diff --git a/.gitignore b/.gitignore
index 31dcf4448..e54ce3717 100644
--- a/.gitignore
+++ b/.gitignore
@@ -20,15 +20,9 @@ examples/**/go.work
 examples/**/go.work.sum
 testdata/**/go.work
 testdata/**/go.work.sum
-
-# Leaving old _ftl for now to avoid old stuff getting checked in
 **/testdata/**/_ftl
 **/examples/**/_ftl
 **/examples/**/types.ftl.go
-**/testdata/**/.ftl
-**/examples/**/.ftl
-/.ftl
-
 buildengine/.gitignore
 go.work*
 junit*.xml
diff --git a/Justfile b/Justfile
index 50af62da2..0f6d1eb3f 100644
--- a/Justfile
+++ b/Justfile
@@ -9,7 +9,7 @@ KT_RUNTIME_RUNNER_TEMPLATE_OUT := "build/template/ftl/jars/ftl-runtime.jar"
 RUNNER_TEMPLATE_ZIP := "backend/controller/scaling/localscaling/template.zip"
 TIMESTAMP := `date +%s`
 SCHEMA_OUT := "backend/protos/xyz/block/ftl/v1/schema/schema.proto"
-ZIP_DIRS := "go-runtime/compile/build-template go-runtime/compile/external-module-template go-runtime/compile/main-work-template common-runtime/scaffolding go-runtime/scaffolding kotlin-runtime/scaffolding kotlin-runtime/external-module-template"
+ZIP_DIRS := "go-runtime/compile/build-template go-runtime/compile/external-module-template common-runtime/scaffolding go-runtime/scaffolding kotlin-runtime/scaffolding kotlin-runtime/external-module-template"
 FRONTEND_OUT := "frontend/dist/index.html"
 EXTENSION_OUT := "extensions/vscode/dist/extension.js"
 PROTOS_IN := "backend/protos/xyz/block/ftl/v1/schema/schema.proto backend/protos/xyz/block/ftl/v1/console/console.proto backend/protos/xyz/block/ftl/v1/ftl.proto backend/protos/xyz/block/ftl/v1/schema/runtime.proto"
diff --git a/buildengine/build.go b/buildengine/build.go
index 3a50e0522..298722399 100644
--- a/buildengine/build.go
+++ b/buildengine/build.go
@@ -22,11 +22,11 @@ const BuildLockTimeout = time.Minute
 // Build a module in the given directory given the schema and module config.
 //
 // A lock file is used to ensure that only one build is running at a time.
-func Build(ctx context.Context, projectRootDir string, sch *schema.Schema, module Module, filesTransaction ModifyFilesTransaction) error {
-	return buildModule(ctx, projectRootDir, sch, module, filesTransaction)
+func Build(ctx context.Context, sch *schema.Schema, module Module, filesTransaction ModifyFilesTransaction) error {
+	return buildModule(ctx, sch, module, filesTransaction)
 }
 
-func buildModule(ctx context.Context, projectRootDir string, sch *schema.Schema, module Module, filesTransaction ModifyFilesTransaction) error {
+func buildModule(ctx context.Context, sch *schema.Schema, module Module, filesTransaction ModifyFilesTransaction) error {
 	release, err := flock.Acquire(ctx, filepath.Join(module.Config.Dir, ".ftl.lock"), BuildLockTimeout)
 	if err != nil {
 		return err
@@ -46,7 +46,7 @@ func buildModule(ctx context.Context, projectRootDir string, sch *schema.Schema,
 
 	switch module.Config.Language {
 	case "go":
-		err = buildGoModule(ctx, projectRootDir, sch, module, filesTransaction)
+		err = buildGoModule(ctx, sch, module, filesTransaction)
 	case "kotlin":
 		err = buildKotlinModule(ctx, sch, module)
 	case "rust":
diff --git a/buildengine/build_go.go b/buildengine/build_go.go
index 8eba01a74..ee8fb1c98 100644
--- a/buildengine/build_go.go
+++ b/buildengine/build_go.go
@@ -8,8 +8,8 @@ import (
 	"github.com/TBD54566975/ftl/go-runtime/compile"
 )
 
-func buildGoModule(ctx context.Context, projectRootDir string, sch *schema.Schema, module Module, transaction ModifyFilesTransaction) error {
-	if err := compile.Build(ctx, projectRootDir, module.Config.Dir, sch, transaction); err != nil {
+func buildGoModule(ctx context.Context, sch *schema.Schema, module Module, transaction ModifyFilesTransaction) error {
+	if err := compile.Build(ctx, module.Config.Dir, sch, transaction); err != nil {
 		return CompilerBuildError{err: fmt.Errorf("failed to build module %q: %w", module.Config.Module, err)}
 	}
 	return nil
diff --git a/buildengine/build_go_test.go b/buildengine/build_go_test.go
index cdfd9c821..498e26e43 100644
--- a/buildengine/build_go_test.go
+++ b/buildengine/build_go_test.go
@@ -11,6 +11,181 @@ import (
 	"github.com/TBD54566975/ftl/backend/schema"
 )
 
+func TestGenerateGoModule(t *testing.T) {
+	if testing.Short() {
+		t.SkipNow()
+	}
+	sch := &schema.Schema{
+		Modules: []*schema.Module{
+			schema.Builtins(),
+			{Name: "other", Decls: []schema.Decl{
+				&schema.Enum{
+					Comments: []string{"This is an enum.", "", "It has 3 variants."},
+					Name:     "Color",
+					Export:   true,
+					Type:     &schema.String{},
+					Variants: []*schema.EnumVariant{
+						{Name: "Red", Value: &schema.StringValue{Value: "Red"}},
+						{Name: "Blue", Value: &schema.StringValue{Value: "Blue"}},
+						{Name: "Green", Value: &schema.StringValue{Value: "Green"}},
+					},
+				},
+				&schema.Enum{
+					Name:   "ColorInt",
+					Export: true,
+					Type:   &schema.Int{},
+					Variants: []*schema.EnumVariant{
+						{Name: "RedInt", Value: &schema.IntValue{Value: 0}},
+						{Name: "BlueInt", Value: &schema.IntValue{Value: 1}},
+						{Name: "GreenInt", Value: &schema.IntValue{Value: 2}},
+					},
+				},
+				&schema.Enum{
+					Comments: []string{"This is type enum."},
+					Name:     "TypeEnum",
+					Export:   true,
+					Variants: []*schema.EnumVariant{
+						{Name: "A", Value: &schema.TypeValue{Value: &schema.Int{}}},
+						{Name: "B", Value: &schema.TypeValue{Value: &schema.String{}}},
+					},
+				},
+				&schema.Data{Name: "EchoRequest", Export: true},
+				&schema.Data{
+					Comments: []string{"This is an echo data response."},
+					Name:     "EchoResponse", Export: true},
+				&schema.Verb{
+					Name:     "echo",
+					Export:   true,
+					Request:  &schema.Ref{Name: "EchoRequest"},
+					Response: &schema.Ref{Name: "EchoResponse"},
+				},
+				&schema.Data{Name: "SinkReq", Export: true},
+				&schema.Verb{
+					Comments: []string{"This is a sink verb.", "", "Here is another line for this comment!"},
+					Name:     "sink",
+					Export:   true,
+					Request:  &schema.Ref{Name: "SinkReq"},
+					Response: &schema.Unit{},
+				},
+				&schema.Data{Name: "SourceResp", Export: true},
+				&schema.Verb{
+					Name:     "source",
+					Export:   true,
+					Request:  &schema.Unit{},
+					Response: &schema.Ref{Name: "SourceResp"},
+				},
+				&schema.Verb{
+					Name:     "nothing",
+					Export:   true,
+					Request:  &schema.Unit{},
+					Response: &schema.Unit{},
+				},
+			}},
+			{Name: "test"},
+		},
+	}
+	expected := `// Code generated by FTL. DO NOT EDIT.
+
+package other
+
+import (
+  "context"
+
+  "github.com/TBD54566975/ftl/go-runtime/ftl/reflection"
+)
+
+var _ = context.Background
+
+// This is an enum.
+//
+// It has 3 variants.
+//
+//ftl:enum
+type Color string
+const (
+  Red Color = "Red"
+  Blue Color = "Blue"
+  Green Color = "Green"
+)
+
+//ftl:enum
+type ColorInt int
+const (
+  RedInt ColorInt = 0
+  BlueInt ColorInt = 1
+  GreenInt ColorInt = 2
+)
+
+// This is type enum.
+//
+//ftl:enum
+type TypeEnum interface { typeEnum() }
+
+type A int
+
+func (A) typeEnum() {}
+
+type B string
+
+func (B) typeEnum() {}
+
+type EchoRequest struct {
+}
+
+// This is an echo data response.
+//
+type EchoResponse struct {
+}
+
+//ftl:verb
+func Echo(context.Context, EchoRequest) (EchoResponse, error) {
+  panic("Verb stubs should not be called directly, instead use github.com/TBD54566975/ftl/runtime-go/ftl.Call()")
+}
+
+type SinkReq struct {
+}
+
+// This is a sink verb.
+//
+// Here is another line for this comment!
+//
+//ftl:verb
+func Sink(context.Context, SinkReq) error {
+  panic("Verb stubs should not be called directly, instead use github.com/TBD54566975/ftl/runtime-go/ftl.CallSink()")
+}
+
+type SourceResp struct {
+}
+
+//ftl:verb
+func Source(context.Context) (SourceResp, error) {
+  panic("Verb stubs should not be called directly, instead use github.com/TBD54566975/ftl/runtime-go/ftl.CallSource()")
+}
+
+//ftl:verb
+func Nothing(context.Context) error {
+  panic("Verb stubs should not be called directly, instead use github.com/TBD54566975/ftl/runtime-go/ftl.CallEmpty()")
+}
+
+func init() {
+  reflection.Register(
+    reflection.SumType[TypeEnum](
+      *new(A),
+      *new(B),
+    ),
+  )
+}
+`
+	bctx := buildContext{
+		moduleDir: "testdata/another",
+		buildDir:  "_ftl",
+		sch:       sch,
+	}
+	testBuild(t, bctx, "", []assertion{
+		assertGeneratedModule("go/modules/other/external_module.go", expected),
+	})
+}
+
 func TestGoBuildClearsBuildDir(t *testing.T) {
 	if testing.Short() {
 		t.SkipNow()
@@ -23,22 +198,82 @@ func TestGoBuildClearsBuildDir(t *testing.T) {
 	}
 	bctx := buildContext{
 		moduleDir: "testdata/another",
-		buildDir:  ".ftl",
+		buildDir:  "_ftl",
 		sch:       sch,
 	}
 	testBuildClearsBuildDir(t, bctx)
 }
 
