diff --git a/editor/js/main.js b/editor/js/main.js
index 582a15494..04270f7be 100644
--- a/editor/js/main.js
+++ b/editor/js/main.js
@@ -131,11 +131,12 @@
                         var project = RED.projects.getActiveProject();
                         var message = {
                             "change-branch":"Change to local branch '"+project.git.branches.local+"'",
-                            "abort-merge":"Git merge aborted",
+                            "merge-abort":"Git merge aborted",
                             "loaded":"Project '"+msg.project+"' loaded",
                             "updated":"Project '"+msg.project+"' updated",
                             "pull":"Project '"+msg.project+"' reloaded",
-                            "revert": "Project '"+msg.project+"' reloaded"
+                            "revert": "Project '"+msg.project+"' reloaded",
+                            "merge-complete":"Git merge completed"
                         }[msg.action];
                         RED.notify("<p>"+message+"</p>");
                         RED.sidebar.info.refresh()
@@ -219,6 +220,20 @@
                                 }
                             ]
                         }
+                    } else if (msg.error === "git_merge_conflict") {
+                        RED.nodes.clear();
+                        RED.sidebar.versionControl.refresh(true);
+                        if (RED.user.hasPermission("projects.write")) {
+                            options.buttons = [
+                                {
+                                    text: "Show merge conflicts",
+                                    click: function() {
+                                        persistentNotifications[notificationId].hideNotification();
+                                        RED.sidebar.versionControl.showLocalChanges();
+                                    }
+                                }
+                            ]
+                        }
                     }
                 }
                 if (!persistentNotifications.hasOwnProperty(notificationId)) {
diff --git a/editor/js/ui/diff.js b/editor/js/ui/diff.js
index 012005a9d..2cc6d8027 100644
--- a/editor/js/ui/diff.js
+++ b/editor/js/ui/diff.js
@@ -21,17 +21,18 @@ RED.diff = (function() {
         RED.keyboard.add("*","ctrl-shift-f 3","core:show-test-flow-diff-3");
 
     }
-    function createDiffTable(container) {
+    function createDiffTable(container,CurrentDiff) {
         var diffList = $('<ol class="node-dialog-view-diff-diff"></ol>').appendTo(container);
         diffList.editableList({
             addButton: false,
+            height: "auto",
             scrollOnAdd: false,
             addItem: function(container,i,object) {
                 var localDiff = object.diff;
                 var remoteDiff = object.remoteDiff;
                 var tab = object.tab.n;
                 var def = object.def;
-                var conflicts = currentDiff.conflicts;
+                var conflicts = CurrentDiff.conflicts;
 
                 var tabDiv = $('<div>',{class:"node-diff-tab"}).appendTo(container);
                 tabDiv.addClass('collapsed');
@@ -150,10 +151,10 @@ RED.diff = (function() {
                             }
                             div.addClass("node-diff-node-entry-conflict");
                         } else {
-                            selectState = currentDiff.resolutions[tab.id];
+                            selectState = CurrentDiff.resolutions[tab.id];
                         }
                         // Tab properties row
-                        createNodeConflictRadioBoxes(tab,div,localNodeDiv,remoteNodeDiv,true,!conflicts[tab.id],selectState);
+                        createNodeConflictRadioBoxes(tab,div,localNodeDiv,remoteNodeDiv,true,!conflicts[tab.id],selectState,CurrentDiff);
                     }
                 }
                 // var stats = $('<span>',{class:"node-diff-tab-stats"}).appendTo(titleRow);
@@ -162,14 +163,14 @@ RED.diff = (function() {
                 var seen = {};
                 object.tab.nodes.forEach(function(node) {
                     seen[node.id] = true;
-                    createNodeDiffRow(node,flowStats).appendTo(nodesDiv)
+                    createNodeDiffRow(node,flowStats,CurrentDiff).appendTo(nodesDiv)
                 });
                 if (object.newTab) {
                     localNodeCount = object.newTab.nodes.length;
                     object.newTab.nodes.forEach(function(node) {
                         if (!seen[node.id]) {
                             seen[node.id] = true;
-                            createNodeDiffRow(node,flowStats).appendTo(nodesDiv)
+                            createNodeDiffRow(node,flowStats,CurrentDiff).appendTo(nodesDiv)
                         }
                     });
                 }
@@ -177,7 +178,7 @@ RED.diff = (function() {
                     remoteNodeCount = object.remoteTab.nodes.length;
                     object.remoteTab.nodes.forEach(function(node) {
                         if (!seen[node.id]) {
-                            createNodeDiffRow(node,flowStats).appendTo(nodesDiv)
+                            createNodeDiffRow(node,flowStats,CurrentDiff).appendTo(nodesDiv)
                         }
                     });
                 }
@@ -269,12 +270,12 @@ RED.diff = (function() {
                     if (flowStats.conflicts > 0) {
                         titleRow.addClass("node-diff-node-entry-conflict");
                     } else {
-                        selectState = currentDiff.resolutions[tab.id];
+                        selectState = CurrentDiff.resolutions[tab.id];
                     }
                     if (tab.id) {
                         var hide = !(flowStats.conflicts > 0 &&(localDiff.deleted[tab.id] || remoteDiff.deleted[tab.id]));
                         // Tab parent row
-                        createNodeConflictRadioBoxes(tab,titleRow,localCell,remoteCell, false, hide, selectState);
+                        createNodeConflictRadioBoxes(tab,titleRow,localCell,remoteCell, false, hide, selectState, CurrentDiff);
                     }
                 }
 
