diff --git a/scripts/mcp_server.py b/scripts/mcp_server.py
index 9bfcd286..83f10d41 100644
--- a/scripts/mcp_server.py
+++ b/scripts/mcp_server.py
@@ -79,16 +79,33 @@ async def call_tool(name: str, arguments: dict) -> list[TextContent]:
   return [TextContent(type="text", text=f"ERROR: {e}")]
 
 async def main() -> None:
- project_root = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
+ # Robust context detection: project_root is os.getcwd() (the directory
+ # the user is actually working in), not just where the script lives.
+ # The script's own home is a secondary fallback. This handles the case
+ # where opencode launches the MCP from a sibling clone (e.g., main repo
+ # launches the tier2 clone's MCP via a hardcoded path in opencode.json)
+ # — the MCP should allow access to the user's working directory too.
+ cwd = os.getcwd()
+ script_root = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
 
- extra_dirs = [project_root]
- mcp_paths_toml = os.path.join(project_root, "mcp_paths.toml")
- if os.path.exists(mcp_paths_toml):
-  import tomllib
-  with open(mcp_paths_toml, "rb") as f:
-   config = tomllib.load(f)
-  allowed = config.get("allowed_paths", {}).get("extra_dirs", [])
-  extra_dirs.extend(allowed)
+ extra_dirs: list[str] = []
+ for d in (cwd, script_root):
+  if d and d not in extra_dirs:
+   extra_dirs.append(d)
+
+ # Read mcp_paths.toml from cwd first (the user's working dir takes
+ # precedence), then fall back to the script's home dir.
+ for mcp_paths_toml in (os.path.join(cwd, "mcp_paths.toml"),
+                          os.path.join(script_root, "mcp_paths.toml")):
+  if os.path.exists(mcp_paths_toml):
+   import tomllib
+   with open(mcp_paths_toml, "rb") as f:
+    config = tomllib.load(f)
+   allowed = config.get("allowed_paths", {}).get("extra_dirs", [])
+   for p in allowed:
+    if p not in extra_dirs:
+     extra_dirs.append(p)
+   break
 
  mcp_client.configure([], extra_base_dirs=extra_dirs)
  async with stdio_server() as (read_stream, write_stream):