diff --git a/.circleci/config.yml b/.circleci/config.yml
index d8d0c51137..e62785641a 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -21,7 +21,7 @@ jobs:
            path: plz-out/results
        - run:
            name: Lint
-           command: ./tools/misc/ci_lint.py && plz-out/bin/src/please buildify --mode=check `git ls-files | grep BUILD`
+           command: plz-out/bin/src/please lint
        - run:
            name: Package
            command: ./plz-out/bin/src/please build //package:all //tools/misc:gen_release --exclude asc -p
diff --git a/.plzconfig b/.plzconfig
index b7fff3b56a..8f5003cd0f 100644
--- a/.plzconfig
+++ b/.plzconfig
@@ -52,7 +52,11 @@ positionallabels = true
 
 [alias "buildify"]
 desc = Runs buildifier, a BUILD file autoformatter.
-cmd = run //src:please -p -- run -p //third_party/go:buildifier --
+cmd = run //tools/misc:buildify -p -- --mode=fix
+
+[alias "lint"]
+desc = Runs the linters for this repo
+cmd = run //tools/misc:lint -p --
 
 [licences]
 accept = MIT
diff --git a/bootstrap.sh b/bootstrap.sh
index ec82a6db17..0a2d5865ca 100755
--- a/bootstrap.sh
+++ b/bootstrap.sh
@@ -119,11 +119,6 @@ if ! hash java 2>/dev/null ; then
     warn "Java not found, excluding Java tests"
     EXCLUDES="${EXCLUDES} --exclude=java"
 fi
-# If the proto files are installed in a different location, their tests won't work.
-if [ ! -d "/usr/include/google/protobuf" ]; then
-    warn "google/protobuf not found, excluding relevant tests"
-    EXCLUDES="${EXCLUDES} --exclude=proto"
-fi
 GCCVER="`cc -dumpversion`"
 if [ ! -d "/usr/lib/gcc/x86_64-linux-gnu/${GCCVER%.*.*}/32" ] && [ ! -d "/usr/lib/gcc/x86_64-pc-linux-gnu/$GCCVER/32" ]; then
     warn "32-bit gcc libraries not found, excluding cross-compile tests"
@@ -135,15 +130,12 @@ plz-out/bin/src/please $PLZ_ARGS ${PLZ_COVER:-test} $EXCLUDES --exclude=e2e --lo
 # We run the end-to-end tests separately to ensure things don't fight with one another; they are
 # finicky about some things due to running plz recursively and disabling the lock.
 notice "Running end-to-end tests..."
-plz-out/bin/src/please $PLZ_ARGS ${PLZ_COVER:-test} $EXCLUDES --include=e2e --log_file plz-out/log/test_build.log --log_file_level 4 --trace_file plz-out/log/trace.json $@
+plz-out/bin/src/please $PLZ_ARGS ${PLZ_COVER:-test} $EXCLUDES --include=e2e --log_file plz-out/log/test_build.log --log_file_level 4 $@
 
 # Lint needs python3.
 if hash python3 2>/dev/null ; then
     # Don't run this in CI or any unusual workflows.
     if [ $# -eq 0 ] ; then
-        tools/misc/ci_lint.py
-        plz-out/bin/src/please buildify --mode=check `git ls-files | grep BUILD`
-        # If the above fails, then the fix is to run:
-        # plz-out/bin/src/please buildify --mode=fix `git ls-files | grep BUILD`
+        plz lint
     fi
 fi
diff --git a/tools/misc/BUILD b/tools/misc/BUILD
index 3a36e68a63..8325809ac3 100644
--- a/tools/misc/BUILD
+++ b/tools/misc/BUILD
@@ -28,3 +28,13 @@ python_test(
     srcs = ["gen_release_test.py"],
     deps = [":gen_release"],
 )
+
+sh_binary(
+    name = "buildify",
+    main = "buildify.sh",
+)
+
+python_binary(
+    name = "lint",
+    main = "ci_lint.py",
+)
diff --git a/tools/misc/buildify.sh b/tools/misc/buildify.sh
new file mode 100644
index 0000000000..5c6597f151
--- /dev/null
+++ b/tools/misc/buildify.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+exec plz-out/bin/src/please run -p -- //third_party/go:buildifier $@ `git ls-files | grep BUILD`
diff --git a/tools/misc/ci_lint.py b/tools/misc/ci_lint.py
index aad80b247a..254bb0f56d 100755
--- a/tools/misc/ci_lint.py
+++ b/tools/misc/ci_lint.py
@@ -71,6 +71,12 @@ def main():
             linter.reset_line()
             sys.exit('Some linters failed')
         linter.reset_line()
+    # Run Buildifier
+    try:
+        subprocess.check_call(['plz-out/bin/src/please', 'run', '//tools/misc:buildify', '-p', '--', '--mode=check'],
+                              stdout=sys.stdout, stderr=sys.stderr)
+    except subprocess.CalledProcessError:
+        sys.exit('Your BUILD files are not correctly formatted, run `plz buildify` to fix.')
 
 
 if __name__ == '__main__':