@@ -291,11 +292,8 @@ RED.diff = (function() {
         var diffHeaders = $('<div class="node-dialog-view-diff-headers"></div>').appendTo(diffPanel);
         if (options.mode === "merge") {
             diffPanel.addClass("node-dialog-view-diff-panel-merge");
-            var toolbar = $('<div class="node-diff-toolbar">'+
-                '<span><span id="node-diff-toolbar-resolved-conflicts"></span></span> '+
-                '</div>').prependTo(diffPanel);
         }
-        var diffList = createDiffTable(diffPanel);
+        var diffList = createDiffTable(diffPanel, diff);
 
         var localDiff = diff.localDiff;
         var remoteDiff = diff.remoteDiff;
@@ -512,10 +510,10 @@ RED.diff = (function() {
         $('<span>',{class:"node-diff-node-label"}).html(nodeLabel).appendTo(contentDiv);
         return nodeTitleDiv;
     }
-    function createNodeDiffRow(node,stats) {
-        var localDiff = currentDiff.localDiff;
-        var remoteDiff = currentDiff.remoteDiff;
-        var conflicted = currentDiff.conflicts[node.id];
+    function createNodeDiffRow(node,stats,CurrentDiff) {
+        var localDiff = CurrentDiff.localDiff;
+        var remoteDiff = CurrentDiff.remoteDiff;
+        var conflicted = CurrentDiff.conflicts[node.id];
 
         var hasChanges = false; // exists in original and local/remote but with changes
         var unChanged = true; // existing in original,local,remote unchanged
@@ -703,10 +701,10 @@ RED.diff = (function() {
             }
             div.addClass("node-diff-node-entry-conflict");
         } else {
-            selectState = currentDiff.resolutions[node.id];
+            selectState = CurrentDiff.resolutions[node.id];
         }
         // Node row
-        createNodeConflictRadioBoxes(node,div,localNodeDiv,remoteNodeDiv,false,!conflicted,selectState);
+        createNodeConflictRadioBoxes(node,div,localNodeDiv,remoteNodeDiv,false,!conflicted,selectState,CurrentDiff);
         row.click(function(evt) {
             $(this).parent().toggleClass('collapsed');
         });
@@ -982,7 +980,7 @@ RED.diff = (function() {
         });
         return nodePropertiesDiv;
     }
-    function createNodeConflictRadioBoxes(node,row,localDiv,remoteDiv,propertiesTable,hide,state) {
+    function createNodeConflictRadioBoxes(node,row,localDiv,remoteDiv,propertiesTable,hide,state,diff) {
         var safeNodeId = "node-diff-selectbox-"+node.id.replace(/\./g,'-')+(propertiesTable?"-props":"");
         var className = "";
         if (node.z||propertiesTable) {
@@ -1019,7 +1017,7 @@ RED.diff = (function() {
                 row.addClass("node-diff-select-remote");
                 row.removeClass("node-diff-select-local");
             }
-            refreshConflictHeader();
+            refreshConflictHeader(diff);
         }
 
         var localSelectDiv = $('<label>',{class:"node-diff-selectbox",for:safeNodeId+"-local"}).click(function(e) { e.stopPropagation();}).appendTo(localDiv);
@@ -1037,7 +1035,7 @@ RED.diff = (function() {
         }
 
     }
-    function refreshConflictHeader() {
+    function refreshConflictHeader(currentDiff) {
         var resolutionCount = 0;
         $(".node-diff-selectbox>input:checked").each(function() {
             if (currentDiff.conflicts[$(this).data('node-id')]) {
@@ -1053,6 +1051,7 @@ RED.diff = (function() {
         }
         if (conflictCount === resolutionCount) {
             $("#node-diff-view-diff-merge").removeClass('disabled');
+            $("#node-diff-view-resolve-diff").removeClass('disabled');
         }
     }
     function getRemoteDiff(callback) {
@@ -1231,7 +1230,7 @@ RED.diff = (function() {
         var localDiff = diff.localDiff;
         var remoteDiff = diff.remoteDiff;
         var conflicts = diff.conflicts;
-        currentDiff = diff;
+        // currentDiff = diff;
 
         var trayOptions = {
             title: options.title||"Review Changes", //TODO: nls
@@ -1250,7 +1249,11 @@ RED.diff = (function() {
             },
             open: function(tray) {
                 var trayBody = tray.find('.editor-tray-body');
-                var diffTable = buildDiffPanel(trayBody,diff,options);
+                var toolbar = $('<div class="node-diff-toolbar">'+
+                    '<span><span id="node-diff-toolbar-resolved-conflicts"></span></span> '+
+                    '</div>').prependTo(trayBody);
+                var diffContainer = $('<div class="node-diff-container"></div>').appendTo(trayBody);
+                var diffTable = buildDiffPanel(diffContainer,diff,options);
                 diffTable.list.hide();
                 if (remoteDiff) {
                     $("#node-diff-view-diff-merge").show();
@@ -1262,7 +1265,7 @@ RED.diff = (function() {
                 } else {
                     $("#node-diff-view-diff-merge").hide();
                 }
-                refreshConflictHeader();
+                refreshConflictHeader(diff);
                 // console.log("--------------");
                 // console.log(localDiff);
                 // console.log(remoteDiff);
@@ -1290,8 +1293,8 @@ RED.diff = (function() {
                     class: "primary disabled",
                     click: function() {
                         if (!$("#node-diff-view-diff-merge").hasClass('disabled')) {
-                            refreshConflictHeader();
-                            mergeDiff(currentDiff);
+                            refreshConflictHeader(diff);
+                            mergeDiff(diff);
                             RED.tray.close();
                         }
                     }
@@ -1302,7 +1305,7 @@ RED.diff = (function() {
         RED.tray.show(trayOptions);
     }
 
