Add --full flag to apply command

When --full is passed, apply also runs 'docker compose up' on all
services (not just missing/migrating ones) to pick up any config
changes (compose file, .env, etc).

- cf apply          # Fast: state reconciliation only
- cf apply --full   # Thorough: also refresh all running services

README.md

@@ -259,6 +259,7 @@ Each command replaces: look up host → SSH → find compose file → run `ssh h
 cf apply               # start missing + migrate + stop orphans
 cf apply --dry-run     # preview what would change
 cf apply --no-orphans  # skip stopping orphaned services
+cf apply --full        # also refresh all services (picks up config changes)
 
 # Or operate on individual services
 cf up plex jellyfin    # start services (auto-migrates if host changed)

src/compose_farm/cli/lifecycle.py

@@ -193,6 +193,14 @@ def _report_pending_starts(cfg: Config, missing: list[str]) -> None:
         console.print(f"  [cyan]{svc}[/] on [magenta]{target}[/]")
 
 
+def _report_pending_refresh(cfg: Config, to_refresh: list[str]) -> None:
+    """Report services that will be refreshed."""
+    console.print(f"[blue]Services to refresh ({len(to_refresh)}):[/]")
+    for svc in to_refresh:
+        target = _format_host(cfg.get_hosts(svc))
+        console.print(f"  [cyan]{svc}[/] on [magenta]{target}[/]")
+
+
 @app.command(rich_help_panel="Lifecycle")
 def apply(
     dry_run: Annotated[
@@ -203,6 +211,10 @@ def apply(
         bool,
         typer.Option("--no-orphans", help="Only migrate, don't stop orphaned services"),
     ] = False,
+    full: Annotated[
+        bool,
+        typer.Option("--full", help="Also run up on all services to apply config changes"),
+    ] = False,
     config: ConfigOption = None,
 ) -> None:
     """Make reality match config (start, migrate, stop as needed).
@@ -216,17 +228,23 @@ def apply(
 
     Use --dry-run to preview changes before applying.
     Use --no-orphans to only migrate/start without stopping orphaned services.
+    Use --full to also run 'up' on all services (picks up compose/env changes).
     """
     cfg = load_config_or_exit(config)
     orphaned = get_orphaned_services(cfg)
     migrations = get_services_needing_migration(cfg)
     missing = get_services_not_in_state(cfg)
 
+    # For --full: refresh all services not already being started/migrated
+    handled = set(migrations) | set(missing)
+    to_refresh = [svc for svc in cfg.services if svc not in handled] if full else []
+
     has_orphans = bool(orphaned) and not no_orphans
     has_migrations = bool(migrations)
     has_missing = bool(missing)
+    has_refresh = bool(to_refresh)
 
-    if not has_orphans and not has_migrations and not has_missing:
+    if not has_orphans and not has_migrations and not has_missing and not has_refresh:
         console.print("[green]✓[/] Nothing to apply - reality matches config")
         return
 
@@ -237,6 +255,8 @@ def apply(
         _report_pending_migrations(cfg, migrations)
     if has_missing:
         _report_pending_starts(cfg, missing)
+    if has_refresh:
+        _report_pending_refresh(cfg, to_refresh)
 
     if dry_run:
         console.print("\n[dim](dry-run: no changes made)[/]")
@@ -265,4 +285,11 @@ def apply(
         all_results.extend(start_results)
         maybe_regenerate_traefik(cfg, start_results)
 
+    # 4. Refresh remaining services (--full: run up to apply config changes)
+    if has_refresh:
+        console.print("[blue]Refreshing services...[/]")
+        refresh_results = run_async(up_services(cfg, to_refresh, raw=True))
+        all_results.extend(refresh_results)
+        maybe_regenerate_traefik(cfg, refresh_results)
+
     report_results(all_results)

tests/test_cli_lifecycle.py

@@ -57,7 +57,7 @@ class TestApplyCommand:
             patch("compose_farm.cli.lifecycle.get_services_needing_migration", return_value=[]),
             patch("compose_farm.cli.lifecycle.get_services_not_in_state", return_value=[]),
         ):
-            apply(dry_run=False, no_orphans=False, config=None)
+            apply(dry_run=False, no_orphans=False, full=False, config=None)
 
         captured = capsys.readouterr()
         assert "Nothing to apply" in captured.out
@@ -83,7 +83,7 @@ class TestApplyCommand:
             patch("compose_farm.cli.lifecycle.stop_orphaned_services") as mock_stop,
             patch("compose_farm.cli.lifecycle.up_services") as mock_up,
         ):
-            apply(dry_run=True, no_orphans=False, config=None)
+            apply(dry_run=True, no_orphans=False, full=False, config=None)
 
         captured = capsys.readouterr()
         assert "Services to migrate" in captured.out
@@ -118,7 +118,7 @@ class TestApplyCommand:
             patch("compose_farm.cli.lifecycle.maybe_regenerate_traefik"),
             patch("compose_farm.cli.lifecycle.report_results"),
         ):
-            apply(dry_run=False, no_orphans=False, config=None)
+            apply(dry_run=False, no_orphans=False, full=False, config=None)
 
             mock_up.assert_called_once()
             call_args = mock_up.call_args
@@ -144,7 +144,7 @@ class TestApplyCommand:
             patch("compose_farm.cli.lifecycle.stop_orphaned_services") as mock_stop,
             patch("compose_farm.cli.lifecycle.report_results"),
         ):
-            apply(dry_run=False, no_orphans=False, config=None)
+            apply(dry_run=False, no_orphans=False, full=False, config=None)
 
             mock_stop.assert_called_once_with(cfg)
 
