refactor: route startup and cli settings through runtime

tests/fixtures/architecture/configuration-debt-baseline.json

@@ -9,17 +9,12 @@
     "root": "app"
   },
   "settings_imports": {
-    "count": 24,
+    "count": 19,
     "files": [
       "app/adapters/system/fsproxy.py",
-      "app/cli.py",
       "app/db/base.py",
       "app/db/engine.py",
       "app/db/session.py",
-      "app/doctor/checks.py",
-      "app/doctor/runner.py",
-      "app/factory.py",
-      "app/main.py",
       "app/modules/filemanager/storages/local.py",
       "app/modules/postgresql/__init__.py",
       "app/modules/qbittorrent/__init__.py",

tests/fixtures/architecture/dependency-baseline.json

@@ -13,8 +13,8 @@
     "runtime_to_db": [],
     "workflow_to_db": []
   },
-  "edge_count": 6425,
-  "edge_sha256": "4d0424aeaa643346981710c4533b4cf546cf07a0d1cb9642707369c60afc4e39",
+  "edge_count": 6427,
+  "edge_sha256": "1d56d5da4d473e3c61cb5501b79619b9ec8a6623c788f629c31efac6972ce948",
   "edges": [
     "app -> app.runtime",
     "app -> app.runtime.compat",
@@ -3413,6 +3413,7 @@
     "app.cli -> app.doctor.formatters",
     "app.cli -> app.runtime",
     "app.cli -> app.runtime.config",
+    "app.cli -> app.runtime.settings",
     "app.cli -> app.runtime.state",
     "app.cli -> app.startup",
     "app.cli -> app.startup.database",
@@ -3691,7 +3692,7 @@
     "app.doctor.checks -> app.doctor",
     "app.doctor.checks -> app.doctor.models",
     "app.doctor.checks -> app.runtime",
-    "app.doctor.checks -> app.runtime.config",
+    "app.doctor.checks -> app.runtime.settings",
     "app.doctor.checks -> app.runtime.topology",
     "app.doctor.formatters -> app.doctor",
     "app.doctor.formatters -> app.doctor.models",
@@ -3702,7 +3703,7 @@
     "app.doctor.runner -> app.doctor.checks",
     "app.doctor.runner -> app.doctor.models",
     "app.doctor.runner -> app.runtime",
-    "app.doctor.runner -> app.runtime.config",
+    "app.doctor.runner -> app.runtime.settings",
     "app.domain.context -> app.domain",
     "app.domain.context -> app.domain.meta",
     "app.domain.context -> app.domain.meta.metabase",
@@ -3810,13 +3811,13 @@
     "app.factory -> app.application.security",
     "app.factory -> app.application.security.token",
     "app.factory -> app.runtime",
-    "app.factory -> app.runtime.config",
     "app.factory -> app.runtime.correlation",
     "app.factory -> app.runtime.extensions",
     "app.factory -> app.runtime.extensions.plugin_manager",
     "app.factory -> app.runtime.localization",
     "app.factory -> app.runtime.log",
     "app.factory -> app.runtime.observability",
+    "app.factory -> app.runtime.settings",
     "app.factory -> app.schemas",
     "app.factory -> app.schemas.mcp",
     "app.factory -> app.schemas.openai",
@@ -3830,6 +3831,7 @@
     "app.main -> app.factory",
     "app.main -> app.runtime",
     "app.main -> app.runtime.config",
+    "app.main -> app.runtime.settings",
     "app.main -> app.runtime.topology",
     "app.modules -> app.runtime",
     "app.modules -> app.runtime.extensions",