-    function mergeDiff(diff) {
+    function applyDiff(diff) {
         var currentConfig = diff.localDiff.currentConfig;
         var localDiff = diff.localDiff;
         var remoteDiff = diff.remoteDiff;
@@ -1356,6 +1359,20 @@ RED.diff = (function() {
                 }
             }
         }
+        return {
+            config: newConfig,
+            nodeChangedStates: nodeChangedStates,
+            localChangedStates: localChangedStates
+        }
+    }
+
+    function mergeDiff(diff) {
+        var appliedDiff = applyDiff(diff);
+
+        var newConfig = appliedDiff.config;
+        var nodeChangedStates = appliedDiff.nodeChangedStates;
+        var localChangedStates = appliedDiff.localChangedStates;
+
         var historyEvent = {
             t:"replace",
             config: RED.nodes.createCompleteNodeSet(),
@@ -1417,7 +1434,7 @@ RED.diff = (function() {
                 var trayBody = tray.find('.editor-tray-body');
                 var diffPanel = $('<div class="node-text-diff"></div>').appendTo(trayBody);
 
-                var codeTable = $("<table>").appendTo(diffPanel);
+                var codeTable = $("<table>",{class:"node-text-diff-content"}).appendTo(diffPanel);
                 $('<colgroup><col width="50"><col width="50%"><col width="50"><col width="50%"></colgroup>').appendTo(codeTable);
                 var codeBody = $('<tbody>').appendTo(codeTable);
                 var diffSummary = diffText(textA||"",textB||"");
@@ -1681,7 +1698,7 @@ RED.diff = (function() {
         files.forEach(function(file) {
             var hunks = file.hunks;
             var isBinary = file.binary;
-            var codeTable = $("<table>").appendTo(diffPanel);
+            var codeTable = $("<table>",{class:"node-text-diff-content"}).appendTo(diffPanel);
             $('<colgroup><col width="50"><col width="50"><col width="100%"></colgroup>').appendTo(codeTable);
             var codeBody = $('<tbody>').appendTo(codeTable);
 
@@ -1700,49 +1717,145 @@ RED.diff = (function() {
             var unresolvedConflicts = 0;
             var resolvedConflicts = 0;
             var conflictResolutions = {};
+            if (commitOptions.project.files && commitOptions.project.files.flow === file.file) {
+                if (commitOptions.unmerged) {
+                    $('<span style="float: right;"><span id="node-diff-toolbar-resolved-conflicts"></span></span>').appendTo(content);
+                }
+                // var tools = $('<span style="float: right;" class="button-group"></span>').appendTo(content);
+                // $('<button class="editor-button editor-button-small">show flow diff</button>').appendTo(tools).click(function(e) {
+                //     e.preventDefault();
+                //     e.stopPropagation();
+                //     var projectName = commitOptions.project.name;
+                //     var filename = commitOptions.project.files.flow;
+                //     var commonVersionUrl = "/projects/"+projectName+"/files/"+commitOptions.commonRev+"/"+filename;
+                //     var oldVersionUrl = "/projects/"+projectName+"/files/"+commitOptions.oldRev+"/"+filename;
+                //     var newVersionUrl = "/projects/"+projectName+"/files/"+commitOptions.newRev+"/"+filename;
+                //     var promises = [];
+                //     if (commitOptions.commonRev) {
+                //         var commonVersionUrl = "/projects/"+projectName+"/files/"+commitOptions.commonRev+"/"+filename;
+                //         promises.push($.getJSON(commonVersionUrl));
+                //     } else {
+                //         promises.push($.when(null));
+                //     }
+                //     promises.push($.getJSON(oldVersionUrl));
+                //     promises.push($.getJSON(newVersionUrl));
+                //     $.when.apply($,promises).done(function(commonVersion, oldVersion,newVersion) {
+                //         var commonFlow;
+                //         var oldFlow;
+                //         var newFlow;
+                //         if (commonVersion) {
+                //             try {
+                //                 commonFlow = JSON.parse(commonVersion[0].content||"[]");
+                //             } catch(err) {
+                //                 console.log("Common Version doesn't contain valid JSON:",commonVersionUrl);
+                //                 console.log(err);
+                //                 return;
+                //             }
+                //         }
+                //         try {
+                //             oldFlow = JSON.parse(oldVersion[0].content||"[]");
+                //         } catch(err) {
+                //             console.log("Old Version doesn't contain valid JSON:",oldVersionUrl);
+                //             console.log(err);
+                //             return;
+                //         }
+                //         if (!commonFlow) {
+                //             commonFlow = oldFlow;
+                //         }
+                //         try {
+                //             newFlow = JSON.parse(newVersion[0].content||"[]");
+                //         } catch(err) {
+                //             console.log("New Version doesn't contain valid JSON:",newFlow);
+                //             console.log(err);
+                //             return;
+                //         }
+                //         var localDiff = generateDiff(commonFlow,oldFlow);
+                //         var remoteDiff = generateDiff(commonFlow,newFlow);
+                //         var diff = resolveDiffs(localDiff,remoteDiff);
+                //         showDiff(diff,{
+                //             title: filename,
+                //             mode: commitOptions.commonRev?'merge':'view',
+                //             oldRevTitle: commitOptions.oldRevTitle,
+                //             newRevTitle: commitOptions.newRevTitle
+                //         });
+                //         // var flowDiffRow = $("<tr>").insertAfter(diffRow);
+                //         // var content = $('<td colspan="3"></td>').appendTo(flowDiffRow);
+                //         // currentDiff = diff;
+                //         // var diffTable = buildDiffPanel(content,diff,{mode:"view"}).finish();
+                //     });
+                // })
+                var diffRow = $('<tr class="node-text-diff-header">').appendTo(codeBody);
+                var flowDiffContent = $('<td class="flow-diff" colspan="3"></td>').appendTo(diffRow);
 
