diff --git a/Sources/Packages/Sources/SecretKit/PublicKeyStandinFileController.swift b/Sources/Packages/Sources/SecretKit/PublicKeyStandinFileController.swift
index 3d84317..cbf40a6 100644
--- a/Sources/Packages/Sources/SecretKit/PublicKeyStandinFileController.swift
+++ b/Sources/Packages/Sources/SecretKit/PublicKeyStandinFileController.swift
@@ -15,15 +15,21 @@ public class PublicKeyFileStoreController {
 
     /// Writes out the keys specified to disk.
     /// - Parameter secrets: The Secrets to generate keys for.
-    /// - Parameter clear: Whether or not the directory should be erased before writing keys.
+    /// - Parameter clear: Whether or not any untracked files in the directory should be removed.
     public func generatePublicKeys(for secrets: [AnySecret], clear: Bool = false) throws {
         logger.log("Writing public keys to disk")
         if clear {
-            try? FileManager.default.removeItem(at: URL(fileURLWithPath: directory))
+            let validPaths = Set(secrets.map { publicKeyPath(for: $0) }).union(Set(secrets.map { sshCertificatePath(for: $0) }))
+            let untracked = Set(try FileManager.default.contentsOfDirectory(atPath: directory)
+                .map { "\(directory)/\($0)" })
+                .subtracting(validPaths)
+            for path in untracked {
+                try? FileManager.default.removeItem(at: URL(fileURLWithPath: path))
+            }
         }
         try? FileManager.default.createDirectory(at: URL(fileURLWithPath: directory), withIntermediateDirectories: false, attributes: nil)
         for secret in secrets {
-            let path = path(for: secret)
+            let path = publicKeyPath(for: secret)
             guard let data = keyWriter.openSSHString(secret: secret).data(using: .utf8) else { continue }
             FileManager.default.createFile(atPath: path, contents: data, attributes: nil)
         }
@@ -34,9 +40,18 @@ public class PublicKeyFileStoreController {
     /// - Parameter secret: The Secret to return the path for.
     /// - Returns: The path to the Secret's public key.
     /// - Warning: This method returning a path does not imply that a key has been written to disk already. This method only describes where it will be written to.
-    public func path<SecretType: Secret>(for secret: SecretType) -> String {
+    public func publicKeyPath<SecretType: Secret>(for secret: SecretType) -> String {
         let minimalHex = keyWriter.openSSHMD5Fingerprint(secret: secret).replacingOccurrences(of: ":", with: "")
         return directory.appending("/").appending("\(minimalHex).pub")
     }
 
+    /// The path for a Secret's SSH Certificate public key.
+    /// - Parameter secret: The Secret to return the path for.
+    /// - Returns: The path to the SSH Certificate public key.
+    /// - Warning: This method returning a path does not imply that a key has a SSH certificates. This method only describes where it will be.
+    public func sshCertificatePath<SecretType: Secret>(for secret: SecretType) -> String {
+        let minimalHex = keyWriter.openSSHMD5Fingerprint(secret: secret).replacingOccurrences(of: ":", with: "")
+        return directory.appending("/").appending("\(minimalHex)-cert.pub")
+    }
+
 }
diff --git a/Sources/Secretive/Views/SecretDetailView.swift b/Sources/Secretive/Views/SecretDetailView.swift
index d756679..52978d7 100644
--- a/Sources/Secretive/Views/SecretDetailView.swift
+++ b/Sources/Secretive/Views/SecretDetailView.swift
@@ -21,7 +21,7 @@ struct SecretDetailView<SecretType: Secret>: View {
                     CopyableView(title: "Public Key", image: Image(systemName: "key"), text: keyString)
                     Spacer()
                         .frame(height: 20)
-                    CopyableView(title: "Public Key Path", image: Image(systemName: "lock.doc"), text: publicKeyFileStoreController.path(for: secret))
+                    CopyableView(title: "Public Key Path", image: Image(systemName: "lock.doc"), text: publicKeyFileStoreController.publicKeyPath(for: secret))
                     Spacer()
                 }
             }