+func TestMetadataImportsExcluded(t *testing.T) {
+	if testing.Short() {
+		t.SkipNow()
+	}
+	sch := &schema.Schema{
+		Modules: []*schema.Module{
+			schema.Builtins(),
+			{Name: "test", Decls: []schema.Decl{
+				&schema.Data{
+					Comments: []string{"Request data type."},
+					Name:     "Req", Export: true},
+				&schema.Data{Name: "Resp", Export: true},
+				&schema.Verb{
+					Comments: []string{"This is a verb."},
+					Name:     "call",
+					Export:   true,
+					Request:  &schema.Ref{Name: "Req"},
+					Response: &schema.Ref{Name: "Resp"},
+					Metadata: []schema.Metadata{
+						&schema.MetadataCalls{Calls: []*schema.Ref{{Name: "verb", Module: "other"}}},
+					},
+				},
+			}},
+		},
+	}
+	expected := `// Code generated by FTL. DO NOT EDIT.
+
+package test
+
+import (
+  "context"
+)
+
+var _ = context.Background
+
+// Request data type.
+//
+type Req struct {
+}
+
+type Resp struct {
+}
+
+// This is a verb.
+//
+//ftl:verb
+func Call(context.Context, Req) (Resp, error) {
+  panic("Verb stubs should not be called directly, instead use github.com/TBD54566975/ftl/runtime-go/ftl.Call()")
+}
+`
+	bctx := buildContext{
+		moduleDir: "testdata/another",
+		buildDir:  "_ftl",
+		sch:       sch,
+	}
+	testBuild(t, bctx, "", []assertion{
+		assertGeneratedModule("go/modules/test/external_module.go", expected),
+	})
+}
+
 func TestExternalType(t *testing.T) {
 	if testing.Short() {
 		t.SkipNow()
 	}
 	bctx := buildContext{
 		moduleDir: "testdata/external",
-		buildDir:  ".ftl",
+		buildDir:  "_ftl",
 		sch:       &schema.Schema{},
 	}
-	testBuild(t, bctx, "", "unsupported external type", []assertion{
+	testBuild(t, bctx, "unsupported external type", []assertion{
 		assertBuildProtoErrors(
 			"unsupported external type \"time.Month\"",
 			"unsupported type \"time.Month\" for field \"Month\"",
@@ -67,10 +302,10 @@ func TestGoModVersion(t *testing.T) {
 	}
 	bctx := buildContext{
 		moduleDir: "testdata/highgoversion",
-		buildDir:  ".ftl",
+		buildDir:  "_ftl",
 		sch:       sch,
 	}
-	testBuild(t, bctx, fmt.Sprintf("go version %q is not recent enough for this module, needs minimum version \"9000.1.1\"", runtime.Version()[2:]), "", []assertion{})
+	testBuild(t, bctx, fmt.Sprintf("go version %q is not recent enough for this module, needs minimum version \"9000.1.1\"", runtime.Version()[2:]), []assertion{})
 }
 
 func TestGeneratedTypeRegistry(t *testing.T) {
@@ -110,10 +345,10 @@ func TestGeneratedTypeRegistry(t *testing.T) {
 	assert.NoError(t, err)
 	bctx := buildContext{
 		moduleDir: "testdata/other",
-		buildDir:  ".ftl",
+		buildDir:  "_ftl",
 		sch:       sch,
 	}
-	testBuild(t, bctx, "", "", []assertion{
+	testBuild(t, bctx, "", []assertion{
 		assertGeneratedMain(string(expected)),
 	})
 }
diff --git a/buildengine/build_test.go b/buildengine/build_test.go
index e29e244ea..83a05b6c0 100644
--- a/buildengine/build_test.go
+++ b/buildengine/build_test.go
@@ -38,7 +38,6 @@ func (t *mockModifyFilesTransaction) End() error {
 func testBuild(
 	t *testing.T,
 	bctx buildContext,
-	expectedGeneratStubsErrMsg string, // emptystr if no error expected
 	expectedBuildErrMsg string, // emptystr if no error expected
 	assertions []assertion,
 ) {
@@ -48,31 +47,12 @@ func testBuild(
 	assert.NoError(t, err, "Error getting absolute path for module directory")
 	module, err := LoadModule(abs)
 	assert.NoError(t, err)
-
-	projectRootDir := t.TempDir()
-
-	configs := []moduleconfig.ModuleConfig{}
-	if bctx.moduleDir != "" {
-		config, err := moduleconfig.LoadModuleConfig(bctx.moduleDir)
-		assert.NoError(t, err, "Error loading project config")
-		configs = append(configs, config)
-	}
-
-	// generate stubs to create the shared modules directory
-	err = GenerateStubs(ctx, projectRootDir, bctx.sch.Modules, configs)
-	if len(expectedGeneratStubsErrMsg) > 0 {
+	err = Build(ctx, bctx.sch, module, &mockModifyFilesTransaction{})
+	if len(expectedBuildErrMsg) > 0 {
 		assert.Error(t, err)
-		assert.Contains(t, err.Error(), expectedGeneratStubsErrMsg)
+		assert.Contains(t, err.Error(), expectedBuildErrMsg)
 	} else {
 		assert.NoError(t, err)
-
-		err = Build(ctx, projectRootDir, bctx.sch, module, &mockModifyFilesTransaction{})
-		if len(expectedBuildErrMsg) > 0 {
-			assert.Error(t, err)
-			assert.Contains(t, err.Error(), expectedBuildErrMsg)
-		} else {
-			assert.NoError(t, err)
-		}
 	}
 
 	for _, a := range assertions {
@@ -90,16 +70,10 @@ func testBuildClearsBuildDir(t *testing.T, bctx buildContext) {
 	abs, err := filepath.Abs(bctx.moduleDir)
 	assert.NoError(t, err, "Error getting absolute path for module directory")
 
-	projectRoot := t.TempDir()
-
-	// generate stubs to create the shared modules directory
-	err = GenerateStubs(ctx, projectRoot, bctx.sch.Modules, []moduleconfig.ModuleConfig{{Dir: bctx.moduleDir}})
-	assert.NoError(t, err)
-
 	// build to generate the build directory
 	module, err := LoadModule(abs)
 	assert.NoError(t, err)
-	err = Build(ctx, projectRoot, bctx.sch, module, &mockModifyFilesTransaction{})
+	err = Build(ctx, bctx.sch, module, &mockModifyFilesTransaction{})
 	assert.NoError(t, err)
 
 	// create a temporary file in the build directory
@@ -111,7 +85,7 @@ func testBuildClearsBuildDir(t *testing.T, bctx buildContext) {
 	// build to clear the old build directory
 	module, err = LoadModule(abs)
 	assert.NoError(t, err)
-	err = Build(ctx, projectRoot, bctx.sch, module, &mockModifyFilesTransaction{})
+	err = Build(ctx, bctx.sch, module, &mockModifyFilesTransaction{})
 	assert.NoError(t, err)
 
 	// ensure the temporary file was removed
diff --git a/buildengine/deploy_test.go b/buildengine/deploy_test.go
index 3550668d2..029f2d33a 100644
--- a/buildengine/deploy_test.go
+++ b/buildengine/deploy_test.go
@@ -10,7 +10,6 @@ import (
 
 	ftlv1 "github.com/TBD54566975/ftl/backend/protos/xyz/block/ftl/v1"
 	"github.com/TBD54566975/ftl/backend/schema"
-	"github.com/TBD54566975/ftl/common/moduleconfig"
 	"github.com/TBD54566975/ftl/internal/log"
 	"github.com/TBD54566975/ftl/internal/sha256"
 )
@@ -72,17 +71,11 @@ func TestDeploy(t *testing.T) {
 	module, err := LoadModule(modulePath)
 	assert.NoError(t, err)
 
