Enhance MCP development features and introduce skills management

- Added configuration options for requiring human approval before applying LLM-generated MCP patches.
- Updated Docker setup to include skills directory.
- Integrated skills management into the backend, allowing for procedural guides and skill matching.
- Refactored database initialization to apply Alembic migrations.
- Enhanced task approval process to handle MCP patch applications with optional approval.
- Introduced new schemas for skills and updated existing APIs to support skills functionality.

This commit lays the groundwork for improved agent capabilities and better management of MCP development processes.

backend/tests/test_device_defaults.py

@@ -3,25 +3,30 @@ from __future__ import annotations
 
 import os
 
-os.environ.setdefault("SECRET_KEY", "test-secret-key-for-unit-tests-only")
-os.environ["DEVICE_SSH_USERNAME"] = "shipadmin"
-os.environ["DEVICE_SSH_PASSWORD"] = "ssh-secret"
-os.environ["DEVICE_PFSENSE_PORT"] = "40443"
-os.environ["DEVICE_PFSENSE_API_KEY"] = "pf-key-123"
-os.environ["DEVICE_PROXMOX_PASSWORD"] = "pve-pass"
-os.environ["DEVICE_PROXMOX_TOKEN_ID"] = "root@pam!agentic"
-os.environ["DEVICE_PROXMOX_TOKEN_SECRET"] = "token-uuid"
+import pytest
 
-from app.inventory_catalog import catalog_by_key  # noqa: E402
-from app.services.device_defaults import (  # noqa: E402
-    merge_selection_with_defaults,
-    proxmox_api_configured,
-    resolve_proxmox_api_defaults,
-    resolve_slot_defaults,
-)
+os.environ.setdefault("SECRET_KEY", "test-secret-key-for-unit-tests-only")
+
+
+@pytest.fixture(autouse=True)
+def device_env(monkeypatch: pytest.MonkeyPatch):
+    monkeypatch.setenv("DEVICE_SSH_USERNAME", "shipadmin")
+    monkeypatch.setenv("DEVICE_SSH_PASSWORD", "ssh-secret")
+    monkeypatch.delenv("DEVICE_PROXMOX_USERNAME", raising=False)
+    monkeypatch.setenv("DEVICE_PFSENSE_PORT", "40443")
+    monkeypatch.setenv("DEVICE_PFSENSE_API_KEY", "pf-key-123")
+    monkeypatch.setenv("DEVICE_PROXMOX_PASSWORD", "pve-pass")
+    monkeypatch.setenv("DEVICE_PROXMOX_TOKEN_ID", "root@pam!agentic")
+    monkeypatch.setenv("DEVICE_PROXMOX_TOKEN_SECRET", "token-uuid")
+    from app.config import get_settings
+
+    get_settings.cache_clear()
 
 
 def test_ssh_slot_uses_global_fallback():
+    from app.inventory_catalog import catalog_by_key
+    from app.services.device_defaults import resolve_slot_defaults
+
     entry = catalog_by_key()["docker_vm"]
     d = resolve_slot_defaults("docker_vm", entry)
     assert d.username == "shipadmin"
@@ -30,6 +35,9 @@ def test_ssh_slot_uses_global_fallback():
 
 
 def test_per_slot_overrides_global():
+    from app.inventory_catalog import catalog_by_key
+    from app.services.device_defaults import resolve_slot_defaults
+
     entry = catalog_by_key()["proxmox"]
     d = resolve_slot_defaults("proxmox", entry)
     assert d.secret == "pve-pass"
@@ -37,32 +45,32 @@ def test_per_slot_overrides_global():
 
 
 def test_api_key_slot():
+    from app.inventory_catalog import catalog_by_key
+    from app.services.device_defaults import resolve_slot_defaults
+
     entry = catalog_by_key()["pfsense"]
     d = resolve_slot_defaults("pfsense", entry)
-    assert d.port == 40443
     assert d.secret == "pf-key-123"
     assert d.secret_kind == "api_key"
+    assert d.port == 40443
 
 
-def test_merge_applies_env_when_blank():
-    entry = catalog_by_key()["pfsense"]
+def test_merge_keeps_existing_secret():
+    from app.inventory_catalog import catalog_by_key
+    from app.services.device_defaults import merge_selection_with_defaults
+
+    entry = catalog_by_key()["docker_vm"]
     port, user, secret = merge_selection_with_defaults(
-        "pfsense", entry, port=None, username=None, secret=None
+        "docker_vm", entry, port=None, username=None, secret=None, existing_secret="stored"
     )
-    assert port == 40443
-    assert secret == "pf-key-123"
+    assert secret == "stored"
+    assert user == "shipadmin"
 
 
-def test_proxmox_api_env():
-    api = resolve_proxmox_api_defaults("10.1.2.3")
-    assert api["proxmox_token_id"] == "root@pam!agentic"
-    assert api["proxmox_token_secret"] == "token-uuid"
-    assert proxmox_api_configured(api)
+def test_proxmox_api_defaults_from_env():
+    from app.services.device_defaults import proxmox_api_configured, resolve_proxmox_api_defaults
 
-
-def test_merge_ui_override_wins():
-    entry = catalog_by_key()["pfsense"]
-    _, _, secret = merge_selection_with_defaults(
-        "pfsense", entry, port=8443, username="admin", secret="custom-key"
-    )
-    assert secret == "custom-key"
+    ctx = resolve_proxmox_api_defaults("10.20.30.254")
+    assert ctx["proxmox_api_url"] == "https://10.20.30.254:8006"
+    assert ctx["proxmox_token_id"] == "root@pam!agentic"
+    assert proxmox_api_configured(ctx)