diff --git a/.travis.yml b/.travis.yml
index 315b799..94a0920 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -17,8 +17,8 @@ before_script:
 script:
     - go test ./...
     - mkdir stage
-    - cd stage 
+    - cd stage
     - ../bootstrap.bash
-    - ninja
+    - ./blueprint.bash
     - diff -us ../build.ninja.in .bootstrap/bootstrap.ninja.in
     - ../tests/test.sh
diff --git a/blueprint.bash b/blueprint.bash
new file mode 100755
index 0000000..7b6b17a
--- /dev/null
+++ b/blueprint.bash
@@ -0,0 +1,61 @@
+#!/bin/bash
+
+# This script is intented to wrap the execution of ninja so that we
+# can do some checks before each ninja run.
+#
+# It can either be run with a standalone Blueprint checkout to generate
+# the minibp binary, or can be used by another script as part of a custom
+# Blueprint-based build system. When used by another script, the following
+# environment variables can be set to configure this script, which are
+# documented below:
+#
+#   BUILDDIR
+#   SKIP_NINJA
+#
+# When run in a standalone Blueprint checkout, bootstrap.bash will install
+# this script into the $BUILDDIR, where it may be executed.
+#
+# For embedding into a custom build system, the current directory when this
+# script executes should be the same directory that $BOOTSTRAP should be
+# called from.
+
+set -e
+
+# BUILDDIR should be set to the path to store build results. By default,
+# this is the directory containing this script, but can be set explicitly
+# if the custom build system only wants to install their own wrapper.
+[ -z "$BUILDDIR" ] && BUILDDIR=`dirname "${BASH_SOURCE[0]}"`
+
+# .blueprint.bootstrap provides saved values from the bootstrap.bash script:
+#
+#   BOOTSTRAP
+#   BOOTSTRAP_MANIFEST
+#
+# If it doesn't exist, we probably just need to re-run bootstrap.bash, which
+# ninja will do when switching stages. So just skip to ninja.
+if [ -f "${BUILDDIR}/.blueprint.bootstrap" ]; then
+    source "${BUILDDIR}/.blueprint.bootstrap"
+
+    # Pick the newer of .bootstrap/bootstrap.ninja.in or $BOOTSTRAP_MANIFEST,
+    # and copy it to .bootstrap/build.ninja.in
+    GEN_BOOTSTRAP_MANIFEST="${BUILDDIR}/.bootstrap/bootstrap.ninja.in"
+    if [ -f "${GEN_BOOTSTRAP_MANIFEST}" ]; then
+        if [ "${GEN_BOOTSTRAP_MANIFEST}" -nt "${BOOTSTRAP_MANIFEST}" ]; then
+            BOOTSTRAP_MANIFEST="${GEN_BOOTSTRAP_MANIFEST}"
+        fi
+    fi
+
+    # Copy the selected manifest to $BUILDDIR/.bootstrap/build.ninja.in
+    mkdir -p "${BUILDDIR}/.bootstrap"
+    cp "${BOOTSTRAP_MANIFEST}" "${BUILDDIR}/.bootstrap/build.ninja.in"
+
+    # Bootstrap it to $BUILDDIR/build.ninja
+    "${BOOTSTRAP}" -i "${BUILDDIR}/.bootstrap/build.ninja.in"
+fi
+
+# SKIP_NINJA can be used by wrappers that wish to run ninja themselves.
+if [ -z "$SKIP_NINJA" ]; then
+    ninja -C "${BUILDDIR}" "$@"
+else
+    exit 0
+fi
diff --git a/bootstrap.bash b/bootstrap.bash
index ff60e21..6e58651 100755
--- a/bootstrap.bash
+++ b/bootstrap.bash
@@ -10,6 +10,7 @@
 # their default values are set:
 #
 #   BOOTSTRAP
+#   WRAPPER
 #   SRCDIR
 #   BUILDDIR
 #   BOOTSTRAP_MANIFEST
@@ -28,7 +29,14 @@ EXTRA_ARGS=""
 # BOOTSTRAP should be set to the path of the bootstrap script.  It can be
 # either an absolute path or one relative to the build directory (which of
 # these is used should probably match what's used for SRCDIR).
-[ -z "$BOOTSTRAP" ] && BOOTSTRAP="${BASH_SOURCE[0]}"
+if [ -z "$BOOTSTRAP" ]; then
+    BOOTSTRAP="${BASH_SOURCE[0]}"
+
+    # WRAPPER should only be set if you want a ninja wrapper script to be
+    # installed into the builddir. It is set to blueprint's blueprint.bash
+    # only if BOOTSTRAP and WRAPPER are unset.
+    [ -z "$WRAPPER" ] && WRAPPER="`dirname "${BOOTSTRAP}"`/blueprint.bash"
+fi
 