-	projectRootDir := t.TempDir()
-
-	// generate stubs to create the shared modules directory
-	err = GenerateStubs(ctx, projectRootDir, sch.Modules, []moduleconfig.ModuleConfig{module.Config})
-	assert.NoError(t, err)
-
 	// Build first to make sure the files are there.
-	err = Build(ctx, projectRootDir, sch, module, &mockModifyFilesTransaction{})
+	err = Build(ctx, sch, module, &mockModifyFilesTransaction{})
 	assert.NoError(t, err)
 
-	sum, err := sha256.SumFile(modulePath + "/.ftl/main")
+	sum, err := sha256.SumFile(modulePath + "/_ftl/main")
 	assert.NoError(t, err)
 
 	client := &mockDeployClient{
diff --git a/buildengine/discover_test.go b/buildengine/discover_test.go
index 0aec6ccc9..b63d7d341 100644
--- a/buildengine/discover_test.go
+++ b/buildengine/discover_test.go
@@ -22,7 +22,7 @@ func TestDiscoverModules(t *testing.T) {
 				Realm:     "home",
 				Module:    "alpha",
 				Deploy:    []string{"main"},
-				DeployDir: ".ftl",
+				DeployDir: "_ftl",
 				Schema:    "schema.pb",
 				Errors:    "errors.pb",
 				Watch:     []string{"**/*.go", "go.mod", "go.sum", "../../../go-runtime/ftl/**/*.go"},
@@ -35,7 +35,7 @@ func TestDiscoverModules(t *testing.T) {
 				Realm:     "home",
 				Module:    "another",
 				Deploy:    []string{"main"},
-				DeployDir: ".ftl",
+				DeployDir: "_ftl",
 				Schema:    "schema.pb",
 				Errors:    "errors.pb",
 				Watch:     []string{"**/*.go", "go.mod", "go.sum", "../../../go-runtime/ftl/**/*.go"},
@@ -48,7 +48,7 @@ func TestDiscoverModules(t *testing.T) {
 				Realm:     "home",
 				Module:    "depcycle1",
 				Deploy:    []string{"main"},
-				DeployDir: ".ftl",
+				DeployDir: "_ftl",
 				Schema:    "schema.pb",
 				Errors:    "errors.pb",
 				Watch:     []string{"**/*.go", "go.mod", "go.sum"},
@@ -61,7 +61,7 @@ func TestDiscoverModules(t *testing.T) {
 				Realm:     "home",
 				Module:    "depcycle2",
 				Deploy:    []string{"main"},
-				DeployDir: ".ftl",
+				DeployDir: "_ftl",
 				Schema:    "schema.pb",
 				Errors:    "errors.pb",
 				Watch:     []string{"**/*.go", "go.mod", "go.sum"},
@@ -100,7 +100,7 @@ func TestDiscoverModules(t *testing.T) {
 				Deploy: []string{
 					"main",
 				},
-				DeployDir: ".ftl",
+				DeployDir: "_ftl",
 				Schema:    "schema.pb",
 				Errors:    "errors.pb",
 				Watch: []string{
@@ -140,7 +140,7 @@ func TestDiscoverModules(t *testing.T) {
 				Realm:     "home",
 				Module:    "highgoversion",
 				Deploy:    []string{"main"},
-				DeployDir: ".ftl",
+				DeployDir: "_ftl",
 				Schema:    "schema.pb",
 				Errors:    "errors.pb",
 				Watch:     []string{"**/*.go", "go.mod", "go.sum", "../../../go-runtime/ftl/**/*.go"},
@@ -153,7 +153,7 @@ func TestDiscoverModules(t *testing.T) {
 				Realm:     "home",
 				Module:    "other",
 				Deploy:    []string{"main"},
-				DeployDir: ".ftl",
+				DeployDir: "_ftl",
 				Schema:    "schema.pb",
 				Errors:    "errors.pb",
 				Watch:     []string{"**/*.go", "go.mod", "go.sum", "../../../go-runtime/ftl/**/*.go"},
diff --git a/buildengine/engine.go b/buildengine/engine.go
index dbc109e15..b9a7b4215 100644
--- a/buildengine/engine.go
+++ b/buildengine/engine.go
@@ -21,7 +21,6 @@ import (
 	ftlv1 "github.com/TBD54566975/ftl/backend/protos/xyz/block/ftl/v1"
 	"github.com/TBD54566975/ftl/backend/protos/xyz/block/ftl/v1/ftlv1connect"
 	"github.com/TBD54566975/ftl/backend/schema"
-	"github.com/TBD54566975/ftl/common/moduleconfig"
 	"github.com/TBD54566975/ftl/internal/log"
 	"github.com/TBD54566975/ftl/internal/rpc"
 	"github.com/TBD54566975/ftl/internal/slices"
@@ -66,7 +65,6 @@ type Listener interface {
 type Engine struct {
 	client           ftlv1connect.ControllerServiceClient
 	moduleMetas      *xsync.MapOf[string, moduleMeta]
-	projectRoot      string
 	moduleDirs       []string
 	watcher          *Watcher
 	controllerSchema *xsync.MapOf[string, *schema.Module]
@@ -99,11 +97,10 @@ func WithListener(listener Listener) Option {
 // pull in missing schemas.
 //
 // "dirs" are directories to scan for local modules.
-func New(ctx context.Context, client ftlv1connect.ControllerServiceClient, projectRoot string, moduleDirs []string, options ...Option) (*Engine, error) {
+func New(ctx context.Context, client ftlv1connect.ControllerServiceClient, moduleDirs []string, options ...Option) (*Engine, error) {
 	ctx = rpc.ContextWithClient(ctx, client)
 	e := &Engine{
 		client:           client,
-		projectRoot:      projectRoot,
 		moduleDirs:       moduleDirs,
 		moduleMetas:      xsync.NewMapOf[string, moduleMeta](),
 		watcher:          NewWatcher(),
@@ -569,21 +566,6 @@ func (e *Engine) buildWithCallback(ctx context.Context, callback buildCallback,
 	}
 	errCh := make(chan error, 1024)
 	for _, group := range topology {
-		groupSchemas := map[string]*schema.Module{}
-		metas, err := e.gatherGroupSchemas(builtModules, group, groupSchemas)
-		if err != nil {
-			return err
-		}
-
-		moduleConfigs := make([]moduleconfig.ModuleConfig, len(metas))
-		for i, meta := range metas {
-			moduleConfigs[i] = meta.module.Config
-		}
-		err = GenerateStubs(ctx, e.projectRoot, maps.Values(groupSchemas), moduleConfigs)
-		if err != nil {
-			return err
-		}
-
 		// Collect schemas to be inserted into "built" map for subsequent groups.
 		schemas := make(chan *schema.Module, len(group))
 
@@ -682,7 +664,7 @@ func (e *Engine) build(ctx context.Context, moduleName string, builtModules map[
 	if e.listener != nil {
 		e.listener.OnBuildStarted(meta.module)
 	}
-	err := Build(ctx, e.projectRoot, sch, meta.module, e.watcher.GetTransaction(meta.module.Config.Dir))
+	err := Build(ctx, sch, meta.module, e.watcher.GetTransaction(meta.module.Config.Dir))
 	if err != nil {
 		return err
 	}
@@ -695,29 +677,6 @@ func (e *Engine) build(ctx context.Context, moduleName string, builtModules map[
 	return nil
 }
 
-// Construct a combined schema for a group of modules and their transitive dependencies.
-func (e *Engine) gatherGroupSchemas(
-	moduleSchemas map[string]*schema.Module,
-	group []string,
-	out map[string]*schema.Module,
-) ([]moduleMeta, error) {
-	var metas []moduleMeta
-	for _, module := range group {
-		if module == "builtin" {
-			continue // Skip the builtin module
-		}
-
-		meta, ok := e.moduleMetas.Load(module)
-		if ok {
-			metas = append(metas, meta)
-			if err := e.gatherSchemas(moduleSchemas, meta.module, out); err != nil {
-				return nil, err
-			}
-		}
-	}
-	return metas, nil
-}
-
 // Construct a combined schema for a module and its transitive dependencies.
 func (e *Engine) gatherSchemas(
 	moduleSchemas map[string]*schema.Module,
diff --git a/buildengine/engine_test.go b/buildengine/engine_test.go
index a44ab8768..73a521134 100644
--- a/buildengine/engine_test.go
+++ b/buildengine/engine_test.go
@@ -16,7 +16,7 @@ func TestEngine(t *testing.T) {
 		t.SkipNow()
 	}
 	ctx := log.ContextWithNewDefaultLogger(context.Background())
-	engine, err := buildengine.New(ctx, nil, t.TempDir(), []string{"testdata/alpha", "testdata/other", "testdata/another"})
+	engine, err := buildengine.New(ctx, nil, []string{"testdata/alpha", "testdata/other", "testdata/another"})
 	assert.NoError(t, err)
 
 	defer engine.Close()
@@ -64,7 +64,7 @@ func TestCycleDetection(t *testing.T) {
 		t.SkipNow()
 	}
 	ctx := log.ContextWithNewDefaultLogger(context.Background())
-	engine, err := buildengine.New(ctx, nil, t.TempDir(), []string{"testdata/depcycle1", "testdata/depcycle2"})
+	engine, err := buildengine.New(ctx, nil, []string{"testdata/depcycle1", "testdata/depcycle2"})
 	assert.NoError(t, err)
 