-            if (!commitOptions.unmerged && commitOptions.project.files && commitOptions.project.files.flow === file.file) {
-                var tools = $('<span style="float: right;" class="button-group"></span>').appendTo(content);
-                $('<button class="editor-button editor-button-small">show flow diff</button>').appendTo(tools).click(function(e) {
-                    e.preventDefault();
-                    e.stopPropagation();
-                    var projectName = commitOptions.project.name;
-                    var filename = commitOptions.project.files.flow;
-                    var oldVersionUrl = "/projects/"+projectName+"/files/"+commitOptions.oldRev+"/"+filename;
-                    var newVersionUrl = "/projects/"+projectName+"/files/"+commitOptions.newRev+"/"+filename;
-                    $.when($.getJSON(oldVersionUrl),$.getJSON(newVersionUrl)).done(function(oldVersion,newVersion) {
-                        var oldFlow;
-                        var newFlow;
+                var projectName = commitOptions.project.name;
+                var filename = commitOptions.project.files.flow;
+                var commonVersionUrl = "/projects/"+projectName+"/files/"+commitOptions.commonRev+"/"+filename;
+                var oldVersionUrl = "/projects/"+projectName+"/files/"+commitOptions.oldRev+"/"+filename;
+                var newVersionUrl = "/projects/"+projectName+"/files/"+commitOptions.newRev+"/"+filename;
+                var promises = [$.Deferred(),$.Deferred(),$.Deferred()];
+                if (commitOptions.commonRev) {
+                    var commonVersionUrl = "/projects/"+projectName+"/files/"+commitOptions.commonRev+"/"+filename;
+                    $.ajax({dataType: "json",url: commonVersionUrl}).then(function(data) { promises[0].resolve(data); }).fail(function() { promises[0].resolve(null);})
+                } else {
+                    promises[0].resolve(null);
+                }
+
+                $.ajax({dataType: "json",url: oldVersionUrl}).then(function(data) { promises[1].resolve(data); }).fail(function() { promises[1].resolve({content:"[]"});})
+                $.ajax({dataType: "json",url: newVersionUrl}).then(function(data) { promises[2].resolve(data); }).fail(function() { promises[2].resolve({content:"[]"});})
+                $.when.apply($,promises).always(function(commonVersion, oldVersion,newVersion) {
+                    var commonFlow;
+                    var oldFlow;
+                    var newFlow;
+                    if (commonVersion) {
                         try {
-                            oldFlow = JSON.parse(oldVersion[0].content||"[]");
+                            commonFlow = JSON.parse(commonVersion.content||"[]");
                         } catch(err) {
-                            console.log("Old Version doesn't contain valid JSON:",oldVersionUrl);
+                            console.log("Common Version doesn't contain valid JSON:",commonVersionUrl);
                             console.log(err);
                             return;
                         }
-                        try {
-                            newFlow = JSON.parse(newVersion[0].content||"[]");
-                        } catch(err) {
-                            console.log("New Version doesn't contain valid JSON:",newFlow);
-                            console.log(err);
-                            return;
-                        }
-                        var localDiff = generateDiff(oldFlow,oldFlow);
-                        var remoteDiff = generateDiff(oldFlow,newFlow);
-                        var diff = resolveDiffs(localDiff,remoteDiff);
-                        showDiff(diff,{
-                            title: filename,
-                            mode: 'view',
-                            oldRevTitle: commitOptions.oldRevTitle,
-                            newRevTitle: commitOptions.newRevTitle
-                        });
-                        // var flowDiffRow = $("<tr>").insertAfter(diffRow);
-                        // var content = $('<td colspan="3"></td>').appendTo(flowDiffRow);
-                        // currentDiff = diff;
-                        // var diffTable = buildDiffPanel(content,diff,{mode:"view"}).finish();
+                    }
+                    try {
+                        oldFlow = JSON.parse(oldVersion.content||"[]");
+                    } catch(err) {
+                        console.log("Old Version doesn't contain valid JSON:",oldVersionUrl);
+                        console.log(err);
+                        return;
+                    }
+                    if (!commonFlow) {
+                        commonFlow = oldFlow;
+                    }
+                    try {
+                        newFlow = JSON.parse(newVersion.content||"[]");
+                    } catch(err) {
+                        console.log("New Version doesn't contain valid JSON:",newFlow);
+                        console.log(err);
+                        return;
+                    }
+                    var localDiff = generateDiff(commonFlow,oldFlow);
+                    var remoteDiff = generateDiff(commonFlow,newFlow);
+                    commitOptions.currentDiff = resolveDiffs(localDiff,remoteDiff);
+                    var diffTable = buildDiffPanel(flowDiffContent,commitOptions.currentDiff,{
+                        title: filename,
+                        mode: commitOptions.commonRev?'merge':'view',
+                        oldRevTitle: commitOptions.oldRevTitle,
+                        newRevTitle: commitOptions.newRevTitle
                     });
-                })
-            }
+                    diffTable.list.hide();
+                    refreshConflictHeader(commitOptions.currentDiff);
+                    setTimeout(function() {
+                        diffTable.finish();
+                        diffTable.list.show();
+                    },300);
+                    // var flowDiffRow = $("<tr>").insertAfter(diffRow);
+                    // var content = $('<td colspan="3"></td>').appendTo(flowDiffRow);
+                    // currentDiff = diff;
+                    // var diffTable = buildDiffPanel(content,diff,{mode:"view"}).finish();
+                });
+
+
+
+            } else
 
             if (isBinary) {
                 var diffBinaryRow = $('<tr class="node-text-diff-header">').appendTo(codeBody);
@@ -1750,6 +1863,9 @@ RED.diff = (function() {
                 $('<span></span>').text("Cannot show binary file contents").appendTo(binaryContent);
 
