Do not use CWD as a fallback for --project-from-cwd

This can be problematic if CWD is, for example, the user's home directory.
Fixes #979

docs/02-usage/020_running.md

@@ -162,8 +162,8 @@ to get a list of all available options.
 Some useful options include:
 
   * `--project <path|name>`: specify the project to work on by name or path.
-  * `--project-from-cwd`: auto-detect the project from current working directory   
-    (looking for a directory containing `.serena/project.yml` or `.git` in parent directories, activating the current directory if none is found);  
+  * `--project-from-cwd`: auto-detect the project from current working directory     
+    (looking for a directory containing `.serena/project.yml` or `.git` in parent directories and activating the containing directory as the project root, if any).
     This option is intended for CLI-based agents like Claude Code, Gemini and Codex, which are typically started from within the project directory
     and which do not change directories during their operation.
   * `--language-backend JetBrains`: use the Serena JetBrains Plugin as the language backend (overriding the default backend configured in the central configuration)

docs/02-usage/030_clients.md

@@ -96,7 +96,7 @@ claude mcp add --scope user serena -- uvx --from git+https://github.com/oraios/s
 ```
 
 Whenever you start Claude Code, Serena will search up from the current directory for `.serena/project.yml` or `.git` markers,
-activating the current directory as the project if neither is found. 
+activating the containing directory as the project (if any). 
 This mechanism makes it suitable for a single global MCP configuration.
 
 **Maximum Token Efficiency.** To maximize token efficiency, you may want to use Claude Code's 

src/serena/cli.py

@@ -55,15 +55,14 @@ Overriding them means that they no longer apply, so you will need to
 re-specify them in addition to further modes if you want to keep them."""
 
 
-def find_project_root(root: str | Path | None = None) -> str:
+def find_project_root(root: str | Path | None = None) -> str | None:
     """Find project root by walking up from CWD.
 
     Checks for .serena/project.yml first (explicit Serena project), then .git (git root).
-    Falls back to CWD if no marker is found.
 
     :param root: If provided, constrains the search to this directory and below
                  (acts as a virtual filesystem root). Search stops at this boundary.
-    :return: absolute path to project root (falls back to CWD if no marker found)
+    :return: absolute path to project root or None if not suitable root is found
     """
     current = Path.cwd().resolve()
     boundary = Path(root).resolve() if root is not None else None
@@ -86,8 +85,7 @@ def find_project_root(root: str | Path | None = None) -> str:
         if (directory / ".git").exists():  # .git can be file (worktree) or dir
             return str(directory)
 
-    # Fall back to CWD
-    return str(current)
+    return None
 
 
 # --------------------- Utilities -------------------------------------
@@ -274,7 +272,10 @@ class TopLevelCommands(AutoRegisteringGroup):
             if project is not None or project_file_arg is not None:
                 raise click.UsageError("--project-from-cwd cannot be used with --project or positional project argument")
             project = find_project_root()
-            log.info("Auto-detected project root: %s", project)
+            if project is not None:
+                log.info("Auto-detected project root: %s", project)
+            else:
+                log.warning("No project root found from %s; not activating any project", os.getcwd())
 
         project_file = project_file_arg or project
         factory = SerenaMCPFactory(context=context, project=project_file, memory_log_handler=memory_log_handler)