 	defer engine.Close()
diff --git a/buildengine/stubs.go b/buildengine/stubs.go
deleted file mode 100644
index 911d00d10..000000000
--- a/buildengine/stubs.go
+++ /dev/null
@@ -1,26 +0,0 @@
-package buildengine
-
-import (
-	"context"
-	"fmt"
-
-	"github.com/TBD54566975/ftl/backend/schema"
-	"github.com/TBD54566975/ftl/common/moduleconfig"
-	"github.com/TBD54566975/ftl/go-runtime/compile"
-)
-
-// GenerateStubs generates stubs for the given modules.
-//
-// Currently, only Go stubs are supported. Kotlin and other language stubs can be added in the future.
-func GenerateStubs(ctx context.Context, projectRoot string, modules []*schema.Module, moduleConfigs []moduleconfig.ModuleConfig) error {
-	return generateGoStubs(ctx, projectRoot, modules, moduleConfigs)
-}
-
-func generateGoStubs(ctx context.Context, projectRoot string, modules []*schema.Module, moduleConfigs []moduleconfig.ModuleConfig) error {
-	sch := &schema.Schema{Modules: modules}
-	err := compile.GenerateStubsForModules(ctx, projectRoot, moduleConfigs, sch)
-	if err != nil {
-		return fmt.Errorf("failed to generate Go stubs: %w", err)
-	}
-	return nil
-}
diff --git a/buildengine/stubs_test.go b/buildengine/stubs_test.go
deleted file mode 100644
index c4c1efe5b..000000000
--- a/buildengine/stubs_test.go
+++ /dev/null
@@ -1,250 +0,0 @@
-package buildengine
-
-import (
-	"context"
-	"os"
-	"path/filepath"
-	"testing"
-
-	"github.com/TBD54566975/ftl/backend/schema"
-	"github.com/TBD54566975/ftl/common/moduleconfig"
-	"github.com/TBD54566975/ftl/internal/log"
-	"github.com/alecthomas/assert/v2"
-)
-
-func TestGenerateGoStubs(t *testing.T) {
-	if testing.Short() {
-		t.SkipNow()
-	}
-
-	modules := []*schema.Module{
-		schema.Builtins(),
-		{Name: "other", Decls: []schema.Decl{
-			&schema.Enum{
-				Comments: []string{"This is an enum.", "", "It has 3 variants."},
-				Name:     "Color",
-				Export:   true,
-				Type:     &schema.String{},
-				Variants: []*schema.EnumVariant{
-					{Name: "Red", Value: &schema.StringValue{Value: "Red"}},
-					{Name: "Blue", Value: &schema.StringValue{Value: "Blue"}},
-					{Name: "Green", Value: &schema.StringValue{Value: "Green"}},
-				},
-			},
-			&schema.Enum{
-				Name:   "ColorInt",
-				Export: true,
-				Type:   &schema.Int{},
-				Variants: []*schema.EnumVariant{
-					{Name: "RedInt", Value: &schema.IntValue{Value: 0}},
-					{Name: "BlueInt", Value: &schema.IntValue{Value: 1}},
-					{Name: "GreenInt", Value: &schema.IntValue{Value: 2}},
-				},
-			},
-			&schema.Enum{
-				Comments: []string{"This is type enum."},
-				Name:     "TypeEnum",
-				Export:   true,
-				Variants: []*schema.EnumVariant{
-					{Name: "A", Value: &schema.TypeValue{Value: &schema.Int{}}},
-					{Name: "B", Value: &schema.TypeValue{Value: &schema.String{}}},
-				},
-			},
-			&schema.Data{Name: "EchoRequest", Export: true},
-			&schema.Data{
-				Comments: []string{"This is an echo data response."},
-				Name:     "EchoResponse", Export: true},
-			&schema.Verb{
-				Name:     "echo",
-				Export:   true,
-				Request:  &schema.Ref{Name: "EchoRequest"},
-				Response: &schema.Ref{Name: "EchoResponse"},
-			},
-			&schema.Data{Name: "SinkReq", Export: true},
-			&schema.Verb{
-				Comments: []string{"This is a sink verb.", "", "Here is another line for this comment!"},
-				Name:     "sink",
-				Export:   true,
-				Request:  &schema.Ref{Name: "SinkReq"},
-				Response: &schema.Unit{},
-			},
-			&schema.Data{Name: "SourceResp", Export: true},
-			&schema.Verb{
-				Name:     "source",
-				Export:   true,
-				Request:  &schema.Unit{},
-				Response: &schema.Ref{Name: "SourceResp"},
-			},
-			&schema.Verb{
-				Name:     "nothing",
-				Export:   true,
-				Request:  &schema.Unit{},
-				Response: &schema.Unit{},
-			},
-		}},
-		{Name: "test"},
-	}
-
-	expected := `// Code generated by FTL. DO NOT EDIT.
-
-package other
-
-import (
-  "context"
-
-  "github.com/TBD54566975/ftl/go-runtime/ftl/reflection"
-)
-
-var _ = context.Background
-
-// This is an enum.
-//
-// It has 3 variants.
-//
-//ftl:enum
-type Color string
-const (
-  Red Color = "Red"
-  Blue Color = "Blue"
-  Green Color = "Green"
-)
-
-//ftl:enum
-type ColorInt int
-const (
-  RedInt ColorInt = 0
-  BlueInt ColorInt = 1
-  GreenInt ColorInt = 2
-)
-
-// This is type enum.
-//
-//ftl:enum
-type TypeEnum interface { typeEnum() }
-
-type A int
-
-func (A) typeEnum() {}
-
-type B string
-
-func (B) typeEnum() {}
-
-type EchoRequest struct {
-}
-
-// This is an echo data response.
-//
-type EchoResponse struct {
-}
-
-//ftl:verb
-func Echo(context.Context, EchoRequest) (EchoResponse, error) {
-  panic("Verb stubs should not be called directly, instead use github.com/TBD54566975/ftl/runtime-go/ftl.Call()")
-}
-
-type SinkReq struct {
-}
-
-// This is a sink verb.
-//
-// Here is another line for this comment!
-//
-//ftl:verb
-func Sink(context.Context, SinkReq) error {
-  panic("Verb stubs should not be called directly, instead use github.com/TBD54566975/ftl/runtime-go/ftl.CallSink()")
-}
-
-type SourceResp struct {
-}
-
-//ftl:verb
-func Source(context.Context) (SourceResp, error) {
-  panic("Verb stubs should not be called directly, instead use github.com/TBD54566975/ftl/runtime-go/ftl.CallSource()")
-}
-
-//ftl:verb
-func Nothing(context.Context) error {
-  panic("Verb stubs should not be called directly, instead use github.com/TBD54566975/ftl/runtime-go/ftl.CallEmpty()")
-}
-
-func init() {
-  reflection.Register(
-    reflection.SumType[TypeEnum](
-      *new(A),
-      *new(B),
-    ),
-  )
-}
-`
-
-	ctx := log.ContextWithNewDefaultLogger(context.Background())
-	projectRoot := t.TempDir()
-	err := GenerateStubs(ctx, projectRoot, modules, []moduleconfig.ModuleConfig{})
-	assert.NoError(t, err)
-
-	generatedPath := filepath.Join(projectRoot, ".ftl/go/modules/other/external_module.go")
-	fileContent, err := os.ReadFile(generatedPath)
-	assert.NoError(t, err)
-	assert.Equal(t, expected, string(fileContent))
-}
-
-func TestMetadataImportsExcluded(t *testing.T) {
-	if testing.Short() {
-		t.SkipNow()
-	}
-	modules := []*schema.Module{
-		schema.Builtins(),
-		{Name: "test", Decls: []schema.Decl{
-			&schema.Data{
-				Comments: []string{"Request data type."},
-				Name:     "Req", Export: true},
-			&schema.Data{Name: "Resp", Export: true},
-			&schema.Verb{
-				Comments: []string{"This is a verb."},
-				Name:     "call",
-				Export:   true,
-				Request:  &schema.Ref{Name: "Req"},
-				Response: &schema.Ref{Name: "Resp"},
-				Metadata: []schema.Metadata{
-					&schema.MetadataCalls{Calls: []*schema.Ref{{Name: "verb", Module: "other"}}},
-				},
-			},
-		}},
-	}
-
-	expected := `// Code generated by FTL. DO NOT EDIT.
-
-package test
-
-import (
-  "context"
-)
-
-var _ = context.Background
-
-// Request data type.
-//
-type Req struct {
-}
-
-type Resp struct {
-}
-
-// This is a verb.
-//
-//ftl:verb
-func Call(context.Context, Req) (Resp, error) {
-  panic("Verb stubs should not be called directly, instead use github.com/TBD54566975/ftl/runtime-go/ftl.Call()")
-}
-`
-	ctx := log.ContextWithNewDefaultLogger(context.Background())
-	projectRoot := t.TempDir()
-	err := GenerateStubs(ctx, projectRoot, modules, []moduleconfig.ModuleConfig{})
-	assert.NoError(t, err)
-
-	generatedPath := filepath.Join(projectRoot, ".ftl/go/modules/test/external_module.go")
-	fileContent, err := os.ReadFile(generatedPath)
-	assert.NoError(t, err)
-	assert.Equal(t, expected, string(fileContent))
-}
diff --git a/cmd/ftl/cmd_box.go b/cmd/ftl/cmd_box.go
index 887eefb76..d09214c88 100644
--- a/cmd/ftl/cmd_box.go
+++ b/cmd/ftl/cmd_box.go
@@ -123,7 +123,7 @@ func (b *boxCmd) Run(ctx context.Context, client ftlv1connect.ControllerServiceC
 	if len(b.Dirs) == 0 {
 		return errors.New("no directories specified")
 	}
-	engine, err := buildengine.New(ctx, client, projConfig.Root(), b.Dirs, buildengine.Parallelism(b.Parallelism))
+	engine, err := buildengine.New(ctx, client, b.Dirs, buildengine.Parallelism(b.Parallelism))
 	if err != nil {
 		return err
 	}
diff --git a/cmd/ftl/cmd_box_run.go b/cmd/ftl/cmd_box_run.go
index 0565edd54..0f9cb08b5 100644
--- a/cmd/ftl/cmd_box_run.go
+++ b/cmd/ftl/cmd_box_run.go
@@ -17,7 +17,6 @@ import (
 	"github.com/TBD54566975/ftl/backend/protos/xyz/block/ftl/v1/ftlv1connect"
 	"github.com/TBD54566975/ftl/backend/schema"
 	"github.com/TBD54566975/ftl/buildengine"
-	"github.com/TBD54566975/ftl/common/projectconfig"
 	"github.com/TBD54566975/ftl/internal/bind"
 	"github.com/TBD54566975/ftl/internal/log"
 	"github.com/TBD54566975/ftl/internal/model"
@@ -34,7 +33,7 @@ type boxRunCmd struct {
 	ControllerTimeout time.Duration `help:"Timeout for Controller start." default:"30s"`
 }
 
