diff --git a/plugins/settings-repository/src/BaseRepositoryManager.kt b/plugins/settings-repository/src/BaseRepositoryManager.kt
index 8d8ca968ebe0..35029871070e 100644
--- a/plugins/settings-repository/src/BaseRepositoryManager.kt
+++ b/plugins/settings-repository/src/BaseRepositoryManager.kt
@@ -130,7 +130,7 @@ abstract class BaseRepositoryManager(protected val dir: Path) : RepositoryManage
    */
   protected abstract fun addToIndex(file: Path, path: String, content: ByteArray, size: Int)
 
-  override fun delete(path: String) {
+  override fun delete(path: String): Boolean {
     LOG.debug { "Remove $path"}
 
     lock.write {
@@ -138,8 +138,11 @@ abstract class BaseRepositoryManager(protected val dir: Path) : RepositoryManage
       // delete could be called for non-existent file
       if (file.exists()) {
         delete(file, path)
+        return true
       }
     }
+
+    return false
   }
 
   private fun delete(file: Path, path: String) {
diff --git a/plugins/settings-repository/src/IcsManager.kt b/plugins/settings-repository/src/IcsManager.kt
index 7e6217b1ed84..568156f900d7 100644
--- a/plugins/settings-repository/src/IcsManager.kt
+++ b/plugins/settings-repository/src/IcsManager.kt
@@ -242,23 +242,26 @@ class IcsApplicationLoadListener : ApplicationLoadListener {
 
     val repositoryManager = icsManager.repositoryManager
     if (repositoryManager.isRepositoryExists() && repositoryManager is GitRepositoryManager) {
-      if (repositoryManager.renameDirectory(linkedMapOf(
-        Pair("\$ROOT_CONFIG$", null),
-        Pair("_mac/\$ROOT_CONFIG$", "_mac"),
-        Pair("_windows/\$ROOT_CONFIG$", "_windows"),
-        Pair("_linux/\$ROOT_CONFIG$", "_linux"),
-        Pair("_freebsd/\$ROOT_CONFIG$", "_freebsd"),
-        Pair("_unix/\$ROOT_CONFIG$", "_unix"),
-        Pair("_unknown/\$ROOT_CONFIG$", "_unknown"),
+      val migrateSchemes = repositoryManager.renameDirectory(linkedMapOf(
+          Pair("\$ROOT_CONFIG$", null),
+          Pair("_mac/\$ROOT_CONFIG$", "_mac"),
+          Pair("_windows/\$ROOT_CONFIG$", "_windows"),
+          Pair("_linux/\$ROOT_CONFIG$", "_linux"),
+          Pair("_freebsd/\$ROOT_CONFIG$", "_freebsd"),
+          Pair("_unix/\$ROOT_CONFIG$", "_unix"),
+          Pair("_unknown/\$ROOT_CONFIG$", "_unknown"),
 
-        Pair("\$APP_CONFIG$", null),
-        Pair("_mac/\$APP_CONFIG$", "_mac"),
-        Pair("_windows/\$APP_CONFIG$", "_windows"),
-        Pair("_linux/\$APP_CONFIG$", "_linux"),
-        Pair("_freebsd/\$APP_CONFIG$", "_freebsd"),
-        Pair("_unix/\$APP_CONFIG$", "_unix"),
-        Pair("_unknown/\$APP_CONFIG$", "_unknown")
-      ))) {
+          Pair("\$APP_CONFIG$", null),
+          Pair("_mac/\$APP_CONFIG$", "_mac"),
+          Pair("_windows/\$APP_CONFIG$", "_windows"),
+          Pair("_linux/\$APP_CONFIG$", "_linux"),
+          Pair("_freebsd/\$APP_CONFIG$", "_freebsd"),
+          Pair("_unix/\$APP_CONFIG$", "_unix"),
+          Pair("_unknown/\$APP_CONFIG$", "_unknown")
+      ))
+
+      val removeOtherXml = repositoryManager.delete("other.xml")
+      if (migrateSchemes || removeOtherXml) {
         // schedule push to avoid merge conflicts
         application.invokeLater({ icsManager.autoSyncManager.autoSync(force = true) })
       }
diff --git a/plugins/settings-repository/src/RepositoryManager.kt b/plugins/settings-repository/src/RepositoryManager.kt
index 223471a6014f..c743e6ae9de1 100644
--- a/plugins/settings-repository/src/RepositoryManager.kt
+++ b/plugins/settings-repository/src/RepositoryManager.kt
@@ -46,7 +46,7 @@ interface RepositoryManager {
    */
   fun write(path: String, content: ByteArray, size: Int): Boolean
 
-  fun delete(path: String)
+  fun delete(path: String): Boolean
 
   fun processChildren(path: String, filter: (name: String) -> Boolean, processor: (name: String, inputStream: InputStream) -> Boolean)