diff --git a/build/appcache.py b/build/appcache.py
index 3c9acfa5..a4861961 100644
--- a/build/appcache.py
+++ b/build/appcache.py
@@ -2,6 +2,7 @@
 import click
 import os
 import re
+import time
 
 
 @wq.command()
@@ -9,13 +10,18 @@
 @wq.pass_config
 def appcache(config, version):
     """
-    Generate an HTML5 appcache manifest.  Should be run after wq optimize, as
-    some of the manifest entries will be inferred from the build log.
+    (DEPRECATED) Generate an HTML5 appcache.  Should be run after
+    wq optimize, as some of the manifest entries will be inferred from the
+    build log.
 
-    A manifest will be created for both the source directory and the build
-    directory, so you can test offline capabilities even when running off of
-    the source AMD files.
+    Note that browser vendors are deprecating support for Application Cache
+    in favor of Service Workers. The `wq appcache` command will be removed in
+    wq.app 2.0.
     """
+
+    click.echo("Warning: Application Cache is deprecated by browser vendors.")
+    time.sleep(10)
+
     if 'appcache' not in config:
         raise click.UsageError(
             "appcache section not found in %s" % config.filename
diff --git a/build/builder.py b/build/builder.py
index 32982315..ec96a20e 100644
--- a/build/builder.py
+++ b/build/builder.py
@@ -1,5 +1,7 @@
 from wq.core import wq
 import click
+import subprocess
+import os
 
 from .collect import collectjson
 from .setversion import setversion
@@ -23,14 +25,27 @@ def build(ctx, config, version):
         wq collectjson (if configured)
         wq scss        (if configured)
         wq mustache    (if configured)
-        wq optimize
-        wq babel       (if configured)
-        wq appcache    (if configured)
+
+    \b
+    Followed by either:
+        wq optimize + wq babel + wq appcache
+    Or:
+        npm build
     """
-    if 'optimize' not in config:
-        raise click.UsageError(
-            "optimize section not found in %s" % config.filename
-        )
+
+    has_package_json = os.path.exists(
+        os.path.join(os.path.dirname(config.filename), 'package.json')
+    )
+    if has_package_json:
+        if 'optimize' in config:
+            raise click.UsageError(
+                "optimize section is not used for npm build"
+            )
+    else:
+        if 'optimize' not in config:
+            raise click.UsageError(
+                "optimize section not found in %s" % config.filename
+            )
 
     def run(command, **kwargs):
         confs = config.get(command.name, {})
@@ -49,13 +64,19 @@ def run(command, **kwargs):
         if command.name in config:
             run(command)
 
-    # Compile Javascript / CSS (using r.js)
-    ctx.invoke(optimize)
+    if has_package_json:
+        subprocess.check_call(
+            ['npm', 'build'],
+            cwd=os.path.abspath(os.path.dirname(config.filename))
+        )
+    else:
+        # Compile Javascript / CSS (using r.js)
+        ctx.invoke(optimize)
 
-    # Convert to ES5 via babel.js
-    if 'babel' in config:
-        ctx.invoke(babel)
+        # Convert to ES5 via babel.js
+        if 'babel' in config:
+            ctx.invoke(babel)
 
