fix: allow git commands in workspace subdirectories

The shell safety guard in _guard_command() checked extracted absolute
paths only against cwd_path (the command's working directory).  When
cwd was a subdirectory like ~/.nanobot/workspace/obsidian_notes, any
absolute path referencing the broader workspace (e.g. a sibling
directory or the workspace root itself) was incorrectly blocked with
"path outside working dir".

Fix: pass the workspace_root from _prepare_command() into
_guard_command() and check absolute paths against it as a fallback
when they are outside cwd_path.  Paths truly outside the workspace
root are still blocked.

Added tests:
- test_exec_allows_workspace_paths_from_subdirectory
- test_exec_blocks_outside_paths_from_subdirectory

nanobot/agent/tools/shell.py

@@ -397,6 +397,7 @@ class ExecTool(Tool):
             command,
             cwd,
             restrict_to_workspace=access.restrict_to_workspace,
+            workspace_root=workspace_root,
         )
         if guard_error:
             return guard_error
@@ -591,6 +592,7 @@ class ExecTool(Tool):
         cwd: str,
         *,
         restrict_to_workspace: bool | None = None,
+        workspace_root: str | None = None,
     ) -> str | None:
         """Best-effort safety guard for potentially destructive commands."""
         cmd = command.strip()
@@ -629,6 +631,11 @@ class ExecTool(Tool):
                 )
 
             cwd_path = Path(cwd).resolve()
+            resolved_workspace = (
+                Path(workspace_root).expanduser().resolve()
+                if workspace_root
+                else None
+            )
 
             for raw in self._extract_absolute_paths(cmd):
                 try:
@@ -646,10 +653,13 @@ class ExecTool(Tool):
                     continue
 
                 media_path = get_media_dir().resolve()
-                if p.is_absolute() and not (
+                allowed = (
                     is_path_within(p, cwd_path)
                     or is_path_within(p, media_path)
-                ):
+                )
+                if not allowed and resolved_workspace is not None:
+                    allowed = is_path_within(p, resolved_workspace)
+                if p.is_absolute() and not allowed:
                     return (
                         "Error: Command blocked by safety guard (path outside working dir)"
                         + _WORKSPACE_BOUNDARY_NOTE

tests/tools/test_exec_security.py

@@ -349,3 +349,49 @@ def test_exec_allows_format_in_url_and_args(command):
     tool = ExecTool()
     result = tool._guard_command(command, "/tmp")
     assert result is None
+
+
+# --- workspace_root allows paths inside workspace but outside cwd ----------
+
+
+def test_exec_allows_workspace_paths_from_subdirectory(tmp_path):
+    """Absolute paths inside the workspace root must be allowed even when cwd
+    is a subdirectory.  This is the scenario reported in the issue: git
+    commands in ``~/.nanobot/workspace/obsidian_notes`` reference paths
+    under the broader workspace that are outside the subdirectory cwd."""
+    workspace = tmp_path / "workspace"
+    subdir = workspace / "obsidian_notes"
+    subdir.mkdir(parents=True)
+    sibling = workspace / "other_project"
+    sibling.mkdir()
+
+    tool = ExecTool(working_dir=str(workspace), restrict_to_workspace=True)
+
+    # A command run from the subdirectory that references a sibling path
+    # inside the workspace should be allowed.
+    result = tool._guard_command(
+        f"git clone {sibling}",
+        str(subdir),
+        workspace_root=str(workspace),
+    )
+    assert result is None
+
+
+def test_exec_blocks_outside_paths_from_subdirectory(tmp_path):
+    """Paths truly outside the workspace must still be blocked even when
+    workspace_root is provided."""
+    workspace = tmp_path / "workspace"
+    subdir = workspace / "project"
+    subdir.mkdir(parents=True)
+    outside = tmp_path / "secrets"
+    outside.mkdir()
+
+    tool = ExecTool(working_dir=str(workspace), restrict_to_workspace=True)
+
+    result = tool._guard_command(
+        f"cat {outside / 'key.pem'}",
+        str(subdir),
+        workspace_root=str(workspace),
+    )
+    assert result is not None
+    assert "path outside working dir" in result