diff --git a/serena_config.template.yml b/serena_config.template.yml
index 269c01f8..33a9cd3b 100644
--- a/serena_config.template.yml
+++ b/serena_config.template.yml
@@ -24,11 +24,13 @@ gui_log_level: 20
 # minimum log level for the GUI log window (10 = debug, 20 = info, 30 = warning, 40 = error)
 
 
-# The list of registered projects (which you can switch between using "activate_project").
-# MANAGED BY SERENA, KEEP AT THE BOTTOM OF THE YAML AND DON'T ADJUST WITHOUT NEED (you may add paths though)
-# Whenever a project is activated (either by using the tool or by starting the server with --project),
-# the project's path will be added here and you will be able to activate it by its name in the future.
+# MANAGED BY SERENA, KEEP AT THE BOTTOM OF THE YAML AND DON'T EDIT WITHOUT NEED
+# The list of registered projects.
+# To add a project, within a chat, simply ask Serena to "activate the project /path/to/project" or,
+# if the project was previously added, "activate the project <project name>".
 # By default, the project's name will be the name of the directory containing the project, but you may change it
-# by changing the entry in the (autogenerated) `.serena/project.yml` file.
-# Note: make sure there are no name collisions in the names of registered projects
+# by editing the (auto-generated) project configuration file `/path/project/project/.serena/project.yml` file.
+# If you want to maintain full control of the project configuration, create the project.yml file manually and then
+# instruct Serena to activate the project by its path for first-time activation.
+# NOTE: Make sure there are no name collisions in the names of registered projects.
 projects: []
diff --git a/src/serena/agent.py b/src/serena/agent.py
index 15124b55..0810448e 100644
--- a/src/serena/agent.py
+++ b/src/serena/agent.py
@@ -340,19 +340,10 @@ class SerenaConfig(SerenaConfigBase):
         num_project_migrations = 0
         for path in loaded_commented_yaml["projects"]:
             path = Path(path).resolve()
-            if not path.exists():
-                log.warning(f"Project path {path} does not exist, skipping.")
+            if not path.exists() or (path.is_dir() and not (path / ProjectConfig.rel_path_to_project_yml()).exists()):
+                log.warning(f"Project path {path} does not exist or does not contain a project configuration file, skipping.")
                 continue
-            if path.is_dir():
-                project_yml_path = path / ProjectConfig.rel_path_to_project_yml()
-                if not project_yml_path.exists():
-                    log.info(f"Project path {path} does not contain a project configuration file, creating one.")
-                    ProjectConfig.autogenerate(path, save_to_disk=True)
-                    continue
             if path.is_file():
-                log.info(
-                    f"Project path {path} is a file, migrating to in-project configuration. This is a legacy feature for backwards compatibility."
-                )
                 path = cls._migrate_out_of_project_config_file(path)
                 if path is None:
                     continue
diff --git a/src/serena/util/general.py b/src/serena/util/general.py
index b350ae18..bfddaf47 100644
--- a/src/serena/util/general.py
+++ b/src/serena/util/general.py
@@ -1,4 +1,3 @@
-import os
 from typing import Literal, overload
 
 from ruamel.yaml import YAML
@@ -27,6 +26,5 @@ def load_yaml(path: str, preserve_comments: bool = False) -> dict | CommentedMap
 
 def save_yaml(path: str, data: dict | CommentedMap, preserve_comments: bool = False) -> None:
     yaml = _create_YAML(preserve_comments)
-    os.makedirs(os.path.dirname(path), exist_ok=True)
     with open(path, "w", encoding="utf-8") as f:
         yaml.dump(data, f)