             } else {
+                if (commitOptions.unmerged) {
+                    conflictHeader = $('<span style="float: right;"><span>'+resolvedConflicts+'</span> of <span>'+unresolvedConflicts+'</span> conflicts resolved</span>').appendTo(content);
+                }
                 hunks.forEach(function(hunk) {
                     var diffRow = $('<tr class="node-text-diff-header">').appendTo(codeBody);
                     var content = $('<td colspan="3"></td>').appendTo(diffRow);
@@ -1886,9 +2002,6 @@ RED.diff = (function() {
                     });
                 });
             }
-            if (commitOptions.unmerged) {
-                conflictHeader = $('<span style="float: right;"><span>'+resolvedConflicts+'</span> of <span>'+unresolvedConflicts+'</span> conflicts resolved</span>').appendTo(content);
-            }
         });
         return diffPanel;
     }
@@ -1914,7 +2027,7 @@ RED.diff = (function() {
                 var trayBody = tray.find('.editor-tray-body');
                 var diffPanel = $('<div class="node-text-diff"></div>').appendTo(trayBody);
 
-                var codeTable = $("<table>").appendTo(diffPanel);
+                var codeTable = $("<table>",{class:"node-text-diff-content"}).appendTo(diffPanel);
                 $('<colgroup><col width="50"><col width="50"><col width="100%"></colgroup>').appendTo(codeTable);
                 var codeBody = $('<tbody>').appendTo(codeTable);
 
@@ -1957,7 +2070,6 @@ RED.diff = (function() {
             }
         }
 
-
         var trayOptions = {
             title: title||"Compare Changes", //TODO: nls
             width: Infinity,
@@ -1996,6 +2108,15 @@ RED.diff = (function() {
                     class: "primary disabled",
                     click: function() {
                         if (!$("#node-diff-view-resolve-diff").hasClass('disabled')) {
+                            if (options.currentDiff) {
+                                // This is a flow file. Need to apply the diff
+                                // and generate the new flow.
+                                var result = applyDiff(options.currentDiff);
+                                currentResolution = {
+                                    resolutions:{}
+                                };
+                                currentResolution.resolutions[options.project.files.flow] = JSON.stringify(result.config,"",4);
+                            }
                             if (options.onresolve) {
                                 options.onresolve(currentResolution);
                             }
diff --git a/editor/js/ui/projects/tab-versionControl.js b/editor/js/ui/projects/tab-versionControl.js
index b9d09be56..7e1f7dd7f 100644
--- a/editor/js/ui/projects/tab-versionControl.js
+++ b/editor/js/ui/projects/tab-versionControl.js
@@ -30,7 +30,6 @@ RED.sidebar.versionControl = (function() {
     var unmergedContent;
     var unmergedChangesList;
     var commitButton;
-    var mergeConflictNotification;
     var localChanges;
 
     var localCommitList;
@@ -76,6 +75,11 @@ RED.sidebar.versionControl = (function() {
                         options.oldRev = "@";
                         options.newRev = ":0";
                     } else {
+                        options.oldRevTitle = "Local";
+                        options.newRevTitle = "Remote";
+                        options.commonRev = ":1";
+                        options.oldRev = ":2";
+                        options.newRev = ":3";
                         options.onresolve = function(resolution) {
                             utils.sendRequest({
                                 url: "projects/"+activeProject.name+"/resolve/"+encodeURIComponent(entry.file),
@@ -358,6 +362,7 @@ RED.sidebar.versionControl = (function() {
                 evt.stopPropagation();
                 var spinner = utils.addSpinnerOverlay(unmergedContent);
                 var activeProject = RED.projects.getActiveProject();
+                RED.deploy.setDeployInflight(true);
                 utils.sendRequest({
                     url: "projects/"+activeProject.name+"/merge",
                     type: "DELETE",
@@ -375,6 +380,10 @@ RED.sidebar.versionControl = (function() {
                             }
                         },
                     }
+                }).always(function() {
+                    setTimeout(function() {
+                        RED.deploy.setDeployInflight(false);
+                    },500);
                 });
             });
         unmergedChangesList = $("<ol>",{style:"position: absolute; top: 30px; bottom: 0; right:0; left:0;"}).appendTo(unmergedContent);
@@ -496,6 +505,7 @@ RED.sidebar.versionControl = (function() {
                 evt.preventDefault();
                 var spinner = utils.addSpinnerOverlay(submitCommitButton).addClass('projects-dialog-spinner-sidebar');
                 var activeProject = RED.projects.getActiveProject();
+                RED.deploy.setDeployInflight(true);
                 utils.sendRequest({
                     url: "projects/"+activeProject.name+"/commit",
                     type: "POST",
@@ -516,10 +526,11 @@ RED.sidebar.versionControl = (function() {
                     }
                 },{
                     message:commitMessage.val()
-                });
-
-
-
+                }).always(function() {
+                    setTimeout(function() {
+                        RED.deploy.setDeployInflight(false);
+                    },500);
+                })
             })
 
