diff --git a/makefiles/targets.mk b/makefiles/targets.mk
index 60952d1..00a620e 100644
--- a/makefiles/targets.mk
+++ b/makefiles/targets.mk
@@ -44,7 +44,7 @@ build-nim: | sanity-checks
 		ARCH_OVERRIDE=$(ARCH_OVERRIDE) \
 		"$(CURDIR)/$(BUILD_SYSTEM_DIR)/scripts/build_nim.sh" "$(NIM_DIR)" ../Nim-csources ../nimble "$(CI_CACHE)"
 
-#- for each submodule, delete checked out files (that might prevent a fresh checkout)
+#- for each submodule, delete checked out files (that might prevent a fresh checkout); skip dotfiles
 #- in case of submodule URL changes, propagates that change in the parent repo's .git directory
 #- initialises and updates the Git submodules
 #- hard-resets the working copies of submodules
@@ -52,7 +52,7 @@ build-nim: | sanity-checks
 #- allows parallel building with the '+' prefix
 #- rebuilds the Nim compiler if the corresponding submodule is updated
 update-common: | sanity-checks
-	git submodule foreach --quiet 'git ls-files --exclude-standard --recurse-submodules -z | xargs -0 rm -rf'
+	git submodule foreach --quiet 'git ls-files --exclude-standard --recurse-submodules -z -- ":!:.*" | xargs -0 rm -rf'
 	git submodule update --init --recursive || true
 	# changing URLs in a submodule's submodule means we have to sync and update twice
 	git submodule sync --quiet --recursive