diff --git a/plugins/c9.core/settings.js b/plugins/c9.core/settings.js
index 4ef877d1..94d526e0 100644
--- a/plugins/c9.core/settings.js
+++ b/plugins/c9.core/settings.js
@@ -50,6 +50,7 @@ define(function(require, exports, module) {
         var KEYS = Object.keys(PATH);
         
         var saveToCloud = {};
+        var defaults = {};
         var model = {};
         var cache = {};
         var diff = 0; // TODO should we allow this to be undefined and get NaN in timestamps?
@@ -67,7 +68,7 @@ define(function(require, exports, module) {
             if (!json) {
                 // Load from TEMPLATE
                 if (options.settings == "defaults" || testing)
-                    json = TEMPLATE;
+                    json = util.cloneObject(TEMPLATE);
                 // Load from parsed settings in the index file
                 else if (options.settings) {
                     json = options.settings;
@@ -80,7 +81,7 @@ define(function(require, exports, module) {
                             try {
                                 json[type] = JSON.parse(json[type]);
                             } catch (e) {
-                                json[type] = TEMPLATE[type];
+                                json[type] = util.cloneObject(TEMPLATE[type]);
                             }
                         }
                     }
@@ -91,8 +92,13 @@ define(function(require, exports, module) {
                 KEYS.forEach(function(type) {
                     if (!skipCloud[type] && json)
                         return --count;
-                    fs.readFile(PATH[type], function(err, data) {
-                        if (!json) json = {};
+                    if (!json) 
+                        json = {};
+                    if (type == "state" && debugMode)
+                        return done(null, localStorage["debugState" + c9.projectName]);
+                    fs.readFile(PATH[type], done);
+                    
+                    function done(err, data) {
                         try {
                             json[type] = err ? {} : JSON.parse(data);
                         } catch (e) {
@@ -103,7 +109,7 @@ define(function(require, exports, module) {
                         
                         if (--count === 0)
                             loadSettings(json);
-                    });
+                    }
                 });
                 if (count > 0)
                     return;
@@ -214,59 +220,31 @@ define(function(require, exports, module) {
         }
     
         function read(json, isReset) {
-            try {
-                if (testing) throw "testing";
-                
+            KEYS.forEach(function(type) {
+                if (json[type])
+                    model[type] = json[type];
+            });
+            
+            if (resetSettings) {
+                var query = (resetSettings == 1 
+                    ? "user|state" : resetSettings).split("|");
+                resetSettings = false;
+                query.forEach(function(type) {
+                    model[type] = util.cloneObject(TEMPLATE[type]);
+                });
+            }
+            
+            if (testing) {
                 KEYS.forEach(function(type) {
-                    if (json[type])
-                        model[type] = json[type];
-                });
-                
-                if (resetSettings) {
-                    var query = (resetSettings == 1 
-                        ? "user|state" : resetSettings).split("|");
-                    query.forEach(function(type) {
-                        model[type] = TEMPLATE[type];
-                    });
-                }
-                
-            } catch (e) {
-                KEYS.forEach(function(type) {
-                    model[type] = TEMPLATE[type];
+                    model[type] = util.cloneObject(TEMPLATE[type]);
                 });
             }
     
-            if (!c9.debug && !testing) {
-                try {
-                    emit("read", {
-                        model: model,
-                        ext: plugin,
-                        reset: isReset
-                    });
-                } catch (e) {
-                    console.error("Error loading settings, reseting to defaults");
-                    console.error(e);
-                    fs.writeFile(PATH.project 
-                        + ".broken", JSON.stringify(json), function() {});
-    
-                    KEYS.forEach(function(type) {
-                        model[type] = TEMPLATE[type];
-                    });
-    
-                    emit("read", {
-                        model: model,
-                        ext: plugin,
-                        reset: isReset
-                    });
-                }
-            }
-            else {
-                emit("read", {
-                    model: model,
-                    ext: plugin,
-                    reset: isReset
-                });
-            }
+            emit("read", {
+                model: model,
+                ext: plugin,
+                reset: isReset
+            });
             
             if (inited)
                 return;
@@ -328,7 +306,7 @@ define(function(require, exports, module) {
         }
 
         function setDefaults(path, attr) {
-            var node = getNode(path) || set(path, {}, true, true) && getNode(path);
+            var node = getNode(path, true) || set(path, {}, true, true) && getNode(path, true);
             var changed;
             
             attr.forEach(function(a) {
@@ -405,7 +383,7 @@ define(function(require, exports, module) {
                 key = "json()";
             }
             
-            var hash = model;
+            var hash = isDefault ? defaults : model;
             if (!parts.every(function(part) {
                 if (!hash[part] && checkDefined) return false;
                 hash = hash[part] || (hash[part] = {});
@@ -474,31 +452,37 @@ define(function(require, exports, module) {
             return parseFloat(double);
         }
         
-        function getNode(query) {
-            return get(query, true);
+        function getNode(query, isDefault) {
+            return get(query, true, isDefault);
         }
         
-        function get(query, isNode) {
+        function getUnsafe(query, isNode, isDefault) {
             var parts = query.split("/");
             if (!isNode && parts[parts.length - 1].charAt(0) !== "@")
                 parts.push("json()");
             
-            var hash = model;
+            var hash = isDefault == true ? {} : model;
             parts.every(function(part) { 
                 hash = hash[part];
                 return hash;
             });
-            
+            if (hash === undefined) {
+                hash = isDefault == false ? {} : defaults;
+                parts.every(function(part) { 
+                    hash = hash[part];
+                    return hash;
+                });
+            }
+            return hash;
+        }
+        
+        function get(query, isNode, isDefault) {
+            var hash = getUnsafe(query, isNode, isDefault);
             return hash === undefined ? "" : hash;
         }
         
         function exist(query) {
-            var parts = query.split("/");
-            var hash = model;
-            return parts.every(function(part) { 
-                hash = hash[part];
-                return hash;
-            });
+            return getUnsafe(query, true) != undefined;
         }
         
         function reset(query) {
@@ -506,10 +490,10 @@ define(function(require, exports, module) {
             
             var info = {};
             query.split("|").forEach(function(type) {
-                info[type] = TEMPLATE[type];
+                info[type] = util.cloneObject(TEMPLATE[type]);
             });
             
-            read(model, true);
+            read(info, true);
             saveToFile();
         }
     
diff --git a/plugins/c9.ide.ace/ace.js b/plugins/c9.ide.ace/ace.js
index 42b572b0..ab9d0ecf 100644
--- a/plugins/c9.ide.ace/ace.js
+++ b/plugins/c9.ide.ace/ace.js
@@ -246,7 +246,7 @@ define(function(require, exports, module) {
             ["wrapToView", true, BOOL, "wrapmodeViewport"],
             
             // Ace
-            ["fontSize", "12", NUMBER, "fontsize"],
+            ["fontSize", 12, NUMBER, "fontsize"],
             ["fontFamily", font, STRING, "fontfamily"],
             ["antialiasedfonts", false, BOOL],
             ["overwrite", false, BOOL, "overwrite"],
@@ -257,17 +257,17 @@ define(function(require, exports, module) {
             ["showInvisibles", false, BOOL, "showinvisibles"],
             ["showPrintMargin", true, BOOL, "showprintmargin"],
             ["displayIndentGuides", true, BOOL, "showindentguides"],
-            ["printMarginColumn", "80", NUMBER, "printmargincolumn"],
+            ["printMarginColumn", 80, NUMBER, "printmargincolumn"],
             ["behavioursEnabled", true, BOOL, "behaviors"],
             ["wrapBehavioursEnabled", false, BOOL, "wrapbehaviors"],
-            ["scrollSpeed", "2", NUMBER, "scrollspeed"],
+            ["scrollSpeed", 2, NUMBER, "scrollspeed"],
             ["showGutter", true, BOOL, "gutter"],
             ["showLineNumbers", true, STRING],
             ["showFoldWidgets", true, BOOL, "folding"],
             ["fadeFoldWidgets", true, BOOL, "fadefoldwidgets"],
             ["highlightSelectedWord", true, BOOL, "highlightselectedword"],
             ["animatedScroll", true, BOOL, "animatedscroll"],
-            ["scrollPastEnd", "0.5", NUMBER],
+            ["scrollPastEnd", 0.5, NUMBER],
             ["mergeUndoDeltas", "off", STRING],
             ["theme", defaultThemes[skin], STRING, "theme"]
         ];
diff --git a/plugins/c9.ide.collab/notifications/bubble.js b/plugins/c9.ide.collab/notifications/bubble.js
index 879d7670..be1010c0 100644
--- a/plugins/c9.ide.collab/notifications/bubble.js
+++ b/plugins/c9.ide.collab/notifications/bubble.js
@@ -29,7 +29,7 @@ define(function(require, exports, module) {
             loaded = true;
             
