try using ember-cli-fastboot-addon

addon/fastboot/index.js

@@ -0,0 +1,6 @@
+import {require} from 'ember-cli-fastboot-addon';
+
+const PouchDB = require('pouchdb');
+PouchDB.plugin(require('relational-pouch'));
+
+export default PouchDB;

index.js

@@ -25,10 +25,18 @@ module.exports = {
     }
   },
 
+  treeForAddon: function(tree) {
+    var fastbootTree = require('ember-cli-fastboot-addon').fastbootTree;
+    return this._super.treeForAddon.call(this, fastbootTree(tree));
+  },
+
+  treeForApp: function(tree) {
+    var fastbootTree = require('ember-cli-fastboot-addon').fastbootTree;
+    return fastbootTree(tree);
+  },
+
   included: function included(app) {
-    if (isFastBoot()) {
-      app.import('vendor/ember-pouch/ember-pouch-fastboot.js');
-    } else {
+    if (!isFastBoot()) {
       var bowerDir = app.bowerDirectory;
 
       app.import(bowerDir + '/pouchdb/dist/pouchdb.js');
@@ -45,7 +53,6 @@ module.exports = {
 
 // Steal *all the things* from github.com/tomdale/ember-network !
 
-var funnel = require('broccoli-funnel');
 
 // Checks to see whether this build is targeting FastBoot. Note that we cannot
 // check this at boot time--the environment variable is only set once the build

package.json

@@ -46,20 +46,23 @@
     "ember-cli-sri": "^1.2.0",
     "ember-cli-uglify": "^1.2.0",
     "ember-data": "~1.13.0 || 2.x",
+    "ember-disable-prototype-extensions": "^1.0.0",
     "ember-disable-proxy-controllers": "^1.0.1",
     "ember-export-application-global": "^1.0.4",
-    "ember-disable-prototype-extensions": "^1.0.0",
     "ember-try": "~0.0.8"
   },
   "dependencies": {
-    "broccoli-funnel": "^1.0.1",
     "ember-cli-babel": "^5.1.5",
     "ember-cli-version-checker": "1.1.5",
     "pouchdb": "^5.2.1",
-    "relational-pouch": "^1.4.0"
+    "relational-pouch": "^1.4.0",
+    "ember-cli-fastboot-addon": "0.1.0"
   },
   "ember-addon": {
     "configPath": "tests/dummy/config",
-    "fastBootDependencies": ["pouchdb", "relational-pouch"]
+    "fastBootDependencies": [
+      "pouchdb",
+      "relational-pouch"
+    ]
   }
 }