = Class("Command", {
      * @param {Object} modifiers Any modifiers to be passed to {@link #action}.
      */
     execute: function (args, modifiers) {
-        if (this.deprecated) {
+        if (this.deprecated && !set.add(this.complained, io.sourcing ? io.sourcing.file : "[Command Line]")) {
             let loc = io.sourcing ? io.sourcing.file + ":" + io.sourcing.line + ": " : "";
-            dactyl.echoerr(loc + ":" + this.name + " is deprecated");
+            dactyl.echoerr(loc + ":" + this.name + " is deprecated" +
+                           (isString(this.deprecated) ? ": " + this.deprecated : ""));
         }
 
         let self = this;
@@ -180,6 +181,8 @@ const Command = Class("Command", {
         extra: extra
     }),
 
+    complained: Class.memoize(function () ({})),
+
     /**
      * @property {string[]} All of this command's name specs. e.g., "com[mand]"
      */

common/content/dactyl.js

@@ -25,16 +25,14 @@ const FailedAssertion = Class("FailedAssertion", Error, {
     }
 });
 
-deprecated.seen = {};
-function deprecated(fn)
+deprecated.seen = { "chrome://dactyl/content/javascript.js": true };
+function deprecated(reason, fn)
     function deprecatedMethod() {
         let frame = Components.stack.caller;
-        let caller = frame.filename + ":" + frame.lineNumber;
-        if (frame.filename != "chrome://dactyl/content/javascript.js" &&
-            !set.add(deprecated.seen, caller))
-            dactyl.echoerr(caller + ": " +
+        if (!set.add(deprecated.seen, frame.filename))
+            dactyl.echoerr(frame.filename + ":" + frame.lineNumber + ": " +
                 (this.className || this.constructor.className) + "." + fn.name +
-                " is deprecated");
+                " is deprecated: " + reason);
         return fn.apply(this, arguments);
     }
 
@@ -691,7 +689,8 @@ const Dactyl = Module("dactyl", {
      */
     _globalVariables: {},
     globalVariables: Class.Property({
-        get: deprecated(function globalVariables() this._globalVariables)
+        get: deprecated("Please use the options system instead",
+            function globalVariables() this._globalVariables)
     }),
 
     loadPlugins: function () {

common/content/options.js

@@ -1307,7 +1307,7 @@ const Options = Module("options", {
                     dactyl.echoerr("E18: Unexpected characters in :let");
             },
             {
-                deprecated: true,
+                deprecated: "Please use the options system instead",
                 literal: 0
             }
         );
@@ -1389,7 +1389,7 @@ const Options = Module("options", {
             {
                 argCount: "+",
                 bang: true,
-                deprecated: true
+                deprecated: "Please use the options system instead"
             });
     },
     completion: function () {