-func (b *boxRunCmd) Run(ctx context.Context, projConfig projectconfig.Config) error {
+func (b *boxRunCmd) Run(ctx context.Context) error {
 	conn, err := databasetesting.CreateForDevel(ctx, b.DSN, b.Recreate)
 	if err != nil {
 		return fmt.Errorf("failed to create database: %w", err)
@@ -75,7 +74,7 @@ func (b *boxRunCmd) Run(ctx context.Context, projConfig projectconfig.Config) er
 		return fmt.Errorf("controller failed to start: %w", err)
 	}
 
-	engine, err := buildengine.New(ctx, client, projConfig.Root(), []string{b.Dir})
+	engine, err := buildengine.New(ctx, client, []string{b.Dir})
 	if err != nil {
 		return fmt.Errorf("failed to create build engine: %w", err)
 	}
diff --git a/cmd/ftl/cmd_build.go b/cmd/ftl/cmd_build.go
index a3f13869b..35e826e74 100644
--- a/cmd/ftl/cmd_build.go
+++ b/cmd/ftl/cmd_build.go
@@ -22,7 +22,7 @@ func (b *buildCmd) Run(ctx context.Context, client ftlv1connect.ControllerServic
 	if len(b.Dirs) == 0 {
 		return errors.New("no directories specified")
 	}
-	engine, err := buildengine.New(ctx, client, projConfig.Root(), b.Dirs, buildengine.Parallelism(b.Parallelism))
+	engine, err := buildengine.New(ctx, client, b.Dirs, buildengine.Parallelism(b.Parallelism))
 	if err != nil {
 		return err
 	}
diff --git a/cmd/ftl/cmd_deploy.go b/cmd/ftl/cmd_deploy.go
index a50c7f25f..0ecd47a6e 100644
--- a/cmd/ftl/cmd_deploy.go
+++ b/cmd/ftl/cmd_deploy.go
@@ -5,7 +5,6 @@ import (
 
 	"github.com/TBD54566975/ftl/backend/protos/xyz/block/ftl/v1/ftlv1connect"
 	"github.com/TBD54566975/ftl/buildengine"
-	"github.com/TBD54566975/ftl/common/projectconfig"
 	"github.com/TBD54566975/ftl/internal/rpc"
 )
 
@@ -16,9 +15,9 @@ type deployCmd struct {
 	NoWait      bool     `help:"Do not wait for deployment to complete." default:"false"`
 }
 
-func (d *deployCmd) Run(ctx context.Context, projConfig projectconfig.Config) error {
+func (d *deployCmd) Run(ctx context.Context) error {
 	client := rpc.ClientFromContext[ftlv1connect.ControllerServiceClient](ctx)
-	engine, err := buildengine.New(ctx, client, projConfig.Root(), d.Dirs, buildengine.Parallelism(d.Parallelism))
+	engine, err := buildengine.New(ctx, client, d.Dirs, buildengine.Parallelism(d.Parallelism))
 	if err != nil {
 		return err
 	}
diff --git a/cmd/ftl/cmd_dev.go b/cmd/ftl/cmd_dev.go
index e596d84fa..2741faecf 100644
--- a/cmd/ftl/cmd_dev.go
+++ b/cmd/ftl/cmd_dev.go
@@ -89,7 +89,7 @@ func (d *devCmd) Run(ctx context.Context, projConfig projectconfig.Config) error
 			})
 		}
 
-		engine, err := buildengine.New(ctx, client, projConfig.Root(), d.Dirs, opts...)
+		engine, err := buildengine.New(ctx, client, d.Dirs, opts...)
 		if err != nil {
 			return err
 		}
diff --git a/cmd/ftl/cmd_init.go b/cmd/ftl/cmd_init.go
index b2cafb64e..b39463979 100644
--- a/cmd/ftl/cmd_init.go
+++ b/cmd/ftl/cmd_init.go
@@ -86,7 +86,7 @@ func updateGitIgnore(ctx context.Context, gitRoot string) error {
 
 	scanner := bufio.NewScanner(f)
 	for scanner.Scan() {
-		if strings.TrimSpace(scanner.Text()) == "**/.ftl" {
+		if strings.TrimSpace(scanner.Text()) == "**/_ftl" {
 			return nil
 		}
 	}
@@ -96,7 +96,7 @@ func updateGitIgnore(ctx context.Context, gitRoot string) error {
 	}
 
 	// append if not already present
-	if _, err = f.WriteString("**/.ftl\n"); err != nil {
+	if _, err = f.WriteString("**/_ftl\n"); err != nil {
 		return err
 	}
 
diff --git a/cmd/ftl/cmd_new.go b/cmd/ftl/cmd_new.go
index 1afa32ad1..831364a03 100644
--- a/cmd/ftl/cmd_new.go
+++ b/cmd/ftl/cmd_new.go
@@ -9,7 +9,6 @@ import (
 	"os"
 	"path/filepath"
 	"regexp"
-	"runtime"
 	"strings"
 
 	"github.com/TBD54566975/scaffolder"
@@ -31,10 +30,9 @@ type newCmd struct {
 }
 
 type newGoCmd struct {
-	Replace   map[string]string `short:"r" help:"Replace a module import path with a local path in the initialised FTL module." placeholder:"OLD=NEW,..." env:"FTL_INIT_GO_REPLACE"`
-	Dir       string            `arg:"" help:"Directory to initialize the module in."`
-	Name      string            `arg:"" help:"Name of the FTL module to create underneath the base directory."`
-	GoVersion string
+	Replace map[string]string `short:"r" help:"Replace a module import path with a local path in the initialised FTL module." placeholder:"OLD=NEW,..." env:"FTL_INIT_GO_REPLACE"`
+	Dir     string            `arg:"" help:"Directory to initialize the module in."`
+	Name    string            `arg:"" help:"Name of the FTL module to create underneath the base directory."`
 }
 
 type newKotlinCmd struct {
@@ -60,8 +58,6 @@ func (i newGoCmd) Run(ctx context.Context) error {
 
 	logger := log.FromContext(ctx)
 	logger.Debugf("Creating FTL Go module %q in %s", name, path)
-
-	i.GoVersion = runtime.Version()[2:]
 	if err := scaffold(ctx, config.Hermit, goruntime.Files(), i.Dir, i, scaffolder.Exclude("^go.mod$")); err != nil {
 		return err
 	}
diff --git a/common/moduleconfig/moduleconfig.go b/common/moduleconfig/moduleconfig.go
index 990e96b73..dddad5134 100644
--- a/common/moduleconfig/moduleconfig.go
+++ b/common/moduleconfig/moduleconfig.go
@@ -133,7 +133,7 @@ func setConfigDefaults(moduleDir string, config *ModuleConfig) error {
 
 	case "go":
 		if config.DeployDir == "" {
-			config.DeployDir = ".ftl"
+			config.DeployDir = "_ftl"
 		}
 		if len(config.Deploy) == 0 {
 			config.Deploy = []string{"main"}
diff --git a/extensions/vscode/package-lock.json b/extensions/vscode/package-lock.json
index a539cf6ee..dbc72146e 100644
--- a/extensions/vscode/package-lock.json
+++ b/extensions/vscode/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "ftl",
-  "version": "0.0.0",
+  "version": "0.1.2",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "ftl",
-      "version": "0.0.0",
+      "version": "0.1.2",
       "dependencies": {
         "lookpath": "^1.2.2",
         "semver": "^7.6.0",
diff --git a/go-runtime/compile/build-template/.ftl.tmpl/go/main/go.mod.tmpl b/go-runtime/compile/build-template/_ftl.tmpl/go/main/go.mod.tmpl
similarity index 94%
rename from go-runtime/compile/build-template/.ftl.tmpl/go/main/go.mod.tmpl
rename to go-runtime/compile/build-template/_ftl.tmpl/go/main/go.mod.tmpl
index df0b6eca7..56b07af1f 100644
--- a/go-runtime/compile/build-template/.ftl.tmpl/go/main/go.mod.tmpl
+++ b/go-runtime/compile/build-template/_ftl.tmpl/go/main/go.mod.tmpl
@@ -8,4 +8,4 @@ require github.com/TBD54566975/ftl v{{ .FTLVersion }}
 