-    # Generate HTML5 Cache manifests
-    if 'appcache' in config:
-        ctx.invoke(appcache, version=version)
+        # Generate HTML5 Cache manifests
+        if 'appcache' in config:
+            ctx.invoke(appcache, version=version)
diff --git a/build/compilers.py b/build/compilers.py
index 9faf0e5c..eb85242b 100644
--- a/build/compilers.py
+++ b/build/compilers.py
@@ -17,10 +17,14 @@
 @wq.pass_config
 def optimize(config):
     """
-    Use r.js to optimize JS and CSS assets.  This command requires an
-    "optimize" section in your configuration file, which will be passed as-is
-    to r.js for compilation.  See http://requirejs.org/docs/optimization.html
-    for available configuration options.
+    (DEPRECATED) Use r.js to optimize JS and CSS. This command requires an
+    "optimize" section in your configuration file, which will be passed to
+    r.js for compilation.  See http://requirejs.org/docs/optimization.html
+    for available options.
+
+    Note that r.js-based compilation is deprecated and will be removed in
+    wq.app 2.0. For full control over the compilation process, use
+    `wq start --with-npm` instead.
     """
     conf = config.get('optimize', None)
     if not conf:
@@ -42,10 +46,14 @@ def optimize(config):
 @wq.pass_config
 def babel(config):
     """
-    Use babel.js to compile ES6/2015+.  Generates ES5-compatible JavaScript for
-    older browsers.  Note that wq babel is run after wq optimize, on the
-    compiled modules created by r.js.  Support for running babel at other
-    stages of the build process may be added in a future version of wq.app.
+    (DEPRECATED) Use babel.js with ES6/2015+.  Generates ES5-compatible
+    JavaScript for older browsers.  Note that wq babel is run after
+    wq optimize, on the compiled modules created by r.js.  For more control
+    over the compilation process, use `wq start --with-npm` instead of
+    an r.js-based build.
+
+    Note that this command will be removed in wq.app 2.0 in favor of
+    `wq start --with-npm`.
     """
     rconf = config.get('optimize', None)
     if not rconf:
@@ -93,9 +101,12 @@ def babel(config):
 )
 def scss(**conf):
     """
-    Render all SCSS/SASS files into CSS.  The input directory will be searched
+    (DEPRECATED) Render SCSS/SASS into CSS.  The input folder will be searched
     for *.scss files, which will be compiled to corresponding *.css files in
     the output directory.
+
+    Note: This command will be removed in wq.app 2.0 in favor of
+    Material UI themes.
     """
     compiler = pyScss.Scss(scss_opts={'compress': 0})
     logging.getLogger("scss").addHandler(logging.StreamHandler())
@@ -133,7 +144,7 @@ def compile(path, source):
 )
 def mustache(**conf):
     """
-    Render a mustache template into static HTML.  The template context can be
+    (DEPRECATED) Render mustache into HTML files.  The template context can be
     provided via a nexted object in wq.yml, or by pointing to a folder
     containing JSON or YAML files.  Similarly, the partials can be defined as a
     nested object in wq.yml or by a folder path.
@@ -154,6 +165,8 @@ def mustache(**conf):
     Example command line configuration:
 
     wq mustache --template tmpl.html --partials partials/ --context conf/
+
+    Note: This command will be removed in wq.app 2.0 in favor of JSX.
     """
     template = conf['template']
     if template is None:
diff --git a/build/phonegap.py b/build/phonegap.py
index 5ae49e03..a809be23 100644
--- a/build/phonegap.py
+++ b/build/phonegap.py
@@ -7,6 +7,7 @@
 import shutil
 import pystache
 from .icons import icons, SIZES
+import time
 
 
 @wq.command()
@@ -37,7 +38,7 @@
 @click.pass_context
 def phonegap(ctx, config, version, **conf):
     """
-    Upload application to PhoneGap Build.  Specifically,
+    (DEPRECATED) Package app for PhoneGap Build.  Specifically,
 
     \b
     1. Create a working directory, if not present.
@@ -48,9 +49,16 @@ def phonegap(ctx, config, version, **conf):
     6. Upload the zip file to PhoneGap build.
     7. Save the returned app ID for future builds.
     \b
-    (Inspired by, but not dependent on, the `phonegap remote` api)
+    Note that PhoneGap Build is no longer online.  The `wq phonegap` command
+    will be removed in wq.app 2.0.  @wq/react and @wq/material support using
+    React Native and/or Expo to deploy native apps.
     """
 
+    click.echo(
+        "Warning: PhoneGap Build is offline; this command will likely fail."
+    )
+    time.sleep(10)
+
     if conf['source']:
         source = conf['source']
     else: