Merge branch 'dev' of ssh://git.commumedia.org:2222/alex/headquarter into dev

- apply_mount_permissions now skips mounts with readonly=true to avoid
  'Read-only file system' warnings on post-start chown/chmod
- Removed the ssh_keys mount from the pi-agent manifest definition;
  instance-level SSH key mounting now handles this exclusively
- Added unit test for read-only mount skipping

Quality gates: pytest (15 passed)

apps/api/alembic/versions/2026_05_28_add_tool_definition_manifests.py

@@ -232,14 +232,6 @@ def upgrade() -> None:
                             "writable": True,
                             "owner": "user",
                         },
-                        {
-                            "name": "ssh_keys",
-                            "target": "/home/user/.ssh",
-                            "source_type": "ssh_key",
-                            "mode": "0700",
-                            "file_mode": "0600",
-                            "readonly": True,
-                        },
                         {
                             "name": "pi_state",
                             "target": "/tmp/.pi/agents",

apps/api/src/api/tool_instances.py

@@ -1341,11 +1341,27 @@ async def start_instance(
         manifest_def = await session.get(ToolDefinitionManifest, tool_type.manifest_id)
         if manifest_def:
             manifest = dict(manifest_def.manifest)
+            # Merge with base definition if referenced (user config is often in base)
+            if manifest_def.base_definition_id:
+                base_def = await session.get(
+                    ToolDefinitionManifest, manifest_def.base_definition_id
+                )
+                if base_def:
+                    manifest = resolve_base(
+                        deep_merge(dict(base_def.manifest), manifest)
+                    )
             home_dir = get_manifest_home_dir(manifest)
             user_cfg = manifest.get("user")
             if user_cfg:
                 container_uid = user_cfg.get("uid", 0)
                 container_gid = user_cfg.get("gid", 0)
+            logger.debug(
+                "Manifest user resolved for instance %s: uid=%s, gid=%s, home=%s",
+                instance.id,
+                container_uid,
+                container_gid,
+                home_dir,
+            )
 
     # Apply selected config profile if any
     instance_dir = os.path.dirname(instance.compose_path)

apps/api/src/services/permission_fixer.py

@@ -40,6 +40,17 @@ def apply_mount_permissions(
             "error": None,
         }
 
+        # Skip read-only mounts — their permissions cannot be changed
+        # post-start because the bind mount is locked.
+        if mount.get("readonly", False):
+            logger.debug(
+                "Skipping permission fix for read-only mount %s (target=%s)",
+                name,
+                target,
+            )
+            results.append(result)
+            continue
+
         # Skip if no permission policy defined
         if not owner and not mode and not file_mode:
             results.append(result)

apps/api/src/services/ssh_keys.py

@@ -1,5 +1,6 @@
 """SSH key service utilities for preparing keys for container use."""
 
+import logging
 import os
 from pathlib import Path
 
@@ -7,6 +8,8 @@ from cryptography.fernet import Fernet
 
 from src.config import Settings
 
+logger = logging.getLogger(__name__)
+
 
 def _get_fernet() -> Fernet:
     """Generate a valid Fernet key from the session secret."""
@@ -75,10 +78,20 @@ def prepare_ssh_key_files(
             os.chown(private_key_path, effective_uid, effective_gid)
             os.chown(public_key_path, effective_uid, effective_gid)
             os.chown(config_path, effective_uid, effective_gid)
-        except PermissionError:
+            logger.debug(
-            # API process may not be running as root; permission fixer will
+                "Set SSH key ownership to uid=%s gid=%s for %s",
-            # handle this post-start if the mount is read-write
+                effective_uid,
-            pass
+                effective_gid,
+                ssh_dir,
+            )
+        except PermissionError as exc:
+            logger.warning(
+                "Cannot chown SSH keys to uid=%s gid=%s (running as uid=%s): %s",
+                effective_uid,
+                effective_gid,
+                os.getuid(),
+                exc,
+            )
 
     return str(ssh_dir)
 

apps/api/tests/unit/test_permission_fixer.py

@@ -64,6 +64,24 @@ class TestApplyMountPermissions:
             "find /home/user/.ssh -type f -exec chmod 0600" in file_mode_call[0][1][2]
         )
 
+    @patch("src.services.permission_fixer._run_in_container")
+    def test_skips_readonly_mount(self, mock_run) -> None:
+        mounts = [
+            {
+                "name": "ssh_keys",
+                "target": "/home/user/.ssh",
+                "readonly": True,
+                "mode": "0700",
+                "file_mode": "0600",
+            },
+        ]
+        results = apply_mount_permissions("abc123", mounts)
+
+        assert len(results) == 1
+        assert results[0]["mount_name"] == "ssh_keys"
+        assert results[0]["success"] is True
+        mock_run.assert_not_called()
+
     @patch("src.services.permission_fixer._run_in_container")
     def test_skips_mount_with_no_policy(self, mock_run) -> None:
         mounts = [

apps/api/tests/unit/test_ssh_keys.py

@@ -13,7 +13,9 @@ class TestPrepareSshKeyFiles:
     """Tests for prepare_ssh_key_files."""
 
     @patch("src.services.ssh_keys._get_fernet")
-    def test_creates_files_with_default_permissions(self, mock_fernet, tmp_path) -> None:
+    def test_creates_files_with_default_permissions(
+        self, mock_fernet, tmp_path
+    ) -> None:
         mock_fernet.return_value.decrypt.return_value = b"private-key-content"
         ssh_key = MagicMock()
         ssh_key.private_key_encrypted = "enc"
@@ -35,9 +37,7 @@ class TestPrepareSshKeyFiles:
         ssh_key.public_key = "ssh-ed25519 AAA test@test"
 
         with patch("os.chown") as mock_chown:
-            ssh_dir = prepare_ssh_key_files(
+            ssh_dir = prepare_ssh_key_files(str(tmp_path), ssh_key, uid=1001, gid=1001)
-                str(tmp_path), ssh_key, uid=1001, gid=1001
-            )
 
         # os.chown is called for the directory and each of the 3 files
         assert mock_chown.call_count == 4
@@ -56,8 +56,6 @@ class TestPrepareSshKeyFiles:
 
         with patch("os.chown", side_effect=PermissionError("not allowed")):
             # Should not raise
-            ssh_dir = prepare_ssh_key_files(
+            ssh_dir = prepare_ssh_key_files(str(tmp_path), ssh_key, uid=1001, gid=1001)
-                str(tmp_path), ssh_key, uid=1001, gid=1001
-            )
 
         assert Path(ssh_dir).exists()