@@ -176,7 +176,7 @@ class TestApplyCommand:
             patch("compose_farm.cli.lifecycle.maybe_regenerate_traefik"),
             patch("compose_farm.cli.lifecycle.report_results"),
         ):
-            apply(dry_run=False, no_orphans=True, config=None)
+            apply(dry_run=False, no_orphans=True, full=False, config=None)
 
             # Should run migrations but not orphan cleanup
             mock_up.assert_called_once()
@@ -201,7 +201,7 @@ class TestApplyCommand:
             patch("compose_farm.cli.lifecycle.get_services_needing_migration", return_value=[]),
             patch("compose_farm.cli.lifecycle.get_services_not_in_state", return_value=[]),
         ):
-            apply(dry_run=False, no_orphans=True, config=None)
+            apply(dry_run=False, no_orphans=True, full=False, config=None)
 
         captured = capsys.readouterr()
         assert "Nothing to apply" in captured.out
@@ -227,7 +227,7 @@ class TestApplyCommand:
             patch("compose_farm.cli.lifecycle.maybe_regenerate_traefik"),
             patch("compose_farm.cli.lifecycle.report_results"),
         ):
-            apply(dry_run=False, no_orphans=False, config=None)
+            apply(dry_run=False, no_orphans=False, full=False, config=None)
 
             mock_up.assert_called_once()
             call_args = mock_up.call_args
@@ -248,13 +248,91 @@ class TestApplyCommand:
                 return_value=["svc1"],
             ),
         ):
-            apply(dry_run=True, no_orphans=False, config=None)
+            apply(dry_run=True, no_orphans=False, full=False, config=None)
 
         captured = capsys.readouterr()
         assert "Services to start" in captured.out
         assert "svc1" in captured.out
         assert "dry-run" in captured.out
 
+    def test_apply_full_refreshes_all_services(self, tmp_path: Path) -> None:
+        """--full runs up on all services to pick up config changes."""
+        cfg = _make_config(tmp_path)
+        mock_results = [_make_result("svc1"), _make_result("svc2")]
+
+        with (
+            patch("compose_farm.cli.lifecycle.load_config_or_exit", return_value=cfg),
+            patch("compose_farm.cli.lifecycle.get_orphaned_services", return_value={}),
+            patch("compose_farm.cli.lifecycle.get_services_needing_migration", return_value=[]),
+            patch("compose_farm.cli.lifecycle.get_services_not_in_state", return_value=[]),
+            patch(
+                "compose_farm.cli.lifecycle.run_async",
+                return_value=mock_results,
+            ),
+            patch("compose_farm.cli.lifecycle.up_services") as mock_up,
+            patch("compose_farm.cli.lifecycle.maybe_regenerate_traefik"),
+            patch("compose_farm.cli.lifecycle.report_results"),
+        ):
+            apply(dry_run=False, no_orphans=False, full=True, config=None)
+
+            mock_up.assert_called_once()
+            call_args = mock_up.call_args
+            # Should refresh all services in config
+            assert set(call_args[0][1]) == {"svc1", "svc2"}
+
+    def test_apply_full_dry_run_shows_refresh(
+        self, tmp_path: Path, capsys: pytest.CaptureFixture[str]
+    ) -> None:
+        """--full --dry-run shows services that would be refreshed."""
+        cfg = _make_config(tmp_path)
+
+        with (
+            patch("compose_farm.cli.lifecycle.load_config_or_exit", return_value=cfg),
+            patch("compose_farm.cli.lifecycle.get_orphaned_services", return_value={}),
+            patch("compose_farm.cli.lifecycle.get_services_needing_migration", return_value=[]),
+            patch("compose_farm.cli.lifecycle.get_services_not_in_state", return_value=[]),
+        ):
+            apply(dry_run=True, no_orphans=False, full=True, config=None)
+
+        captured = capsys.readouterr()
+        assert "Services to refresh" in captured.out
+        assert "svc1" in captured.out
+        assert "svc2" in captured.out
+        assert "dry-run" in captured.out
+
+    def test_apply_full_excludes_already_handled_services(self, tmp_path: Path) -> None:
+        """--full doesn't double-process services that are migrating or starting."""
+        cfg = _make_config(tmp_path, {"svc1": "host1", "svc2": "host2", "svc3": "host1"})
+        mock_results = [_make_result("svc1"), _make_result("svc3")]
+
+        with (
+            patch("compose_farm.cli.lifecycle.load_config_or_exit", return_value=cfg),
+            patch("compose_farm.cli.lifecycle.get_orphaned_services", return_value={}),
+            patch(
+                "compose_farm.cli.lifecycle.get_services_needing_migration",
+                return_value=["svc1"],
+            ),
+            patch(
+                "compose_farm.cli.lifecycle.get_services_not_in_state",
+                return_value=["svc2"],
+            ),
+            patch("compose_farm.cli.lifecycle.get_service_host", return_value="host2"),
+            patch(
+                "compose_farm.cli.lifecycle.run_async",
+                return_value=mock_results,
+            ),
+            patch("compose_farm.cli.lifecycle.up_services") as mock_up,
+            patch("compose_farm.cli.lifecycle.maybe_regenerate_traefik"),
+            patch("compose_farm.cli.lifecycle.report_results"),
+        ):
+            apply(dry_run=False, no_orphans=False, full=True, config=None)
+
+            # up_services should be called 3 times: migrate, start, refresh
+            assert mock_up.call_count == 3
+            # Get the third call (refresh) and check it only has svc3
+            refresh_call = mock_up.call_args_list[2]
+            assert refresh_call[0][1] == ["svc3"]
+
 
 class TestDownOrphaned:
     """Tests for down --orphaned flag."""