diff --git a/deps/README b/deps/README
deleted file mode 100644
index 8c81cbbaa..000000000
--- a/deps/README
+++ /dev/null
@@ -1,11 +0,0 @@
-ZephyrJS Dependencies
-=====================
-
-This directory contains projects that the ZephyrJS work depends on so we can
-maintain our own patches to them when necessary.
-
-File Descriptions
------------------
-getrepos - This will check out all the other cloned repos we have.
-repos.txt - A list of all the upstream repos we have cloned locally.
-update - Updates all the cloned repos with the latest code.
diff --git a/deps/README.md b/deps/README.md
new file mode 100644
index 000000000..2f61eaf83
--- /dev/null
+++ b/deps/README.md
@@ -0,0 +1,24 @@
+ZJS Dependencies
+================
+
+This directory contains projects that the ZJS work depends on so we can
+maintain our own patches to them when necessary.
+
+Now we use git submodules to maintain these dependencies, so the old scripts
+that were here have been removed. Use `make update` to sync the dependencies
+to the commits they are supposed to be on given the version of ZJS you have
+checked out. This update target runs automatically when you build normally.
+
+To update the commit for a dependency directory, change to the `deps`
+subdirectory and check out the desired commit. Then when you look at your
+`git diff` back at the root level, you will see the change and can commit it.
+
+For example:
+
+```bash
+$ cd deps/zephyr
+$ git checkout v1.6.0
+$ cd ../..
+$ git add deps/zephyr
+$ git commit
+```
diff --git a/deps/getrepos b/deps/getrepos
deleted file mode 100755
index 55b4f84ff..000000000
--- a/deps/getrepos
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/usr/bin/env python3
-
-# getrepos: Checks out the repos listed in repos.txt
-
-import os
-import shutil
-import subprocess
-import sys
-
-cwd = os.getcwd()
-srcdir = os.path.dirname(os.path.realpath(__file__))
-if cwd != srcdir:
-    print("Error: getrepos is not in the current directory")
-    sys.exit(1)
-
-with open('repos.txt', 'r') as f:
-    for line in f:
-        line = line.strip()
-        if not line or  line[0] == '#':
-            continue
-        try:
-            (subdir, repo, commit) = line.split()
-        except ValueError:
-            print("Warning: line %d invalid in repos.txt, skipping..." % count)
-            continue
-
-        if os.path.exists(subdir):
-            print("Warning: directory '%s' found, skipping..." % subdir)
-            continue
-
-        subprocess.call(['git', 'clone', repo, subdir])
-        os.chdir(subdir)
-        subprocess.call(['git', 'checkout', commit])
-        os.chdir('..')
-
-        # copy overlay, if any
-        overlaydir = os.path.join('overlay-%s' % subdir)
-        relpath = os.path.join('..', subdir)
-        if os.path.isdir(overlaydir):
-            print("Copying overlay into %s..." % subdir, end='')
-            sys.stdout.flush()
-            os.chdir(overlaydir)
-            for (dirpath, dirnames, filenames) in os.walk('.'):
-                for filename in filenames:
-                    fullpath = os.path.join(dirpath, filename)
-                    shutil.copy(fullpath, os.path.join(relpath, dirpath))
-            os.chdir('..')
-            print(" done.")
diff --git a/deps/update b/deps/update
deleted file mode 100755
index 17ac3166b..000000000
--- a/deps/update
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/usr/bin/env python3
-
-# update: Updates the repos listed in repos.txt
-
-import os
-import shutil
-import subprocess
-import sys
-
-cwd = os.getcwd()
-srcdir = os.path.dirname(os.path.realpath(__file__))
-if cwd != srcdir:
-    print("Error: update is not in the current directory")
-    sys.exit(1)
-
-repos = []
-with open('repos.txt', 'r') as f:
-    count = 0
-    for line in f:
-        count += 1
-        line = line.strip()
-        if not line or  line[0] == '#':
-            continue
-        try:
-            (subdir, repo, commit) = line.split()
-        except ValueError:
-            print("Warning: line %d invalid in repos.txt, skipping..." % count)
-            continue
-
-        os.chdir(subdir)
-        subprocess.call(['git', 'checkout', 'master'])
-        subprocess.call(['git', 'pull'])
-        if commit != 'master':
-            subprocess.call(['git', 'checkout', commit])
-        os.chdir('..')
-
-        # copy overlay, if any
-        overlaydir = os.path.join('overlay-%s' % subdir)
-        relpath = os.path.join('..', subdir)
-        if os.path.isdir(overlaydir):
-            print("Copying overlay into %s..." % subdir, end='')
-            sys.stdout.flush()
-            os.chdir(overlaydir)
-            for (dirpath, dirnames, filenames) in os.walk('.'):
-                for filename in filenames:
-                    fullpath = os.path.join(dirpath, filename)
-                    shutil.copy(fullpath, os.path.join(relpath, dirpath))
-            os.chdir('..')
-            print(" done.")