             settings.on("read", function() {
-                settings.setDefaults("user/collab", [["showbubbles", "true"]]);
+                settings.setDefaults("user/collab", [["showbubbles", true]]);
             });
             
             prefs.add({
diff --git a/plugins/c9.ide.configuration/configure.js b/plugins/c9.ide.configuration/configure.js
index 2b066a5c..4d98fee9 100644
--- a/plugins/c9.ide.configuration/configure.js
+++ b/plugins/c9.ide.configuration/configure.js
@@ -302,16 +302,36 @@ define(function(require, exports, module) {
             openTab("~/.c9/styles.css", css, "css");
         }
         
+        function stringifySettings(query) {
+            var model = settings.get(query, true);
+            var defaults = settings.get(query, true, true);
+            var merged = merge({}, defaults, model);
+            function merge(result) {
+                var args = arguments;
+                for (var i = 1; i < args.length; i++) {
+                    var o = args[i];
+                    for (var key in o) {
+                        if (!o[key] || typeof o[key] !== "object") {
+                            result[key] = o[key];
+                        } else {
+                            if (!result[key] || typeof result[key] != "object")
+                                result[key] = {};
+                            merge(result[key], o[key]);
+                        }
+                    }
+                }
+                return result;
+            }
+            return util.stableStringify(merged, null, 4)
+                .replace(/ "(true|false)"/g, " $1");
+        }
+        
         function editProjectSettings() {
-            var value = JSON.stringify(settings.model.project, 0, "    ")
-                .replace(/"true"/g, "true")
-                .replace(/"false"/g, "false");
+            var value = stringifySettings("project");
             openTab(settings.paths.project, value, "javascript");
         }
         function editUserSettings() {
-            var value = JSON.stringify(settings.model.user, 0, "    ")
-                .replace(/"true"/g, "true")
-                .replace(/"false"/g, "false");
+            var value = stringifySettings("user");
             openTab(settings.paths.user, value, "javascript");
         }
         
diff --git a/plugins/c9.ide.console/console.js b/plugins/c9.ide.console/console.js
index 3aa30085..992c9bd1 100644
--- a/plugins/c9.ide.console/console.js
+++ b/plugins/c9.ide.console/console.js
@@ -75,9 +75,9 @@ define(function(require, module, exports) {
             settings.on("read", function(e) {
                 // Defaults
                 settings.setDefaults("state/console", [
-                    ["expanded", "true"],
-                    ["maximized", "false"],
-                    ["height", "153"]
+                    ["expanded", true],
+                    ["maximized", false],
+                    ["height", 153]
                 ]);
                 
                 // Height
diff --git a/plugins/c9.ide.editors/metadata.js b/plugins/c9.ide.editors/metadata.js
index 51f149a6..d9fee162 100644
--- a/plugins/c9.ide.editors/metadata.js
+++ b/plugins/c9.ide.editors/metadata.js
@@ -112,8 +112,8 @@ define(function(require, exports, module) {
             
             settings.on("read", function(e) {
                 settings.setDefaults("user/metadata", [
-                    // ["enabled", "true"],
-                    ["undolimit", "100"],
+                    // ["enabled", true],
+                    ["undolimit", 100],
                 ]);
             }, plugin);
             
diff --git a/plugins/c9.ide.panels/panel.js b/plugins/c9.ide.panels/panel.js
index f5f28bbd..4744da23 100644
--- a/plugins/c9.ide.panels/panel.js
+++ b/plugins/c9.ide.panels/panel.js
@@ -73,7 +73,7 @@ define(function(require, module, exports) {
                 settings.on("read", function() {
                     settings.setDefaults(xpath, [
                         ["name", plugin.name],
-                        ["enabled", "true"]
+                        ["enabled", true]
                     ]);
                     