 {{- range .Replacements }}
 replace {{ .Old }} => {{ .New }}
-{{- end }}
+{{- end }}
\ No newline at end of file
diff --git a/go-runtime/compile/build-template/.ftl.tmpl/go/main/main.go.tmpl b/go-runtime/compile/build-template/_ftl.tmpl/go/main/main.go
similarity index 100%
rename from go-runtime/compile/build-template/.ftl.tmpl/go/main/main.go.tmpl
rename to go-runtime/compile/build-template/_ftl.tmpl/go/main/main.go
diff --git a/go-runtime/compile/build-template/go.work.tmpl b/go-runtime/compile/build-template/go.work.tmpl
index cbd6143cf..683cd1d34 100644
--- a/go-runtime/compile/build-template/go.work.tmpl
+++ b/go-runtime/compile/build-template/go.work.tmpl
@@ -2,8 +2,6 @@ go {{ .GoVersion }}
 
 use (
 	.
-{{- range .SharedModulesPaths }}
-    {{ . }}
-{{- end }}
-	.ftl/go/main
+	_ftl/go/modules
+	_ftl/go/main
 )
diff --git a/go-runtime/compile/build.go b/go-runtime/compile/build.go
index 4b3774294..4a234a356 100644
--- a/go-runtime/compile/build.go
+++ b/go-runtime/compile/build.go
@@ -3,6 +3,7 @@ package compile
 import (
 	"context"
 	"fmt"
+	"maps"
 	"os"
 	"path"
 	"path/filepath"
@@ -14,7 +15,7 @@ import (
 	"unicode"
 
 	sets "github.com/deckarep/golang-set/v2"
-	"golang.org/x/exp/maps"
+	gomaps "golang.org/x/exp/maps"
 	"golang.org/x/mod/modfile"
 	"golang.org/x/mod/semver"
 	"golang.org/x/sync/errgroup"
@@ -34,16 +35,12 @@ import (
 	"github.com/TBD54566975/ftl/internal/reflect"
 )
 
-type MainWorkContext struct {
-	GoVersion          string
-	SharedModulesPaths []string
-}
-
 type ExternalModuleContext struct {
+	ModuleDir string
 	*schema.Schema
 	GoVersion    string
 	FTLVersion   string
-	Module       *schema.Module
+	Main         string
 	Replacements []*modfile.Replace
 }
 
@@ -56,14 +53,13 @@ type goVerb struct {
 }
 
 type mainModuleContext struct {
-	GoVersion          string
-	FTLVersion         string
-	Name               string
-	SharedModulesPaths []string
-	Verbs              []goVerb
-	Replacements       []*modfile.Replace
-	SumTypes           []goSumType
-	LocalSumTypes      []goSumType
+	GoVersion     string
+	FTLVersion    string
+	Name          string
+	Verbs         []goVerb
+	Replacements  []*modfile.Replace
+	SumTypes      []goSumType
+	LocalSumTypes []goSumType
 }
 
 type goSumType struct {
@@ -83,14 +79,25 @@ type ModifyFilesTransaction interface {
 	End() error
 }
 
-const buildDirName = ".ftl"
+func (b ExternalModuleContext) NonMainModules() []*schema.Module {
+	modules := make([]*schema.Module, 0, len(b.Modules))
+	for _, module := range b.Modules {
+		if module.Name == b.Main {
+			continue
+		}
+		modules = append(modules, module)
+	}
+	return modules
+}
+
+const buildDirName = "_ftl"
 
 func buildDir(moduleDir string) string {
 	return filepath.Join(moduleDir, buildDirName)
 }
 
 // Build the given module.
-func Build(ctx context.Context, projectRootDir, moduleDir string, sch *schema.Schema, filesTransaction ModifyFilesTransaction) (err error) {
+func Build(ctx context.Context, moduleDir string, sch *schema.Schema, filesTransaction ModifyFilesTransaction) (err error) {
 	if err := filesTransaction.Begin(); err != nil {
 		return err
 	}
@@ -123,27 +130,19 @@ func Build(ctx context.Context, projectRootDir, moduleDir string, sch *schema.Sc
 
 	funcs := maps.Clone(scaffoldFuncs)
 
-	buildDir := buildDir(moduleDir)
-	err = os.MkdirAll(buildDir, 0750)
-	if err != nil {
-		return fmt.Errorf("failed to create build directory: %w", err)
-	}
-
-	var sharedModulesPaths []string
-	for _, mod := range sch.Modules {
-		if mod.Name == config.Module {
-			continue
-		}
-		sharedModulesPaths = append(sharedModulesPaths, filepath.Join(projectRootDir, buildDirName, "go", "modules", mod.Name))
-	}
-
-	if err := internal.ScaffoldZip(mainWorkTemplateFiles(), moduleDir, MainWorkContext{
-		GoVersion:          goModVersion,
-		SharedModulesPaths: sharedModulesPaths,
-	}, scaffolder.Exclude("^go.mod$"), scaffolder.Functions(funcs)); err != nil {
-		return fmt.Errorf("failed to scaffold zip: %w", err)
+	logger.Debugf("Generating external modules")
+	if err := generateExternalModules(ExternalModuleContext{
+		ModuleDir:    moduleDir,
+		GoVersion:    goModVersion,
+		FTLVersion:   ftlVersion,
+		Schema:       sch,
+		Main:         config.Module,
+		Replacements: replacements,
+	}); err != nil {
+		return fmt.Errorf("failed to generate external modules: %w", err)
 	}
 
+	buildDir := buildDir(moduleDir)
 	logger.Debugf("Extracting schema")
 	result, err := ExtractModuleSchema(config.Dir, sch)
 	if err != nil {
@@ -187,14 +186,13 @@ func Build(ctx context.Context, projectRootDir, moduleDir string, sch *schema.Sc
 		goVerbs = append(goVerbs, goverb)
 	}
 	if err := internal.ScaffoldZip(buildTemplateFiles(), moduleDir, mainModuleContext{
-		GoVersion:          goModVersion,
-		FTLVersion:         ftlVersion,
-		Name:               result.Module.Name,
-		SharedModulesPaths: sharedModulesPaths,
-		Verbs:              goVerbs,
-		Replacements:       replacements,
-		SumTypes:           getSumTypes(result.Module, sch, result.NativeNames),
-		LocalSumTypes:      getLocalSumTypes(result.Module),
+		GoVersion:     goModVersion,
+		FTLVersion:    ftlVersion,
+		Name:          result.Module.Name,
+		Verbs:         goVerbs,
+		Replacements:  replacements,
+		SumTypes:      getSumTypes(result.Module, sch, result.NativeNames),
+		LocalSumTypes: getLocalSumTypes(result.Module),
 	}, scaffolder.Exclude("^go.mod$"), scaffolder.Functions(funcs)); err != nil {
 		return err
 	}
@@ -202,7 +200,7 @@ func Build(ctx context.Context, projectRootDir, moduleDir string, sch *schema.Sc
 	logger.Debugf("Tidying go.mod files")
 	wg, wgctx := errgroup.WithContext(ctx)
 	wg.Go(func() error {
-		if err := exec.Command(wgctx, log.Debug, moduleDir, "go", "mod", "tidy").RunBuffered(wgctx); err != nil {
+		if err := exec.Command(ctx, log.Debug, moduleDir, "go", "mod", "tidy").RunBuffered(ctx); err != nil {
 			return fmt.Errorf("%s: failed to tidy go.mod: %w", moduleDir, err)
 		}
 		return filesTransaction.ModifiedFiles(filepath.Join(moduleDir, "go.mod"), filepath.Join(moduleDir, "go.sum"))
@@ -214,6 +212,13 @@ func Build(ctx context.Context, projectRootDir, moduleDir string, sch *schema.Sc
 		}
 		return filesTransaction.ModifiedFiles(filepath.Join(mainDir, "go.mod"), filepath.Join(moduleDir, "go.sum"))
 	})
+	modulesDir := filepath.Join(buildDir, "go", "modules")
+	wg.Go(func() error {
+		if err := exec.Command(wgctx, log.Debug, modulesDir, "go", "mod", "tidy").RunBuffered(wgctx); err != nil {
+			return fmt.Errorf("%s: failed to tidy go.mod: %w", modulesDir, err)
+		}
+		return filesTransaction.ModifiedFiles(filepath.Join(modulesDir, "go.mod"), filepath.Join(moduleDir, "go.sum"))
+	})
 	if err := wg.Wait(); err != nil {
 		return err
 	}
@@ -222,16 +227,10 @@ func Build(ctx context.Context, projectRootDir, moduleDir string, sch *schema.Sc
 	return exec.Command(ctx, log.Debug, mainDir, "go", "build", "-o", "../../main", ".").RunBuffered(ctx)
 }
 
