diff --git a/lib/blockchain.js b/lib/cmds/blockchain/blockchain.js
similarity index 97%
rename from lib/blockchain.js
rename to lib/cmds/blockchain/blockchain.js
index 2081e1ba..82333fd9 100644
--- a/lib/blockchain.js
+++ b/lib/cmds/blockchain/blockchain.js
@@ -1,9 +1,11 @@
-var fs = require('./fs.js');
 var colors = require('colors');
-var GethCommands = require('./geth_commands.js');
-var utils = require('./utils.js');
 var shelljs = require('shelljs');
 
+var fs = require('../../core/fs.js');
+var utils = require('../../core/utils.js');
+
+var GethCommands = require('./geth_commands.js');
+
 var Blockchain = function(blockchainConfig, Client) {
   this.blockchainConfig = blockchainConfig;
 
diff --git a/lib/geth_commands.js b/lib/cmds/blockchain/geth_commands.js
similarity index 100%
rename from lib/geth_commands.js
rename to lib/cmds/blockchain/geth_commands.js
diff --git a/lib/simulator.js b/lib/cmds/simulator.js
similarity index 100%
rename from lib/simulator.js
rename to lib/cmds/simulator.js
diff --git a/lib/template_generator.js b/lib/cmds/template_generator.js
similarity index 93%
rename from lib/template_generator.js
rename to lib/cmds/template_generator.js
index c61dc136..2f48c6e7 100644
--- a/lib/template_generator.js
+++ b/lib/cmds/template_generator.js
@@ -1,5 +1,5 @@
-var fs = require('./fs.js');
-var utils = require('./utils.js');
+var fs = require('../core/fs.js');
+var utils = require('../core/utils.js');
 
 var TemplateGenerator = function(templateName) {
   this.templateName = templateName;
diff --git a/lib/abi.js b/lib/contracts/abi.js
similarity index 100%
rename from lib/abi.js
rename to lib/contracts/abi.js
diff --git a/lib/compiler.js b/lib/contracts/compiler.js
similarity index 100%
rename from lib/compiler.js
rename to lib/contracts/compiler.js
diff --git a/lib/contracts.js b/lib/contracts/contracts.js
similarity index 100%
rename from lib/contracts.js
rename to lib/contracts/contracts.js
diff --git a/lib/deploy.js b/lib/contracts/deploy.js
similarity index 99%
rename from lib/deploy.js
rename to lib/contracts/deploy.js
index 66de8604..9ea5d580 100644
--- a/lib/deploy.js
+++ b/lib/contracts/deploy.js
@@ -1,7 +1,7 @@
 var async = require('async');
 var DeployTracker = require('./deploy_tracker.js');
 var ABIGenerator = require('./abi.js');
-var RunCode = require('./runCode.js');
+var RunCode = require('../core/runCode.js');
 
 var Deploy = function(options) {
   this.web3 = options.web3;
diff --git a/lib/deploy_tracker.js b/lib/contracts/deploy_tracker.js
similarity index 97%
rename from lib/deploy_tracker.js
rename to lib/contracts/deploy_tracker.js
index 35a7048b..ac09890b 100644
--- a/lib/deploy_tracker.js
+++ b/lib/contracts/deploy_tracker.js
@@ -1,4 +1,4 @@
-var fs = require('./fs.js');
+var fs = require('../core/fs.js');
 
