diff --git a/lib/core/Project.js b/lib/core/Project.js
index 33fb4f2b..ee884441 100644
--- a/lib/core/Project.js
+++ b/lib/core/Project.js
@@ -47,10 +47,6 @@ Project.prototype.install = function (endpoints, options) {
     // Analyse the project
     .then(that.analyse.bind(this))
     .spread(function (json, tree, flattened) {
-        var targets = {};
-        var resolved = {};
-        var installed;
-
         // Mark targets
         endpoints.forEach(function (endpoint) {
             var decEndpoint = endpointParser.decompose(endpoint);
@@ -65,6 +61,7 @@ Project.prototype.install = function (endpoints, options) {
             if (targets[name]) {
                 return false;  // Abort traversal
             }
+
             resolved[name] = node.pkgMeta;
         });
 
@@ -78,19 +75,26 @@ Project.prototype.install = function (endpoints, options) {
     })
     // Handle save and saveDev options
     .then(function (installed) {
-        var jsonKey;
-
         if (!options.save && !options.saveDev) {
             return;
         }
 
-        jsonKey = options.save ? 'dependencies' : 'devDependencies';
-        that._json[jsonKey] = that._json[jsonKey] || {};
-
+        // Cycle through the initial targets and not the installed
+        // ones because some targets could already be installed
         mout.object.forOwn(targets, function (decEndpoint) {
             var source = decEndpoint.registry ? '' : decEndpoint.source;
             var target = decEndpoint.pkgMeta.version ? '~' + decEndpoint.pkgMeta.version : decEndpoint.target;
-            that._json[jsonKey][decEndpoint.name] = mout.string.ltrim(source + '#' + target, ['#']);
+            var endpoint = mout.string.ltrim(source + '#' + target, ['#']);
+
+            if (options.save) {
+                that._json.dependencies = that._json.dependencies || {};
+                that._json.dependencies[decEndpoint.name] = endpoint;
+            }
+
+            if (options.saveDev) {
+                that._json.devDependencies = that._json.devDependencies || {};
+                that._json.devDependencies[decEndpoint.name] = endpoint;
+            }
         });
 
         return that._saveJson()
@@ -164,8 +168,7 @@ Project.prototype.update = function (names, options) {
                     return;
                 }
 
-                // Use json entry if available,
-                // fallbacking to the installed one
+                // Use json entry if available, fallbacking to the installed one
                 jsonEntry = json.dependencies && json.dependencies[name];
                 if (jsonEntry) {
                     targets[name] = endpointParser.json2decomposed(name, jsonEntry);
@@ -180,6 +183,7 @@ Project.prototype.update = function (names, options) {
                 if (targets[name]) {
                     return false;  // Abort traversal
                 }
+
                 resolved[name] = node.pkgMeta;
             });
 
@@ -307,7 +311,6 @@ Project.prototype.analyse = function () {
             name: json.name,
             source: this._config.cwd,
             target: json.version,
-            dir: this._config.cwd,
             pkgMeta: json,
             root: true
         };
@@ -334,6 +337,12 @@ Project.prototype.analyse = function () {
             }
         }, this);
 
+        // The package meta set above is not really a package meta
+        // so we delete it from the root
+        // Also remove it from the flattened tree
+        delete root.pkgMeta;
+        delete flattened[json.name];
+
         return [json, root, flattened];
     }.bind(this));
 };
@@ -481,8 +490,8 @@ Project.prototype._readInstalled = function () {
                 decEndpoints[name] = {
                     name: name,
                     source: pkgMeta._source,
-                    target: pkgMeta.version,
-                    dir: path.dirname(jsonFile),
+                    target: pkgMeta.version || '*',
+                    canonicalPkg: path.dirname(jsonFile),
                     pkgMeta: pkgMeta
                 };
             });
@@ -501,7 +510,6 @@ Project.prototype._readInstalled = function () {
 
 Project.prototype._removePackages = function (packages, options) {
     var promises = [];
-    var jsonKey = options.save ? 'dependencies' : (options.saveDev ? 'devDependencies' : null);
     var deferred = Q.defer();
 
     mout.object.forOwn(packages, function (dir, name) {
@@ -536,10 +544,17 @@ Project.prototype._removePackages = function (packages, options) {
         }
 
         // Remove from json only if successfully deleted
-        if (jsonKey && this._json[jsonKey]) {
+        if (options.save && this._json.dependencies) {
             promise = promise
             .then(function () {
-                delete this._json[jsonKey][name];
+                delete this._json.dependencies[name];
+            }.bind(this));
+        }
+
+        if (options.saveDev && this._json.devDependencies) {
+            promise = promise
+            .then(function () {
+                delete this._json.devDependencies[name];
             }.bind(this));
         }
 
@@ -559,7 +574,7 @@ Project.prototype._removePackages = function (packages, options) {
 };
 
 Project.prototype._walkTree = function (node, fn) {
-    var queue = [node];
+    var queue = mout.object.values(node.dependencies);
     var result;
 
     while (queue.length) {