diff --git a/cmd/flux/bootstrap_bitbucket_server.go b/cmd/flux/bootstrap_bitbucket_server.go
index 9279994e..af93f8f0 100644
--- a/cmd/flux/bootstrap_bitbucket_server.go
+++ b/cmd/flux/bootstrap_bitbucket_server.go
@@ -22,7 +22,6 @@ import (
 	"os"
 	"time"
 
-	"github.com/ProtonMail/go-crypto/openpgp"
 	"github.com/go-git/go-git/v5/plumbing/transport/http"
 	"github.com/spf13/cobra"
 
diff --git a/cmd/flux/bootstrap_git.go b/cmd/flux/bootstrap_git.go
index b7a250f1..8d975749 100644
--- a/cmd/flux/bootstrap_git.go
+++ b/cmd/flux/bootstrap_git.go
@@ -24,7 +24,6 @@ import (
 	"strings"
 	"time"
 
-	"github.com/ProtonMail/go-crypto/openpgp"
 	"github.com/go-git/go-git/v5/plumbing/transport"
 	"github.com/go-git/go-git/v5/plumbing/transport/http"
 	"github.com/go-git/go-git/v5/plumbing/transport/ssh"
diff --git a/cmd/flux/bootstrap_github.go b/cmd/flux/bootstrap_github.go
index a2459437..34ad8e2f 100644
--- a/cmd/flux/bootstrap_github.go
+++ b/cmd/flux/bootstrap_github.go
@@ -22,7 +22,6 @@ import (
 	"os"
 	"time"
 
-	"github.com/ProtonMail/go-crypto/openpgp"
 	"github.com/go-git/go-git/v5/plumbing/transport/http"
 	"github.com/spf13/cobra"
 
diff --git a/cmd/flux/bootstrap_gitlab.go b/cmd/flux/bootstrap_gitlab.go
index e6c94f6e..cb38cdae 100644
--- a/cmd/flux/bootstrap_gitlab.go
+++ b/cmd/flux/bootstrap_gitlab.go
@@ -24,7 +24,6 @@ import (
 	"strings"
 	"time"
 
-	"github.com/ProtonMail/go-crypto/openpgp"
 	"github.com/go-git/go-git/v5/plumbing/transport/http"
 	"github.com/spf13/cobra"
 
diff --git a/pkg/bootstrap/git/gogit/gogit.go b/pkg/bootstrap/git/gogit/gogit.go
index c1c6200a..324e8f02 100644
--- a/pkg/bootstrap/git/gogit/gogit.go
+++ b/pkg/bootstrap/git/gogit/gogit.go
@@ -160,7 +160,13 @@ func (g *GoGit) Commit(message git.Commit, opts ...git.Option) (string, error) {
 	// modified. There's no circumstance in which we want to commit a
 	// change to a broken symlink: so, detect and skip those.
 	var changed bool
-	for file, _ := range status {
+	for file, fileStatus := range status {
+		if fileStatus.Worktree == gogit.Deleted {
+			_, _ = wt.Add(file)
+			changed = true
+			continue
+		}
+
 		abspath := filepath.Join(g.path, file)
 		info, err := os.Lstat(abspath)
 		if err != nil {