diff --git a/src/dstack/_internal/cli/services/configurators/run.py b/src/dstack/_internal/cli/services/configurators/run.py
index 3c7c03be9f..53e8c5e494 100644
--- a/src/dstack/_internal/cli/services/configurators/run.py
+++ b/src/dstack/_internal/cli/services/configurators/run.py
@@ -97,7 +97,8 @@ def apply_configuration(
             # is not set (emulate pre-0.19.27 JobConfigutor logic), otherwise fall back to
             # `/workflow`.
             if isinstance(conf, DevEnvironmentConfiguration) or conf.commands:
-                conf.working_dir = LEGACY_REPO_DIR
+                # relative path for compatibility with pre-0.19.27 servers
+                conf.working_dir = "."
                 warn(
                     "[code]working_dir[/code] is not set."
                     f" Using legacy working directory [code]{LEGACY_REPO_DIR}[/code]\n\n"
@@ -117,6 +118,12 @@ def apply_configuration(
                 f"To keep using legacy working directory, set"
                 f" [code]working_dir[/code] to [code]{legacy_working_dir}[/code]\n"
             )
+        else:
+            # relative path for compatibility with pre-0.19.27 servers
+            try:
+                conf.working_dir = str(PurePosixPath(working_dir).relative_to(LEGACY_REPO_DIR))
+            except ValueError:
+                pass
 
         if conf.repos and conf.repos[0].path is None:
             warn(
diff --git a/src/dstack/_internal/core/compatibility/runs.py b/src/dstack/_internal/core/compatibility/runs.py
index 4edd28808e..fa34fbaa22 100644
--- a/src/dstack/_internal/core/compatibility/runs.py
+++ b/src/dstack/_internal/core/compatibility/runs.py
@@ -104,6 +104,8 @@ def get_run_spec_excludes(run_spec: RunSpec) -> IncludeExcludeDictType:
 
     if run_spec.repo_dir in [None, LEGACY_REPO_DIR]:
         spec_excludes["repo_dir"] = True
+    elif run_spec.repo_dir == "." and configuration.working_dir in [None, LEGACY_REPO_DIR, "."]:
+        spec_excludes["repo_dir"] = True
 
     if configuration.fleets is None:
         configuration_excludes["fleets"] = True