Save changed user config back to disk in integration tests

At the moment, the user config is only read once at startup, so there's no point
in writing it back to disk. However, later in this branch we will add code that
reloads the user config when switching repos, which does happen quite a bit in
integration tests; this would undo the changes that a test made in its
SetupConfig function, so write those changes to disk to prevent that from
happening.

pkg/app/entry_point.go

@@ -136,6 +136,12 @@ func Start(buildInfo *BuildInfo, integrationTest integrationTypes.IntegrationTes
 
 	if integrationTest != nil {
 		integrationTest.SetupConfig(appConfig)
+
+		// Preserve the changes that the test setup just made to the config, so
+		// they don't get lost when we reload the config while running the test
+		// (which happens when switching between repos, going in and out of
+		// submodules, etc).
+		appConfig.SaveGlobalUserConfig()
 	}
 
 	common, err := NewCommon(appConfig)

pkg/config/app_config.go

@@ -2,6 +2,7 @@ package config
 
 import (
 	"fmt"
+	"log"
 	"os"
 	"path/filepath"
 	"strings"
@@ -361,6 +362,24 @@ func loadAppState() (*AppState, error) {
 	return appState, nil
 }
 
+// SaveGlobalUserConfig saves the UserConfig back to disk. This is only used in
+// integration tests, so we are a bit sloppy with error handling.
+func (c *AppConfig) SaveGlobalUserConfig() {
+	if len(c.userConfigFiles) != 1 {
+		panic("expected exactly one global user config file")
+	}
+
+	yamlContent, err := yaml.Marshal(c.userConfig)
+	if err != nil {
+		log.Fatalf("error marshalling user config: %v", err)
+	}
+
+	err = os.WriteFile(c.userConfigFiles[0].Path, yamlContent, 0o644)
+	if err != nil {
+		log.Fatalf("error saving user config: %v", err)
+	}
+}
+
 // AppState stores data between runs of the app like when the last update check
 // was performed and which other repos have been checked out
 type AppState struct {