 
@@ -1108,31 +1119,9 @@ RED.sidebar.versionControl = (function() {
         }
         isMerging = !!result.merging;
         if (isMerging) {
-            if (!mergeConflictNotification) {
-                var text = "<p>Automatic merging of changes failed.</p><p>Fix the unmerged conflicts then commit the results.</p>";
-                var options = {
-                    type: 'error',
-                    fixed: true,
-                    id: 'merge-conflict',
-                    buttons: [
-                        {
-                            text: "Show merge conflicts",
-                            click: function() {
-                                mergeConflictNotification.hideNotification();
-                                RED.sidebar.versionControl.showLocalChanges();
-                            }
-                        }
-                    ]
-                }
-                mergeConflictNotification = RED.notify(text,options);
-            }
             sidebarContent.addClass("sidebar-version-control-merging");
             unmergedContent.show();
         } else {
-            if (mergeConflictNotification) {
-                mergeConflictNotification.close();
-                mergeConflictNotification = null;
-            }
             sidebarContent.removeClass("sidebar-version-control-merging");
             unmergedContent.hide();
         }
@@ -1307,6 +1296,8 @@ RED.sidebar.versionControl = (function() {
                 }
                 refreshInProgress = false;
                 $('.sidebar-version-control-shade').hide();
+            }).fail(function() {
+                refreshInProgress = false;
             });
         } else {
             $('.sidebar-version-control-shade').show();
diff --git a/editor/sass/diff.scss b/editor/sass/diff.scss
index a4c0f5f1f..48a1492c4 100644
--- a/editor/sass/diff.scss
+++ b/editor/sass/diff.scss
@@ -16,17 +16,16 @@
 
 
 .node-dialog-view-diff-panel {
+    padding: 5px;
+    padding-top: 30px;
+    position: relative;
+
     .red-ui-editableList-container {
         border-radius:1px;
         padding:0;
         background: #f9f9f9;
     }
     .node-dialog-view-diff-diff {
-        position: absolute;
-        top:30px;
-        bottom:10px;
-        left:10px;
-        right:10px;
         li {
             background: #f9f9f9;
             padding: 0px;
@@ -38,21 +37,20 @@
         padding: 5px;
         // padding-bottom: 5px;
     }
-    &.node-dialog-view-diff-panel-merge {
-        .node-dialog-view-diff-diff {
-            top: 80px
-        }
-        .node-dialog-view-diff-headers {
-            top: 55px;
-        }
-
-    }
+}
+.node-diff-container {
+    position: absolute;
+    top: 40px;
+    right:0;
+    bottom: 0;
+    left: 0;
+    overflow-y: scroll;
 }
 
 .node-dialog-view-diff-headers {
     position: absolute;
-    left:237px;
-    right:18px;
+    left:232px;
+    right:12px;
     top: 5px;
     height: 25px;
     div {
@@ -76,11 +74,6 @@
 }
 
 .node-diff-toolbar {
-    position:absolute;
-    top:0;
-    left:0;
-    right:0;
-    height: 43px;
     box-sizing: border-box;
     color: #666;
     text-align: right;
@@ -555,129 +548,129 @@ ul.node-dialog-configm-deploy-list {
 .node-text-diff {
     height: 100%;
     overflow-y:auto;
-    table {
+
+    table.node-text-diff-content {
         margin: 10px;
         border: 1px solid $secondary-border-color;
         border-radius: 3px;
         table-layout: fixed;
         width: calc(100% - 20px);
-    }
-    td {
-        vertical-align: top;
-        word-wrap: break-word;
-    }
-    td.lineno {
-        font-family: monospace;
-        text-align: right;
-        color: #aaa;
-        background: #f6f6f6;
-        padding: 1px 5px;
-    }
-    td.lineno:nth-child(3) {
-        border-left: 1px solid $secondary-border-color;
-    }
-    td.linetext {
-        font-family: monospace;
-        white-space: pre-wrap;
-        padding: 1px 5px;
-        span.prefix {
-            width: 30px;
-            display: inline-block;
-            text-align: center;
-            color: #999;
+        td {
+            vertical-align: top;
+            word-wrap: break-word;
         }
-    }
-    td.blank {
-        background: #f6f6f6;
-    }
-    td.added {
-        background: #eefaee;
-    }
-    td.removed {
-        background: #fadddd;
-    }
-    tr.mergeHeader td {
-        color: #800080;
-        background: #e5f9ff;
-        height: 26px;
-        vertical-align: middle;
-    }
-    tr.mergeHeader-separator td {
-        color: #800080;
-        background: darken(#e5f9ff, 10%);
-        height: 0px;
-    }
-    tr.mergeHeader-ours td {
-        border-top: 2px solid darken(#e5f9ff, 10%);
-    }
-    tr.mergeHeader-theirs td {
-        border-bottom: 2px solid darken(#e5f9ff, 10%);
-    }
-    td.unchanged {
-        color: #999;
-    }
-    tr.unchanged {
-        background: #fefefe;
-    }
-    tr.start-block {
-        border-top: 1px solid #f0f0f0;
-    }
-    tr.end-block {
-        border-bottom: 1px solid #f0f0f0;
-    }
-    tr.node-text-diff-file-header td {
-        .filename {
+        td.lineno {
             font-family: monospace;
+            text-align: right;
+            color: #aaa;
+            background: #f6f6f6;
+            padding: 1px 5px;
         }
-        background: #f3f3f3;
-        padding: 5px 10px 5px 0;
-        color: #333;
-        cursor: pointer;
-        i.node-diff-chevron {
-            width: 30px;
+        td.lineno:nth-child(3) {
+            border-left: 1px solid $secondary-border-color;
         }
-    }
-    tr.node-text-diff-file-header.collapsed {
-        td i.node-diff-chevron {
-            transform: rotate(-90deg);
+        td.linetext {
+            font-family: monospace;
+            white-space: pre-wrap;
+            padding: 1px 5px;
+            span.prefix {
+                width: 30px;
+                display: inline-block;
+                text-align: center;
+                color: #999;
+            }
         }
-    }
-    tr.node-text-diff-commit-header td {
-        background: #f3f3f3;
-        padding: 5px 10px;
-        color: #333;
-        h3 {
-            font-size: 1.4em;
-            margin: 0;
+        td.blank {
+            background: #f6f6f6;
         }
-        .commit-summary {
-            border-top: 1px solid $secondary-border-color;
-            padding-top: 5px;
+        td.added {
+            background: #eefaee;
+        }
+        td.removed {
+            background: #fadddd;
+        }
+        tr.mergeHeader td {
+            color: #800080;
+            background: #e5f9ff;
+            height: 26px;
+            vertical-align: middle;
+        }
+        tr.mergeHeader-separator td {
+            color: #800080;
+            background: darken(#e5f9ff, 10%);
+            height: 0px;
+        }
+        tr.mergeHeader-ours td {
+            border-top: 2px solid darken(#e5f9ff, 10%);
+        }
+        tr.mergeHeader-theirs td {
+            border-bottom: 2px solid darken(#e5f9ff, 10%);
+        }
+        td.unchanged {
             color: #999;
         }
-        .commit-body {
-            margin-bottom:15px;
-            white-space: pre;
-            line-height: 1.2em;
+        tr.unchanged {
+            background: #fefefe;
+        }
+        tr.start-block {
+            border-top: 1px solid #f0f0f0;
+        }
+        tr.end-block {
+            border-bottom: 1px solid #f0f0f0;
+        }
+        tr.node-text-diff-file-header td {
+            .filename {
+                font-family: monospace;
+            }
+            background: #f3f3f3;
+            padding: 5px 10px 5px 0;
+            color: #333;
+            cursor: pointer;
+            i.node-diff-chevron {
+                width: 30px;
+            }
+        }
+        tr.node-text-diff-file-header.collapsed {
+            td i.node-diff-chevron {
+                transform: rotate(-90deg);
+            }
+        }
+        tr.node-text-diff-commit-header td {
+            background: #f3f3f3;
+            padding: 5px 10px;
+            color: #333;
+            h3 {
+                font-size: 1.4em;
+                margin: 0;
+            }
+            .commit-summary {
+                border-top: 1px solid $secondary-border-color;
+                padding-top: 5px;
+                color: #999;
+            }
+            .commit-body {
+                margin-bottom:15px;
+                white-space: pre;
+                line-height: 1.2em;
+            }
+        }
+
+        tr.node-text-diff-header > td:not(.flow-diff) {
+            font-family: monospace;
+            padding: 5px 10px;
+            text-align: left;
+            color: #666;
+            background: #ffd;
+            height: 30px;
+            vertical-align: middle;
+            border-top: 1px solid #f0f0f0;
+            border-bottom: 1px solid #f0f0f0;
+        }
+        tr.node-text-diff-expand td {
+            cursor: pointer;
+            &:hover {
+                background: #ffc;
+            }
         }
     }
-
-    tr.node-text-diff-header td {
-        font-family: monospace;
-        padding: 5px 10px;
-        text-align: left;
-        color: #666;
-        background: #ffd;
-        height: 30px;
-        vertical-align: middle;
-        border-top: 1px solid #f0f0f0;
-        border-bottom: 1px solid #f0f0f0;
-    }
-    tr.node-text-diff-expand td {
-        cursor: pointer;
-        &:hover {
-            background: #ffc;
-        }
-    }
-
 }
diff --git a/red/api/admin/flows.js b/red/api/admin/flows.js
index 475448fbd..4f596d212 100644
--- a/red/api/admin/flows.js
+++ b/red/api/admin/flows.js
@@ -80,7 +80,7 @@ module.exports = {
             }).catch(function(err) {
                 log.warn(log._("api.flows.error-save",{message:err.message}));
                 log.warn(err.stack);
-                res.status(500).json({error:"unexpected_error", message:err.message});
+                res.status(500).json({error:err.code || "unexpected_error", message:err.message});
             });
         }
     }
diff --git a/red/api/editor/locales/en-US/editor.json b/red/api/editor/locales/en-US/editor.json
index 5a4b8c81b..882e2808d 100644
--- a/red/api/editor/locales/en-US/editor.json
+++ b/red/api/editor/locales/en-US/editor.json
@@ -93,7 +93,8 @@
             "credentials_load_failed": "<p>Flows stopped as the credentials could not be decrypted.</p><p>The flow credential file is encrypted, but the project's encryption key is missing or invalid.</p>",
             "missing_flow_file": "<p>Project flow file not found.</p><p>The project is not configured with a flow file.</p>",
             "project_empty": "<p>The project is empty.</p><p>Do you want to create a default set of project files?<br/>Otherwise, you will have to manually add files to the project outside of the editor.</p>",
-            "project_not_found": "<p>Project '__project__' not found.</p>"
+            "project_not_found": "<p>Project '__project__' not found.</p>",
+            "git_merge_conflict": "<p>Automatic merging of changes failed.</p><p>Fix the unmerged conflicts then commit the results.</p>"
         },
 
         "error": "<strong>Error</strong>: __message__",
diff --git a/red/runtime/storage/localfilesystem/projects/Project.js b/red/runtime/storage/localfilesystem/projects/Project.js
index d3a0c0cb1..aa2693001 100644
--- a/red/runtime/storage/localfilesystem/projects/Project.js
+++ b/red/runtime/storage/localfilesystem/projects/Project.js
@@ -127,7 +127,7 @@ Project.prototype.load = function () {
 
         promises.push(project.loadRemotes());
 
-        return when.settle(promises).then(function() {
+        return when.settle(promises).then(function(results) {
             return project;
         })
     });
@@ -218,6 +218,9 @@ Project.prototype.parseRemoteBranch = function (remoteBranch) {
 Project.prototype.isEmpty = function () {
     return this.empty;
 };
+Project.prototype.isMerging = function() {
+    return this.merging;
+}
 