 # SRCDIR should be set to the path of the root source directory.  It can be
 # either an absolute path or a path relative to the build directory.  Whether
@@ -128,3 +136,10 @@ sed -e "s|@@SrcDir@@|$SRCDIR|g"                        \
     -e "s|@@Bootstrap@@|$BOOTSTRAP|g"                  \
     -e "s|@@BootstrapManifest@@|$BOOTSTRAP_MANIFEST|g" \
     $IN > $BUILDDIR/build.ninja
+
+echo "BOOTSTRAP=\"${BOOTSTRAP}\"" > $BUILDDIR/.blueprint.bootstrap
+echo "BOOTSTRAP_MANIFEST=\"${BOOTSTRAP_MANIFEST}\"" >> $BUILDDIR/.blueprint.bootstrap
+
+if [ ! -z "$WRAPPER" ]; then
+    cp $WRAPPER $BUILDDIR/
+fi
diff --git a/tests/expected_wrapper_all b/tests/expected_wrapper_all
new file mode 100644
index 0000000..43f2d35
--- /dev/null
+++ b/tests/expected_wrapper_all
@@ -0,0 +1,2 @@
+Choosing primary.ninja.in for next stage
+Choosing main.ninja.in for next stage
diff --git a/tests/expected_wrapper_regen b/tests/expected_wrapper_regen
new file mode 100644
index 0000000..4c339e2
--- /dev/null
+++ b/tests/expected_wrapper_regen
@@ -0,0 +1,4 @@
+Stage bootstrap.ninja.in has changed, restarting
+Choosing bootstrap.ninja.in for next stage
+Choosing primary.ninja.in for next stage
+Choosing main.ninja.in for next stage
diff --git a/tests/expected_wrapper_start b/tests/expected_wrapper_start
new file mode 100644
index 0000000..43f2d35
--- /dev/null
+++ b/tests/expected_wrapper_start
@@ -0,0 +1,2 @@
+Choosing primary.ninja.in for next stage
+Choosing main.ninja.in for next stage
diff --git a/tests/expected_wrapper_start2 b/tests/expected_wrapper_start2
new file mode 100644
index 0000000..43f2d35
--- /dev/null
+++ b/tests/expected_wrapper_start2
@@ -0,0 +1,2 @@
+Choosing primary.ninja.in for next stage
+Choosing main.ninja.in for next stage
diff --git a/tests/test.sh b/tests/test.sh
index e27ae97..8880a86 100755
--- a/tests/test.sh
+++ b/tests/test.sh
@@ -29,7 +29,26 @@ function testcase()
   fi
 }
 
-
+# Run wrapper, filter the output, and compare against expectations
+# $1: Name of test
+function testcase_wrapper()
+{
+  echo -n "Running wrapper_$1..."
+  if ! ./blueprint.bash -v -d explain >log_wrapper_$1 2>&1; then
+    echo " Failed."
+    echo "Test wrapper_$1 Failed:" >>failed
+    tail log_wrapper_$1 >>failed
+    return
+  fi
+  grep -E "^(Choosing|Newer|Stage)" log_wrapper_$1 >test_wrapper_$1
+  if ! cmp -s test_wrapper_$1 ../tests/expected_wrapper_$1; then
+    echo " Failed."
+    echo "Test wrapper_$1 Failed:" >>failed
+    diff -u ../tests/expected_wrapper_$1 test_wrapper_$1 >>failed
+  else
+    echo " Passed."
+  fi
+}
 
 
 testcase start
@@ -85,8 +104,36 @@ sleep 2
 touch ../parser/parser_test.go
 testcase rebuild_test
 
+# Restart testing using the wrapper instead of going straight to ninja. This
+# will force each test to start in the correct bootstrap stage, so there are
+# less cases to test.
+cd ..
+rm -rf out.test
+mkdir -p out.test
+cd out.test
+../bootstrap.bash
 
+testcase_wrapper start
 
+# This test affects all bootstrap stages
+sleep 2
+touch ../Blueprints
+testcase_wrapper all
+
+# From now on, we're going to be modifying the build.ninja.in, so let's make our
+# own copy
+sleep 2
+../tests/bootstrap.bash -r
+
+sleep 2
+testcase_wrapper start2
+
+# This is similar to the last test, but incorporates a change into the source
+# build.ninja.in, so that we'll restart into the new version created by the
+# build.
+sleep 2
+echo "# test" >>src.build.ninja.in
+testcase_wrapper regen
 
 if [ -f failed ]; then
   cat failed