                     // Start disabled
diff --git a/plugins/c9.ide.preferences/general.js b/plugins/c9.ide.preferences/general.js
index 79517aad..78cc1636 100644
--- a/plugins/c9.ide.preferences/general.js
+++ b/plugins/c9.ide.preferences/general.js
@@ -61,13 +61,13 @@ define(function(require, exports, module) {
                             caption: "Reset to Defaults",
                             width: 140,
                             onclick: function() {
-                                confirm("Reset Settings", 
+                                confirm("Reset User Settings", 
                                     "Are you sure you want to reset your settings?", 
                                     "By resetting your settings to their "
                                     + "defaults you will lose all custom settings. "
                                     + "Cloud9 will return to it's original configuration", 
                                     function() {
-                                        settings.reset();
+                                        settings.reset("user");
                                     }, function() {},
                                     { yes: "Reset settings", no: "Cancel" });
                             }
diff --git a/plugins/c9.ide.run.build/gui.js b/plugins/c9.ide.run.build/gui.js
index 7a72b69c..55e66947 100644
--- a/plugins/c9.ide.run.build/gui.js
+++ b/plugins/c9.ide.run.build/gui.js
@@ -61,7 +61,7 @@ define(function(require, module, exports) {
             // Settings
             settings.on("read", function() {
                 settings.setDefaults("project/build", [
-                    ["saveall", "true"],
+                    ["saveall", true],
                     ["builder", "auto"]
                 ]);
                 settings.setDefaults("user/build", [
diff --git a/plugins/c9.ide.run.debug/breakpoints.js b/plugins/c9.ide.run.debug/breakpoints.js
index 30b3f6ff..0b304d3d 100644
--- a/plugins/c9.ide.run.debug/breakpoints.js
+++ b/plugins/c9.ide.run.debug/breakpoints.js
@@ -201,7 +201,7 @@ define(function(require, exports, module) {
             // restore the breakpoints from the IDE settings
             settings.on("read", function (e) {
                 settings.setDefaults("user/breakpoints", [
-                    ["active", "true"]
+                    ["active", true]
                 ]);
 
                 var bps = settings.getJson("state/breakpoints");
@@ -483,7 +483,7 @@ define(function(require, exports, module) {
             codebox = new apf.codebox({
                 skin: "simplebox",
                 "class": "dark",
-                focusselect: "true",
+                focusselect: true,
                 htmlNode: hInput,
                 "initial-message": "Your Expression"
             });
diff --git a/plugins/c9.ide.run.debug/debuggers/debugger.js b/plugins/c9.ide.run.debug/debuggers/debugger.js
index 593f9049..34ac8b85 100644
--- a/plugins/c9.ide.run.debug/debuggers/debugger.js
+++ b/plugins/c9.ide.run.debug/debuggers/debugger.js
@@ -58,8 +58,8 @@ define(function(require, exports, module) {
             
             settings.on("read", function() {
                 settings.setDefaults("user/debug", [
-                    ["pause", "0"],
-                    ["autoshow", "true"]
+                    ["pause", 0],
+                    ["autoshow", true]
                 ]);
                 
                 pauseOnBreaks = settings.getNumber("user/debug/@pause");
diff --git a/plugins/c9.ide.run.debug/debuggers/gdb/gdbdebugger.js b/plugins/c9.ide.run.debug/debuggers/gdb/gdbdebugger.js
index cad04d87..ab026d7d 100755
--- a/plugins/c9.ide.run.debug/debuggers/gdb/gdbdebugger.js
+++ b/plugins/c9.ide.run.debug/debuggers/gdb/gdbdebugger.js
@@ -58,7 +58,7 @@ define(function(require, exports, module) {
 
             settings.on("read", function() {
                 settings.setDefaults("user/debug", [
-                    ["autoshow", "true"]
+                    ["autoshow", true]
                 ]);
             });
 