-func GenerateStubsForModules(ctx context.Context, projectRoot string, moduleConfigs []moduleconfig.ModuleConfig, sch *schema.Schema) error {
-	logger := log.FromContext(ctx)
-	logger.Debugf("Generating stubs for modules")
-
-	sharedFtlDir := filepath.Join(projectRoot, buildDirName)
-
-	// Wipe the modules directory to ensure we don't have any stale modules.
-	err := os.RemoveAll(sharedFtlDir)
+func GenerateStubsForExternalLibrary(ctx context.Context, dir string, schema *schema.Schema) error {
+	goModFile, replacements, err := goModFileWithReplacements(filepath.Join(dir, "go.mod"))
 	if err != nil {
-		return fmt.Errorf("failed to remove %s: %w", sharedFtlDir, err)
+		return fmt.Errorf("failed to propagate replacements for library %q: %w", dir, err)
 	}
 
 	ftlVersion := ""
@@ -239,64 +238,27 @@ func GenerateStubsForModules(ctx context.Context, projectRoot string, moduleConf
 		ftlVersion = ftl.Version
 	}
 
-	for _, module := range sch.Modules {
-		var moduleConfig *moduleconfig.ModuleConfig
-		for _, mc := range moduleConfigs {
-			mcCopy := mc
-			if mc.Module == module.Name {
-				moduleConfig = &mcCopy
-				break
-			}
-		}
-
-		var goModVersion string
-		var replacements []*modfile.Replace
-
-		// If there's no module config, use the go.mod file for the first config we find.
-		if moduleConfig == nil {
-			if len(moduleConfigs) > 0 {
-				_, goModVersion, err = updateGoModule(filepath.Join(moduleConfigs[0].Dir, "go.mod"))
-				if err != nil {
-					return err
-				}
-			} else {
-				// The best we can do here if we don't have a module to read from is to use the current Go version.
-				goModVersion = runtime.Version()[2:]
-			}
-
-			replacements = []*modfile.Replace{}
-		} else {
-			replacements, goModVersion, err = updateGoModule(filepath.Join(moduleConfig.Dir, "go.mod"))
-			if err != nil {
-				return err
-			}
-		}
-
-		goVersion := runtime.Version()[2:]
-		if semver.Compare("v"+goVersion, "v"+goModVersion) < 0 {
-			return fmt.Errorf("go version %q is not recent enough for this module, needs minimum version %q", goVersion, goModVersion)
-		}
-
-		context := ExternalModuleContext{
-			Schema:       sch,
-			GoVersion:    goModVersion,
-			FTLVersion:   ftlVersion,
-			Module:       module,
-			Replacements: replacements,
-		}
-
-		funcs := maps.Clone(scaffoldFuncs)
-		err = internal.ScaffoldZip(externalModuleTemplateFiles(), projectRoot, context, scaffolder.Exclude("^go.mod$"), scaffolder.Functions(funcs))
-		if err != nil {
-			return fmt.Errorf("failed to scaffold zip: %w", err)
-		}
+	return generateExternalModules(ExternalModuleContext{
+		ModuleDir:    dir,
+		GoVersion:    goModFile.Go.Version,
+		FTLVersion:   ftlVersion,
+		Schema:       schema,
+		Replacements: replacements,
+	})
+}
 
-		modulesDir := filepath.Join(sharedFtlDir, "go", "modules", module.Name)
-		if err := exec.Command(ctx, log.Debug, modulesDir, "go", "mod", "tidy").RunBuffered(ctx); err != nil {
-			return fmt.Errorf("failed to tidy go.mod: %w", err)
-		}
+func generateExternalModules(context ExternalModuleContext) error {
+	// Wipe the modules directory to ensure we don't have any stale modules.
+	err := os.RemoveAll(filepath.Join(buildDir(context.ModuleDir), "go", "modules"))
+	if err != nil {
+		return fmt.Errorf("could not remove old external modules: %w", err)
 	}
 
+	funcs := maps.Clone(scaffoldFuncs)
+	err = internal.ScaffoldZip(externalModuleTemplateFiles(), context.ModuleDir, context, scaffolder.Exclude("^go.mod$"), scaffolder.Functions(funcs))
+	if err != nil {
+		return fmt.Errorf("failed to scaffold external modules: %w", err)
+	}
 	return nil
 }
 
@@ -613,7 +575,7 @@ func getLocalSumTypes(module *schema.Module) []goSumType {
 			}
 		}
 	}
-	out := maps.Values(sumTypes)
+	out := gomaps.Values(sumTypes)
 	slices.SortFunc(out, func(a, b goSumType) int {
 		return strings.Compare(a.Discriminator, b.Discriminator)
 	})
@@ -656,7 +618,7 @@ func getSumTypes(module *schema.Module, sch *schema.Schema, nativeNames NativeNa
 			Variants:      variants,
 		}
 	}
-	out := maps.Values(sumTypes)
+	out := gomaps.Values(sumTypes)
 	slices.SortFunc(out, func(a, b goSumType) int {
 		return strings.Compare(a.Discriminator, b.Discriminator)
 	})
diff --git a/go-runtime/compile/devel.go b/go-runtime/compile/devel.go
index 345309da6..c6f2f6270 100644
--- a/go-runtime/compile/devel.go
+++ b/go-runtime/compile/devel.go
@@ -8,14 +8,9 @@ import (
 	"github.com/TBD54566975/ftl/internal"
 )
 
-func mainWorkTemplateFiles() *zip.Reader {
-	return internal.ZipRelativeToCaller("main-work-template")
-}
-
 func externalModuleTemplateFiles() *zip.Reader {
 	return internal.ZipRelativeToCaller("external-module-template")
 }
-
 func buildTemplateFiles() *zip.Reader {
 	return internal.ZipRelativeToCaller("build-template")
 }
diff --git a/go-runtime/compile/external-module-template/.ftl/go/modules/{{ .Module.Name }}/go.mod.tmpl b/go-runtime/compile/external-module-template/_ftl/go/modules/go.mod.tmpl
similarity index 80%
rename from go-runtime/compile/external-module-template/.ftl/go/modules/{{ .Module.Name }}/go.mod.tmpl
rename to go-runtime/compile/external-module-template/_ftl/go/modules/go.mod.tmpl
index be3d76079..2f1d05e47 100644
--- a/go-runtime/compile/external-module-template/.ftl/go/modules/{{ .Module.Name }}/go.mod.tmpl	
+++ b/go-runtime/compile/external-module-template/_ftl/go/modules/go.mod.tmpl
@@ -1,4 +1,4 @@
-module ftl/{{ .Module.Name }}
+module ftl
 
 go {{ .GoVersion }}
 
@@ -8,4 +8,4 @@ require github.com/TBD54566975/ftl v{{ .FTLVersion }}
 
 {{- range .Replacements }}
 replace {{ .Old }} => {{ .New }}
-{{- end }}
+{{- end }}
\ No newline at end of file
diff --git a/go-runtime/compile/external-module-template/.ftl/go/modules/{{ .Module.Name }}/external_module.go.tmpl b/go-runtime/compile/external-module-template/_ftl/go/modules/{{ range .NonMainModules }}{{ push .Name . }}{{ end }}/external_module.go.tmpl
similarity index 66%
rename from go-runtime/compile/external-module-template/.ftl/go/modules/{{ .Module.Name }}/external_module.go.tmpl
rename to go-runtime/compile/external-module-template/_ftl/go/modules/{{ range .NonMainModules }}{{ push .Name . }}{{ end }}/external_module.go.tmpl
index 657e8f20a..a7c7c1b2d 100644
--- a/go-runtime/compile/external-module-template/.ftl/go/modules/{{ .Module.Name }}/external_module.go.tmpl	
+++ b/go-runtime/compile/external-module-template/_ftl/go/modules/{{ range .NonMainModules }}{{ push .Name . }}{{ end }}/external_module.go.tmpl	
@@ -1,13 +1,13 @@
 // Code generated by FTL. DO NOT EDIT.
 
-package {{.Module.Name}}
+package {{.Name}}
 
 import (
   "context"
-{{- range $import, $alias := (.Module | imports)}}
+{{- range $import, $alias := (.|imports)}}
   {{if $alias}}{{$alias}} {{end}}"{{$import}}"
 {{- end}}
-{{- $sumTypes := (.Module | sumTypes)}}
+{{- $sumTypes := $ | sumTypes}}
 {{- if $sumTypes}}
 