 var DeployTracker = function(options) {
   this.logger = options.logger;
diff --git a/lib/config.js b/lib/core/config.js
similarity index 91%
rename from lib/config.js
rename to lib/core/config.js
index f2a589a3..80e47023 100644
--- a/lib/config.js
+++ b/lib/core/config.js
@@ -155,12 +155,12 @@ Config.prototype.loadFiles = function(files) {
     return file.indexOf('.') >= 0;
   }).filter(function(file) {
     if (file === 'embark.js') {
-      readFiles.push({filename: 'web3.js',   content: fs.readFileSync(utils.joinPath(__dirname, "/../js/web3.js")).toString(), path: utils.joinPath(__dirname, "/../js/web3.js")});
-      readFiles.push({filename: 'ipfs.js',   content: fs.readFileSync(utils.joinPath(__dirname, "/../js/ipfs.js")).toString(), path: utils.joinPath(__dirname, "/../js/ipfs.js")});
+      readFiles.push({filename: 'web3.js',   content: fs.readFileSync(utils.joinPath(__dirname, "/../../js/web3.js")).toString(), path: utils.joinPath(__dirname, "/../../js/web3.js")});
+      readFiles.push({filename: 'ipfs.js',   content: fs.readFileSync(utils.joinPath(__dirname, "/../../js/ipfs.js")).toString(), path: utils.joinPath(__dirname, "/../../js/ipfs.js")});
       // TODO: remove duplicated files if funcitonality is the same for storage and orbit
-      readFiles.push({filename: 'ipfs-api.js',   content: fs.readFileSync(utils.joinPath(__dirname, "/../js/ipfs-api.min.js")).toString(), path: utils.joinPath(__dirname, "/../js/ipfs-api.min.js")});
-      readFiles.push({filename: 'orbit.js',  content: fs.readFileSync(utils.joinPath(__dirname, "/../js/orbit.min.js")).toString(), path: utils.joinPath(__dirname, "/../js/orbit.min.js")});
-      readFiles.push({filename: 'embark.js', content: fs.readFileSync(utils.joinPath(__dirname, "/../js/build/embark.bundle.js")).toString(), path: utils.joinPath(__dirname, "/../js/build/embark.bundle.js")});
+      readFiles.push({filename: 'ipfs-api.js',   content: fs.readFileSync(utils.joinPath(__dirname, "/../../js/ipfs-api.min.js")).toString(), path: utils.joinPath(__dirname, "/../../js/ipfs-api.min.js")});
+      readFiles.push({filename: 'orbit.js',  content: fs.readFileSync(utils.joinPath(__dirname, "/../../js/orbit.min.js")).toString(), path: utils.joinPath(__dirname, "/../../js/orbit.min.js")});
+      readFiles.push({filename: 'embark.js', content: fs.readFileSync(utils.joinPath(__dirname, "/../../js/build/embark.bundle.js")).toString(), path: utils.joinPath(__dirname, "/../../js/build/embark.bundle.js")});
     }
   });
 
diff --git a/lib/fs.js b/lib/core/fs.js
similarity index 83%
rename from lib/fs.js
rename to lib/core/fs.js
index 77bfb3de..3c7e5fa3 100644
--- a/lib/fs.js
+++ b/lib/core/fs.js
@@ -8,6 +8,10 @@ function copySync() {
   return fs.copySync.apply(fs.copySync, arguments);
 }
 
+function writeFileSync() {
+  return fs.writeFileSync.apply(fs.writeFileSync, arguments);
+}
+
 function readFileSync() {
   return fs.readFileSync.apply(fs.readFileSync, arguments);
 }
@@ -24,6 +28,7 @@ module.exports = {
   mkdirpSync: mkdirpSync,
   copySync: copySync,
   readFileSync: readFileSync,
+  writeFileSync: writeFileSync,
   readJSONSync: readJSONSync,
   writeJSONSync: writeJSONSync
 };
diff --git a/lib/logger.js b/lib/core/logger.js
similarity index 100%
rename from lib/logger.js
rename to lib/core/logger.js
diff --git a/lib/plugin.js b/lib/core/plugin.js
similarity index 100%
rename from lib/plugin.js
rename to lib/core/plugin.js
diff --git a/lib/plugins.js b/lib/core/plugins.js
similarity index 100%
rename from lib/plugins.js
rename to lib/core/plugins.js
diff --git a/lib/runCode.js b/lib/core/runCode.js
similarity index 100%
rename from lib/runCode.js
rename to lib/core/runCode.js
diff --git a/lib/services.js b/lib/core/services.js
similarity index 100%
rename from lib/services.js
rename to lib/core/services.js
diff --git a/lib/test.js b/lib/core/test.js
similarity index 94%
rename from lib/test.js
rename to lib/core/test.js
index dac0bc1c..ac3c5483 100644
--- a/lib/test.js
+++ b/lib/core/test.js
@@ -1,11 +1,11 @@
 var async = require('async');
 var Web3 = require('web3');
-var Embark = require('./index.js');
-var ContractsManager = require('./contracts.js');
-var Deploy = require('./deploy.js');
+var Embark = require('../index.js');
+var ContractsManager = require('../contracts/contracts.js');
+var Deploy = require('../contracts/deploy.js');
 var TestLogger = require('./test_logger.js');
 var Config = require('./config.js');
-var ABIGenerator = require('./abi.js');
+var ABIGenerator = require('../contracts/abi.js');
 var RunCode = require('./runCode.js');
 