diff --git a/plugins/c9.ide.run/gui.js b/plugins/c9.ide.run/gui.js
index 33f9f0fb..2a326d3d 100644
--- a/plugins/c9.ide.run/gui.js
+++ b/plugins/c9.ide.run/gui.js
@@ -536,9 +536,9 @@ define(function(require, module, exports) {
             // settings
             settings.on("read", function(e) {
                 settings.setDefaults("user/runconfig", [
-                    ["saveallbeforerun", "true"],
-                    ["debug", "true"],
-                    ["showruncfglist", "false"]
+                    ["saveallbeforerun", true],
+                    ["debug", true],
+                    ["showruncfglist", false]
                 ]);
 
                 if (!settings.getBool("project/run/configs/@inited")) {
diff --git a/plugins/c9.ide.run/output.js b/plugins/c9.ide.run/output.js
index 0bb1b30a..a27c4370 100644
--- a/plugins/c9.ide.run/output.js
+++ b/plugins/c9.ide.run/output.js
@@ -129,8 +129,8 @@ define(function(require, exports, module) {
                     ["backgroundColor", colors[0]],
                     ["foregroundColor", colors[1]],
                     ["selectionColor", colors[2]],
-                    ["nosavequestion", "false"],
-                    ["keepOutput", "false"]
+                    ["nosavequestion", false],
+                    ["keepOutput", false]
                 ]);
 
                 setSettings();
@@ -1037,13 +1037,13 @@ define(function(require, exports, module) {
                                 tab.close();
 
                                 if (question.dontAsk)
-                                    settings.set("user/output/nosavequestion", "true");
+                                    settings.set("user/output/nosavequestion", true);
                             },
                             function() { // No
                                 // do nothing; allow user to set a name
 
                                 if (question.dontAsk)
-                                    settings.set("user/output/nosavequestion", "true");
+                                    settings.set("user/output/nosavequestion", true);
                             },
                             { showDontAsk: true, yes: "Close", no: "Cancel" });
                         return false;
diff --git a/plugins/c9.ide.terminal/terminal.js b/plugins/c9.ide.terminal/terminal.js
index 77b9208f..ffd9185b 100644
--- a/plugins/c9.ide.terminal/terminal.js
+++ b/plugins/c9.ide.terminal/terminal.js
@@ -249,8 +249,8 @@ define(function(require, exports, module) {
                     ["selectionColor", colors[2]],
                     ["antialiasedfonts", colors[3]],
                     ["fontfamily", "Ubuntu Mono, Menlo, Consolas, monospace"], // Monaco, 
-                    ["fontsize", "12"],
-                    ["blinking", "false"],
+                    ["fontsize", 12],
+                    ["blinking", false],
                     ["scrollback", 1000]
                 ]);
                 
diff --git a/plugins/c9.ide.tree/favorites.js b/plugins/c9.ide.tree/favorites.js
index c9e385db..54e44037 100644
--- a/plugins/c9.ide.tree/favorites.js
+++ b/plugins/c9.ide.tree/favorites.js
@@ -481,10 +481,10 @@ define(function(require, exports, module) {
             var init = false;
             settings.on("read", function() {
                 settings.setDefaults("state/projecttree", [
-                    ["showfs", startEmpty ? "false" : "true"]
+                    ["showfs", startEmpty ? false : true]
                 ]);
                 settings.setDefaults("user/projecttree", [
-                    ["scope", "false"]
+                    ["scope", false]
                 ]);
                 
                 if (settings.getBool("state/projecttree/@showfs"))
diff --git a/plugins/c9.ide.watcher/gui.js b/plugins/c9.ide.watcher/gui.js
index f7c296a3..aab71037 100644
--- a/plugins/c9.ide.watcher/gui.js
+++ b/plugins/c9.ide.watcher/gui.js
@@ -47,8 +47,8 @@ define(function(require, exports, module) {
     
             settings.on("read", function(e) {
                 settings.setDefaults("user/general", [
-                    ["automerge", "false"],
-                    ["confirmmerge", "true"]
+                    ["automerge", false],
+                    ["confirmmerge", true]
                 ]);
             });