diff --git a/constraints.txt b/constraints.txt
index 311a753fd..247daa922 100644
--- a/constraints.txt
+++ b/constraints.txt
@@ -1,2 +1,21 @@
+# This file allows our dependencies to be against specific versions
+# or git tags. Each line is similar to a requirements.txt line, 
+# except that when installing the dependencies, the constraints.txt
+# is converted into the `dependency_links` of the setuptools
+# packaging script. This allows us to maintain dependencies across
+# repositories.
+#
+# For example, during development the we use the development version
+# of the schemas with the line:
+#
+# git+git://github.com/ga4gh/ga4gh-schemas.git@master#egg=ga4gh_schemas
+#
+# When one has proposed a schema modification, they can change this
+# constraint to point at the branch of their proposed change:
+#
+# git+git://github.com/david4096/schemas.git@protobuf31#egg=ga4gh_schemas
+#
+# Then, when the change has been accepted at the schemas repository
+# you can change this to point back at the master branch!
 git+git://github.com/david4096/ga4gh-client.git@protobuf31#egg=ga4gh_client
-git+git://github.com/david4096/schemas.git@protobuf31#egg=ga4gh_schemas
\ No newline at end of file
+git+git://github.com/david4096/schemas.git@protobuf31#egg=ga4gh_schemas
diff --git a/requirements.txt b/requirements.txt
index f209ff2f2..84a79999e 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -8,6 +8,11 @@
 # these libraries are the set listed by pipdeptree -f -w
 # that are dependencies of libraries listed in the next section
 
+# Adding the constraints.txt allows you to choose a specific 
+# way to resolve our internal dependencies. During development,
+# the constraints file will point at the current master branch 
+# of the respective module.
+-c constraints.txt
 ga4gh-common==0.0.5
 ga4gh-schemas
 ga4gh-client
diff --git a/setup.py b/setup.py
index df44bdd06..af7ec72a5 100644
--- a/setup.py
+++ b/setup.py
@@ -20,8 +20,9 @@
             continue
         if line[0] == '#':
             continue
-        pinnedVersion = line.split()[0]
-        install_requires.append(pinnedVersion)
+        if line.find('-c constraints.txt') == -1:
+            pinnedVersion = line.split()[0]
+            install_requires.append(pinnedVersion)
 
 dependency_links = []
 try:
@@ -32,8 +33,7 @@
                 continue
             if line[0] == '#':
                 continue
-            if line.find('git') != -1:
-                dependency_links.append(line)
+            dependency_links.append(line)
 except EnvironmentError:
     print('No constraints file found, proceeding without '
           'creating dependency links.')