 var Test = function(_options) {
diff --git a/lib/test_logger.js b/lib/core/test_logger.js
similarity index 100%
rename from lib/test_logger.js
rename to lib/core/test_logger.js
diff --git a/lib/utils.js b/lib/core/utils.js
similarity index 100%
rename from lib/utils.js
rename to lib/core/utils.js
diff --git a/lib/console.js b/lib/dashboard/console.js
similarity index 94%
rename from lib/console.js
rename to lib/dashboard/console.js
index d0c7bc07..1e7e3919 100644
--- a/lib/console.js
+++ b/lib/dashboard/console.js
@@ -1,5 +1,5 @@
-var utils = require('./utils.js');
-var RunCode = require('./runCode.js');
+var utils = require('../core/utils.js');
+var RunCode = require('../core/runCode.js');
 
 var Console = function(options) {
   this.plugins = options.plugins;
diff --git a/lib/monitor.js b/lib/dashboard/monitor.js
similarity index 100%
rename from lib/monitor.js
rename to lib/dashboard/monitor.js
diff --git a/lib/index.js b/lib/index.js
index 827c112d..b0388809 100644
--- a/lib/index.js
+++ b/lib/index.js
@@ -3,24 +3,30 @@ var async = require('async');
 var Web3 = require('web3');
 var colors = require('colors');
 
+var Blockchain = require('./cmds/blockchain/blockchain.js');
+var Simulator = require('./cmds/simulator.js');
+var TemplateGenerator = require('./cmds/template_generator.js');
+
+var Deploy = require('./contracts/deploy.js');
+var ContractsManager = require('./contracts/contracts.js');
+var ABIGenerator = require('./contracts/abi.js');
+
+var Test = require('./core/test.js');
+var Logger = require('./core/logger.js');
+var Config = require('./core/config.js');
+var ServicesMonitor = require('./core/services.js');
+
+var Monitor = require('./dashboard/monitor.js');
+var Console = require('./dashboard/console.js');
+
+var Pipeline = require('./pipeline/pipeline.js');
+var Server = require('./pipeline/server.js');
+var Watch = require('./pipeline/watch.js');
+
+var IPFS = require('./upload/ipfs.js');
+var Swarm = require('./upload/swarm.js');
+
 var Cmd = require('./cmd.js');
-var Deploy = require('./deploy.js');
-var ContractsManager = require('./contracts.js');
-var ABIGenerator = require('./abi.js');
-var TemplateGenerator = require('./template_generator.js');
-var Blockchain = require('./blockchain.js');
-var Server = require('./server.js');
-var Watch = require('./watch.js');
-var Pipeline = require('./pipeline.js');
-var Test = require('./test.js');
-var Logger = require('./logger.js');
-var Config = require('./config.js');
-var Monitor = require('./monitor.js');
-var ServicesMonitor = require('./services.js');
-var Console = require('./console.js');
-var IPFS = require('./ipfs.js');
-var Swarm = require('./swarm.js');
-var Simulator = require('./simulator.js');
 
 var Embark = {
 
diff --git a/lib/pipeline.js b/lib/pipeline/pipeline.js
similarity index 98%
rename from lib/pipeline.js
rename to lib/pipeline/pipeline.js
index 51d76b2e..68861c03 100644
--- a/lib/pipeline.js
+++ b/lib/pipeline/pipeline.js
@@ -1,5 +1,5 @@
 /*jshint esversion: 6, loopfunc: true */
-var fs = require('./fs.js');
+var fs = require('../core/fs.js');
 