 Project.prototype.update = function (user, data) {
     var username;
@@ -374,7 +377,13 @@ Project.prototype.unstageFile = function(file) {
     return gitTools.unstageFile(this.path,file);
 }
 Project.prototype.commit = function(user, options) {
-    return gitTools.commit(this.path,options.message,getGitUser(user));
+    var self = this;
+    return gitTools.commit(this.path,options.message,getGitUser(user)).then(function() {
+        if (self.merging) {
+            self.merging = false;
+            return
+        }
+    });
 }
 Project.prototype.getFileDiff = function(file,type) {
     return gitTools.getFileDiff(this.path,file,type);
@@ -440,6 +449,21 @@ Project.prototype.status = function(user, includeRemote) {
             var result = results[0];
             if (results[1]) {
                 result.merging = true;
+                if (!self.merging) {
+                    self.merging = true;
+                    runtime.events.emit("runtime-event",{
+                        id:"runtime-state",
+                        payload:{
+                            type:"warning",
+                            error:"git_merge_conflict",
+                            project:self.name,
+                            text:"notification.warnings.git_merge_conflict"
+                        },
+                        retain:true}
+                    );
+                }
+            } else {
+                self.merging = false;
             }
             self.branches.local = result.branches.local;
             self.branches.remote = result.branches.remote;
@@ -534,6 +558,11 @@ Project.prototype.pull = function (user,remoteBranchName,setRemote,allowUnrelate
 Project.prototype.resolveMerge = function (file,resolutions) {
     var filePath = fspath.join(this.path,file);
     var self = this;
+    if (typeof resolutions === 'string') {
+        return util.writeFile(filePath, resolutions).then(function() {
+            return self.stageFile(file);
+        })
+    }
     return fs.readFile(filePath,"utf8").then(function(content) {
         var lines = content.split("\n");
         var result = [];
@@ -573,7 +602,10 @@ Project.prototype.resolveMerge = function (file,resolutions) {
     });
 };
 Project.prototype.abortMerge = function () {
-    return gitTools.abortMerge(this.path);
+    var self = this;
+    return gitTools.abortMerge(this.path).then(function() {
+        self.merging = false;
+    })
 };
 
 Project.prototype.getBranches = function (user, isRemote) {
diff --git a/red/runtime/storage/localfilesystem/projects/git/index.js b/red/runtime/storage/localfilesystem/projects/git/index.js
index dfa6a03f7..717a1a235 100644
--- a/red/runtime/storage/localfilesystem/projects/git/index.js
+++ b/red/runtime/storage/localfilesystem/projects/git/index.js
@@ -454,18 +454,19 @@ module.exports = {
         } else {
             promise = runGitCommand(args,cwd)
         }
-        return promise.catch(function(err) {
-            if (/CONFLICT/.test(err.stdout)) {
-                var e = new Error("NLS: pull failed - merge conflict");
-                e.code = "git_pull_merge_conflict";
-                throw e;
-            } else if (/Please commit your changes or stash/i.test(err.message)) {
-                var e = new Error("NLS: Pull failed - local changes would be overwritten");
-                e.code = "git_pull_overwrite";
-                throw e;
-            }
-            throw err;
-        });
+        return promise;
+        // .catch(function(err) {
+        //     if (/CONFLICT/.test(err.stdout)) {
+        //         var e = new Error("pull failed - merge conflict");
+        //         e.code = "git_pull_merge_conflict";
+        //         throw e;
+        //     } else if (/Please commit your changes or stash/i.test(err.message)) {
+        //         var e = new Error("Pull failed - local changes would be overwritten");
+        //         e.code = "git_pull_overwrite";
+        //         throw e;
+        //     }
+        //     throw err;
+        // });
     },
     push: function(cwd,remote,branch,setUpstream, auth) {
         var args = ["push"];
diff --git a/red/runtime/storage/localfilesystem/projects/index.js b/red/runtime/storage/localfilesystem/projects/index.js
index 9c1fb97fa..361784987 100644
--- a/red/runtime/storage/localfilesystem/projects/index.js
+++ b/red/runtime/storage/localfilesystem/projects/index.js
@@ -212,7 +212,13 @@ function unstageFile(user, project,file) {
 }
 function commit(user, project,options) {
     checkActiveProject(project);
-    return activeProject.commit(user, options);
+    var isMerging = activeProject.isMerging();
+    return activeProject.commit(user, options).then(function() {
+        // The project was merging, now it isn't. Lets reload.
+        if (isMerging && !activeProject.isMerging()) {
+            return reloadActiveProject("merge-complete");
+        }
+    })
 }
 function getFileDiff(user, project,file,type) {
     checkActiveProject(project);
@@ -258,7 +264,7 @@ function resolveMerge(user, project,file,resolution) {
 function abortMerge(user, project) {
     checkActiveProject(project);
     return activeProject.abortMerge().then(function() {
-        return reloadActiveProject("abort-merge")
+        return reloadActiveProject("merge-abort")
     });
 }
 function getBranches(user, project,isRemote) {
@@ -478,6 +484,13 @@ function getFlows() {
             error.code = "missing_flow_file";
             return when.reject(error);
         }
+        if (activeProject.isMerging()) {
+            log.warn("Project has unmerged changes");
+            error = new Error("Project has unmerged changes. Cannot load flows");
+            error.code = "git_merge_conflict";
+            return when.reject(error);
+        }
+
     }
     return util.readFile(flowsFullPath,flowsFileBackup,[],'flow');
 }
@@ -486,6 +499,11 @@ function saveFlows(flows) {
     if (settings.readOnly) {
         return when.resolve();
     }
+    if (activeProject && activeProject.isMerging()) {
+        var error = new Error("Project has unmerged changes. Cannot deploy new flows");
+        error.code = "git_merge_conflict";
+        return when.reject(error);
+    }
 
     try {
         fs.renameSync(flowsFullPath,flowsFileBackup);