diff --git a/package.json b/package.json
index 21adf40c1..aad454ba9 100644
--- a/package.json
+++ b/package.json
@@ -68,7 +68,7 @@
     "cross-fetch": "0.0.8",
     "deep-extend": "^0.4.1",
     "encode-3986": "^1.0.0",
-    "fast-json-patch": "1.1.8",
+    "fast-json-patch": "^1.2.2",
     "isomorphic-form-data": "0.0.1",
     "js-yaml": "^3.8.1",
     "lodash": "^4.16.2",
@@ -77,4 +77,4 @@
     "utf8-bytes": "0.0.1",
     "utfstring": "^2.0.0"
   }
-}
\ No newline at end of file
+}
diff --git a/src/specmap/index.js b/src/specmap/index.js
index fcf1431e8..c18c03247 100644
--- a/src/specmap/index.js
+++ b/src/specmap/index.js
@@ -212,8 +212,10 @@ class SpecMap {
   }
 
   updateMutations(patch) {
-    if (lib.applyPatch(this.state, patch, {allowMetaPatches: this.allowMetaPatches})) {
+    const result = lib.applyPatch(this.state, patch, {allowMetaPatches: this.allowMetaPatches})
+    if (result) {
       this.mutations.push(patch)
+      this.state = result
     }
   }
 
diff --git a/src/specmap/lib/index.js b/src/specmap/lib/index.js
index cbd865f79..26d23a241 100644
--- a/src/specmap/lib/index.js
+++ b/src/specmap/lib/index.js
@@ -37,15 +37,14 @@ function applyPatch(obj, patch, opts) {
   })
 
   if (patch.op === 'merge') {
-    const valPatch = _get(patch.path)
-    jsonPatch.apply(obj, [valPatch])
-    Object.assign(valPatch.value, patch.value)
+    const newValue = getInByJsonPath(obj, patch.path)
+    Object.assign(newValue, patch.value)
+    jsonPatch.applyPatch(obj, [replace(patch.path, newValue)])
   }
   else if (patch.op === 'mergeDeep') {
-    const valPatch = _get(patch.path)
-    jsonPatch.apply(obj, [valPatch])
-    const origValPatchValue = Object.assign({}, valPatch.value)
-    deepExtend(valPatch.value, patch.value)
+    const currentValue = getInByJsonPath(obj, patch.path)
+    const origValPatchValue = Object.assign({}, currentValue)
+    deepExtend(currentValue, patch.value)
 
     // deepExtend doesn't merge arrays, so we will do it manually
     for (const prop in patch.value) {
@@ -53,20 +52,47 @@ function applyPatch(obj, patch, opts) {
         const propVal = patch.value[prop]
         if (Array.isArray(propVal)) {
           const existing = origValPatchValue[prop] || []
-          valPatch.value[prop] = existing.concat(propVal)
+          currentValue[prop] = existing.concat(propVal)
         }
       }
     }
   }
+  else if (patch.op === 'add' && patch.path === '' && isObject(patch.value)) {
+    // { op: 'add', path: '', value: { a: 1, b: 2 }}
+    // has no effect: json patch refuses to do anything.
+    // so let's break that patch down into a set of patches,
+    // one for each key in the intended root value.
+
+    const patches = Object.keys(patch.value)
+      .reduce((arr, key) => {
+        arr.push({
+          op: 'add',
+          path: `/${normalizeJSONPath(key)}`,
+          value: patch.value[key]
+        })
+        return arr
+      }, [])
+
+    jsonPatch.applyPatch(obj, patches)
+  }
+  else if (patch.op === 'replace' && patch.path === '') {
+    let value = patch.value
+
+    if (opts.allowMetaPatches && patch.meta && isAdditiveMutation(patch) &&
+        (Array.isArray(patch.value) || isObject(patch.value))) {
+      value = Object.assign({}, value, patch.meta)
+    }
+    obj = value
+  }
   else {
-    jsonPatch.apply(obj, [patch])
+    jsonPatch.applyPatch(obj, [patch])
 
     // Attach metadata to the resulting value.
     if (opts.allowMetaPatches && patch.meta && isAdditiveMutation(patch) &&
         (Array.isArray(patch.value) || isObject(patch.value))) {
-      const valPatch = _get(patch.path)
-      jsonPatch.apply(obj, [valPatch])
-      Object.assign(valPatch.value, patch.meta)
+      const currentValue = getInByJsonPath(obj, patch.path)
+      const newValue = Object.assign({}, currentValue, patch.meta)
+      jsonPatch.applyPatch(obj, [replace(patch.path, newValue)])
     }
   }
 
@@ -302,3 +328,13 @@ function isContextPatch(patch) {
 function isPatch(patch) {
   return patch && typeof patch === 'object'
 }
+
+function getInByJsonPath(obj, jsonPath) {
+  try {
+    return jsonPatch.getValueByPointer(obj, jsonPath)
+  }
+  catch (e) {
+    console.error(e) // eslint-disable-line no-console
+    return {}
+  }
+}
diff --git a/test/resolver.js b/test/resolver.js
index c86dab181..19129ea08 100644
--- a/test/resolver.js
+++ b/test/resolver.js
@@ -447,7 +447,6 @@ describe('resolver', () => {
           },
           definitions: {
             Category: {
-              $$ref: '#/definitions/Category', // FIXME: benign, but this should not be present
               type: 'object',
               properties: {
                 id: {
@@ -460,14 +459,13 @@ describe('resolver', () => {
               }
             },
             Pet: {
-              $$ref: '#/definitions/Pet',
               type: 'object',
               required: [
                 'category'
               ],
               properties: {
                 category: {
-                  $$ref: '#/definitions/Category', // FIXME: benign, but this should not be present
+                  $$ref: '#/definitions/Category',
                   type: 'object',
                   properties: {
                     id: {
diff --git a/test/specmap/all-of.js b/test/specmap/all-of.js
index 8c5293c6f..60de3e514 100644
--- a/test/specmap/all-of.js
+++ b/test/specmap/all-of.js
@@ -128,7 +128,6 @@ describe('allOf', function () {
         errors: [],
         spec: {
           Pet: {
-            $$ref: '#/Pet',
             type: 'object',
             properties: {
               name: {
@@ -137,7 +136,6 @@ describe('allOf', function () {
             }
           },
           Cat: {
-            $$ref: '#/Cat',
             properties: {
               meow: {
                 type: 'string'
diff --git a/test/specmap/index.js b/test/specmap/index.js
index d8cf9afd9..2d341fc98 100644
--- a/test/specmap/index.js
+++ b/test/specmap/index.js
@@ -549,6 +549,7 @@ describe('specmap', function () {
           })
             .then((res) => {
               expect(res.spec.one.$$ref).toEqual('#/two')
+              expect(res.spec.two.$$ref).toEqual(undefined)
             })
         })