 var Pipeline = function(options) {
   this.buildDir = options.buildDir;
diff --git a/lib/server.js b/lib/pipeline/server.js
similarity index 100%
rename from lib/server.js
rename to lib/pipeline/server.js
diff --git a/lib/watch.js b/lib/pipeline/watch.js
similarity index 98%
rename from lib/watch.js
rename to lib/pipeline/watch.js
index 56b92f0c..f75933c1 100644
--- a/lib/watch.js
+++ b/lib/pipeline/watch.js
@@ -1,5 +1,5 @@
 /*jshint esversion: 6 */
-var fs = require('./fs.js');
+var fs = require('../core/fs.js');
 var chokidar = require('chokidar');
 
 // TODO: this should be receiving the config object not re-reading the
diff --git a/lib/ipfs.js b/lib/upload/ipfs.js
similarity index 100%
rename from lib/ipfs.js
rename to lib/upload/ipfs.js
diff --git a/lib/swarm.js b/lib/upload/swarm.js
similarity index 100%
rename from lib/swarm.js
rename to lib/upload/swarm.js
diff --git a/test/abi.js b/test/abi.js
index 133402ce..4d2533ba 100644
--- a/test/abi.js
+++ b/test/abi.js
@@ -1,5 +1,5 @@
 /*globals describe, it*/
-var ABIGenerator = require('../lib/abi.js');
+var ABIGenerator = require('../lib/contracts/abi.js');
 var assert = require('assert');
 
 // TODO: instead 'eval' the code with a fake web3 object
diff --git a/test/blockchain.js b/test/blockchain.js
index 1183d963..43fefaf5 100644
--- a/test/blockchain.js
+++ b/test/blockchain.js
@@ -1,5 +1,5 @@
 /*globals describe, it*/
-var Blockchain = require('../lib/blockchain.js');
+var Blockchain = require('../lib/cmds/blockchain/blockchain.js');
 var assert = require('assert');
 
 describe('embark.Blockchain', function() {
diff --git a/test/compiler.js b/test/compiler.js
index e5e6724c..3d4621e3 100644
--- a/test/compiler.js
+++ b/test/compiler.js
@@ -1,5 +1,5 @@
 /*globals describe, it*/
-var Compiler = require('../lib/compiler.js');
+var Compiler = require('../lib/contracts/compiler.js');
 var assert = require('assert');
 var fs = require('fs');
 
diff --git a/test/config.js b/test/config.js
index 78aca2de..3d34e466 100644
--- a/test/config.js
+++ b/test/config.js
@@ -1,6 +1,6 @@
 /*globals describe, it*/
-var Config = require('../lib/config.js');
-var Plugins = require('../lib/plugins.js');
+var Config = require('../lib/core/config.js');
+var Plugins = require('../lib/core/plugins.js');
 var assert = require('assert');
 var fs = require('fs');
 
diff --git a/test/console.js b/test/console.js
index 96eaa4a4..a1d987e1 100644
--- a/test/console.js
+++ b/test/console.js
@@ -1,6 +1,6 @@
 /*globals describe, it*/
-var Console = require('../lib/console.js');
-var Plugins = require('../lib/plugins.js');
+var Console = require('../lib/dashboard/console.js');
+var Plugins = require('../lib/core/plugins.js');
 var assert = require('assert');
 
 describe('embark.Console', function() {
diff --git a/test/contracts.js b/test/contracts.js
index 54d0a464..056d46b9 100644
--- a/test/contracts.js
+++ b/test/contracts.js
@@ -1,6 +1,6 @@
 /*globals describe, it*/
-var ContractsManager = require('../lib/contracts.js');
-var Logger = require('../lib/logger.js');
+var ContractsManager = require('../lib/contracts/contracts.js');
+var Logger = require('../lib/core/logger.js');
 var assert = require('assert');
 var fs = require('fs');