Fix Permission denied errors in bin/upgrade

Data directories are now created in `bin/up`.

.gitignore

@@ -9,8 +9,3 @@ config/**/*
 
 data/**/*
 !data/.gitkeep
-
-!data/git-bridge/.gitkeep
-!data/mongo/.gitkeep
-!data/overleaf/.gitkeep
-!data/redis/.gitkeep

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Changelog
 
+## 2025-08-04
+### Fixed
+- Fix `Permission denied` errors when running `bin/upgrade`.
+
 ## 2025-07-29
 ### Added
 - Updated default [`version`](https://github.com/overleaf/toolkit/blob/master/lib/config-seed/version) to `5.5.3`.

bin/up

@@ -35,6 +35,13 @@ function check_config() {
   fi
 }
 
+function ensure_data_dirs_exist() {
+  mkdir -p "$TOOLKIT_ROOT/data/git-bridge"
+  mkdir -p "$TOOLKIT_ROOT/data/mongo"
+  mkdir -p "$TOOLKIT_ROOT/data/overleaf"
+  mkdir -p "$TOOLKIT_ROOT/data/redis"
+}
+
 function initiate_mongo_replica_set() {
   echo "Initiating Mongo replica set..."
   env SKIP_WARNINGS=true "$TOOLKIT_ROOT/bin/docker-compose" up -d mongo
@@ -98,6 +105,8 @@ function __main__() {
   check_config
   read_config
 
+  ensure_data_dirs_exist
+
   if [[ "$MONGO_ENABLED" == "true" && "$IMAGE_VERSION_MAJOR" -ge 4 ]]; then
     initiate_mongo_replica_set
   fi