   "github.com/TBD54566975/ftl/go-runtime/ftl/reflection"
@@ -16,18 +16,18 @@ import (
 
 var _ = context.Background
 
-{{- range .Module.Decls }}
+{{- range .Decls }}
 {{- if .IsExported}}
 {{if .Comments}}
 {{.Comments|comment -}}
 //
 {{- end}}
 {{- if is "Topic" .}}
-var {{.Name|title}} = ftl.Topic[{{type $.Module .Event}}]("{{.Name}}")
+var {{.Name|title}} = ftl.Topic[{{type $ .Event}}]("{{.Name}}")
 {{- else if and (is "Enum" .) .IsValueEnum}}
 {{- $enumName := .Name}}
 //ftl:enum
-type {{.Name|title}} {{type $.Module .Type}}
+type {{.Name|title}} {{type $ .Type}}
 const (
   {{- range .Variants }}
   {{.Name|title}} {{$enumName}} = {{.Value|value}}
@@ -38,14 +38,14 @@ const (
 {{$enumInterfaceFuncName := enumInterfaceFunc . -}}
 type {{.Name|title}} interface { {{$enumInterfaceFuncName}}() }
 {{- range .Variants }}
-{{if (or (basicType $.Module .) (isStandaloneEnumVariant .))}}
-type {{.Name|title}} {{type $.Module .Value.Value}}
+{{if (or (basicType $ .) (isStandaloneEnumVariant .))}}
+type {{.Name|title}} {{type $ .Value.Value}}
 {{end}}
 func ({{.Name|title}}) {{$enumInterfaceFuncName}}() {}
 {{- end}}
 {{- else if is "TypeAlias" .}}
 //ftl:typealias
-type {{.Name|title}} {{type $.Module .Type}}
+type {{.Name|title}} {{type $ .Type}}
 {{- else if is "Data" .}}
 type {{.Name|title}}
 {{- if .TypeParameters}}[
@@ -54,25 +54,25 @@ type {{.Name|title}}
 {{- end -}}
 ]{{- end}} struct {
   {{- range .Fields}}
-  {{.Name|title}} {{type $.Module .Type}} `json:"{{.Name}}"`
+  {{.Name|title}} {{type $ .Type}} `json:"{{.Name}}"`
   {{- end}}
 }
 {{- else if is "Verb" .}}
 //ftl:verb
-{{- if and (eq (type $.Module .Request) "ftl.Unit") (eq (type $.Module .Response) "ftl.Unit")}}
+{{- if and (eq (type $ .Request) "ftl.Unit") (eq (type $ .Response) "ftl.Unit")}}
 func {{.Name|title}}(context.Context) error {
   panic("Verb stubs should not be called directly, instead use github.com/TBD54566975/ftl/runtime-go/ftl.CallEmpty()")
 }
-{{- else if eq (type $.Module .Request) "ftl.Unit"}}
-func {{.Name|title}}(context.Context) ({{type $.Module .Response}}, error) {
+{{- else if eq (type $ .Request) "ftl.Unit"}}
+func {{.Name|title}}(context.Context) ({{type $ .Response}}, error) {
   panic("Verb stubs should not be called directly, instead use github.com/TBD54566975/ftl/runtime-go/ftl.CallSource()")
 }
-{{- else if eq (type $.Module .Response) "ftl.Unit"}}
-func {{.Name|title}}(context.Context, {{type $.Module .Request}}) error {
+{{- else if eq (type $ .Response) "ftl.Unit"}}
+func {{.Name|title}}(context.Context, {{type $ .Request}}) error {
   panic("Verb stubs should not be called directly, instead use github.com/TBD54566975/ftl/runtime-go/ftl.CallSink()")
 }
 {{- else}}
-func {{.Name|title}}(context.Context, {{type $.Module .Request}}) ({{type $.Module .Response}}, error) {
+func {{.Name|title}}(context.Context, {{type $ .Request}}) ({{type $ .Response}}, error) {
   panic("Verb stubs should not be called directly, instead use github.com/TBD54566975/ftl/runtime-go/ftl.Call()")
 }
 {{- end}}
diff --git a/go-runtime/compile/external-module-template/go.mod b/go-runtime/compile/external-module-template/go.mod
new file mode 100644
index 000000000..8da40da65
--- /dev/null
+++ b/go-runtime/compile/external-module-template/go.mod
@@ -0,0 +1,3 @@
+module exclude
+
+go 1.22.2
diff --git a/go-runtime/compile/external-module-template/go.work.tmpl b/go-runtime/compile/external-module-template/go.work.tmpl
new file mode 100644
index 000000000..204b39b25
--- /dev/null
+++ b/go-runtime/compile/external-module-template/go.work.tmpl
@@ -0,0 +1,6 @@
+go {{ .GoVersion }}
+
+use (
+	.
+	_ftl/go/modules
+)
diff --git a/go-runtime/compile/main-work-template/go.work.tmpl b/go-runtime/compile/main-work-template/go.work.tmpl
deleted file mode 100644
index 1dbed607a..000000000
--- a/go-runtime/compile/main-work-template/go.work.tmpl
+++ /dev/null
@@ -1,8 +0,0 @@
-go {{ .GoVersion }}
-
-use (
-	.
-{{- range .SharedModulesPaths }}
-    {{ . }}
-{{- end }}
-)
diff --git a/go-runtime/compile/release.go b/go-runtime/compile/release.go
index a258dd217..8b909688c 100644
--- a/go-runtime/compile/release.go
+++ b/go-runtime/compile/release.go
@@ -8,23 +8,12 @@ import (
 	_ "embed"
 )
 
-//go:embed main-work-template.zip
-var mainWorkTemplateBytes []byte
-
 //go:embed external-module-template.zip
 var externalModuleTemplateBytes []byte
 
 //go:embed build-template.zip
 var buildTemplateBytes []byte
 
-func mainWorkTemplateFiles() *zip.Reader {
-	zr, err := zip.NewReader(bytes.NewReader(mainWorkTemplateBytes), int64(len(mainWorkTemplateBytes)))
-	if err != nil {
-		panic(err)
-	}
-	return zr
-}
-
 func externalModuleTemplateFiles() *zip.Reader {
 	zr, err := zip.NewReader(bytes.NewReader(externalModuleTemplateBytes), int64(len(externalModuleTemplateBytes)))
 	if err != nil {
diff --git a/go-runtime/compile/schema_test.go b/go-runtime/compile/schema_test.go
index abbc0d83d..8c974259b 100644
--- a/go-runtime/compile/schema_test.go
+++ b/go-runtime/compile/schema_test.go
@@ -56,7 +56,7 @@ func TestExtractModuleSchema(t *testing.T) {
 	assert.NoError(t, err)
 	actual := schema.Normalise(r.Module)
 	expected := `module one {
-  config configValue one.Config 
+  config configValue one.Config
   secret secretValue String
 
   database postgres testDb
@@ -184,9 +184,6 @@ func TestExtractModuleSchemaTwo(t *testing.T) {
 	if testing.Short() {
 		t.SkipNow()
 	}
-
-	assert.NoError(t, prebuildTestModule(t, "testdata/two"))
-
 	r, err := ExtractModuleSchema("testdata/two", &schema.Schema{})
 	assert.NoError(t, err)
 	assert.Equal(t, r.Errors, nil)
@@ -368,9 +365,6 @@ func TestExtractModulePubSub(t *testing.T) {
 	if testing.Short() {
 		t.SkipNow()
 	}
-
-	assert.NoError(t, prebuildTestModule(t, "testdata/pubsub"))
-
 	r, err := ExtractModuleSchema("testdata/pubsub", &schema.Schema{})
 	assert.NoError(t, err)
 	assert.Equal(t, nil, r.Errors, "expected no schema errors")
diff --git a/go-runtime/scaffolding/{{ .Name | camel | lower }}/go.mod.tmpl b/go-runtime/scaffolding/{{ .Name | camel | lower }}/go.mod.tmpl
index 7d6b63f1d..372814bd3 100644
--- a/go-runtime/scaffolding/{{ .Name | camel | lower }}/go.mod.tmpl	
+++ b/go-runtime/scaffolding/{{ .Name | camel | lower }}/go.mod.tmpl	
@@ -1,9 +1,9 @@
 module ftl/{{ .Name }}
 
-go {{ .GoVersion }}
+go 1.21
 
 require github.com/TBD54566975/ftl latest
 
 {{- range $old, $new := .Replace }}
 replace {{ $old }} => {{ $new }}
-{{- end }}
+{{- end }}
\ No newline at end of file
diff --git a/integration/harness.go b/integration/harness.go
index 6cb0af336..d4c55fc95 100644
--- a/integration/harness.go
+++ b/integration/harness.go
@@ -17,7 +17,6 @@ import (
 	"connectrpc.com/connect"
 	"github.com/alecthomas/assert/v2"
 	"github.com/alecthomas/types/optional"
-	"github.com/otiai10/copy"
 
 	ftlv1 "github.com/TBD54566975/ftl/backend/protos/xyz/block/ftl/v1"
 	"github.com/TBD54566975/ftl/backend/protos/xyz/block/ftl/v1/ftlv1connect"
@@ -74,23 +73,11 @@ func run(t *testing.T, ftlConfigPath string, startController bool, actions ...Ac
 	assert.True(t, ok)
 
 	if ftlConfigPath != "" {
-		ftlConfigPath = filepath.Join(cwd, "testdata", "go", ftlConfigPath)
-		projectPath := filepath.Join(tmpDir, "ftl-project.toml")
-
-		// Copy the specified FTL config to the temporary directory.
-		err = copy.Copy(ftlConfigPath, projectPath)
-		if err == nil {
-			t.Setenv("FTL_CONFIG", projectPath)
-		} else {
-			// Use a path into the testdata directory instead of one relative to
-			// tmpDir. Otherwise we have a chicken and egg situation where the config
-			// can't be loaded until the module is copied over, and the config itself
-			// is used by FTL during startup.
-			// Some tests still rely on this behavior, so we can't remove it entirely.
-			t.Logf("Failed to copy %s to %s: %s", ftlConfigPath, projectPath, err)
-			t.Setenv("FTL_CONFIG", ftlConfigPath)
-		}
-
+		// Use a path into the testdata directory instead of one relative to
+		// tmpDir. Otherwise we have a chicken and egg situation where the config
+		// can't be loaded until the module is copied over, and the config itself
+		// is used by FTL during startup.
+		t.Setenv("FTL_CONFIG", filepath.Join(cwd, "testdata", "go", ftlConfigPath))
 	} else {
 		err = os.WriteFile(filepath.Join(tmpDir, "ftl-project.toml"), []byte(`name = "integration"`), 0644)
 		assert.NoError(t, err)