diff --git a/agentuity.schema.json b/agentuity.schema.json
index b1644407..c2617378 100644
--- a/agentuity.schema.json
+++ b/agentuity.schema.json
@@ -220,4 +220,4 @@
 			"description": "The agents that are part of this project"
 		}
 	}
-}
\ No newline at end of file
+}
diff --git a/cmd/project.go b/cmd/project.go
index b97732ac..995c6819 100644
--- a/cmd/project.go
+++ b/cmd/project.go
@@ -38,6 +38,31 @@ Use the subcommands to manage your projects.`,
 	},
 }
 
+// detectRuntime auto-detects the runtime based on lockfiles in the directory
+// If no lockfile is found, falls back to the default runtime from the template
+func detectRuntime(dir string, defaultRuntime string) string {
+	// Only auto-detect for JavaScript-based runtimes
+	if defaultRuntime != "nodejs" && defaultRuntime != "bunjs" {
+		return defaultRuntime
+	}
+
+	// Check for bun lockfiles - use bunjs runtime
+	if util.Exists(filepath.Join(dir, "bun.lockb")) ||
+		util.Exists(filepath.Join(dir, "bun.lock")) {
+		return "bunjs"
+	}
+
+	// Check for nodejs runtime
+	if util.Exists(filepath.Join(dir, "pnpm-lock.yaml")) ||
+		util.Exists(filepath.Join(dir, "package-lock.json")) ||
+		util.Exists(filepath.Join(dir, "yarn.lock")) {
+		return "nodejs"
+	}
+
+	// No lockfile found, use the template default
+	return defaultRuntime
+}
+
 func saveEnv(dir string, apikey string, projectKey string) {
 	filename := filepath.Join(dir, ".env")
 	envLines, err := env.ParseEnvFile(filename)
@@ -140,7 +165,7 @@ func initProject(ctx context.Context, logger logger.Logger, args InitProjectArgs
 		Identifier: args.Provider.Identifier,
 		Language:   args.Provider.Language,
 		Framework:  args.Provider.Framework,
-		Runtime:    args.Provider.Runtime,
+		Runtime:    detectRuntime(args.Dir, args.Provider.Runtime),
 		Ignore:     args.Provider.Bundle.Ignore,
 		AgentConfig: project.AgentBundlerConfig{
 			Dir: args.Provider.SrcDir,
diff --git a/internal/bundler/bundler.go b/internal/bundler/bundler.go
index 15328680..9fe579b3 100644
--- a/internal/bundler/bundler.go
+++ b/internal/bundler/bundler.go
@@ -141,6 +141,38 @@ func runTypecheck(ctx BundleContext, dir string) error {
 	return nil
 }
 
+// detectPackageManager detects which package manager to use based on lockfiles
+func detectPackageManager(projectDir string) string {
+	if util.Exists(filepath.Join(projectDir, "pnpm-lock.yaml")) {
+		return "pnpm"
+	} else if util.Exists(filepath.Join(projectDir, "bun.lockb")) || util.Exists(filepath.Join(projectDir, "bun.lock")) {
+		return "bun"
+	} else if util.Exists(filepath.Join(projectDir, "yarn.lock")) {
+		return "yarn"
+	} else {
+		return "npm"
+	}
+}
+
+// jsInstallCommandSpec returns the base command name and arguments for installing JavaScript dependencies
+// This function returns the base command without CI-specific modifications
+func jsInstallCommandSpec(projectDir string) (string, []string, error) {
+	packageManager := detectPackageManager(projectDir)
+
+	switch packageManager {
+	case "pnpm":
+		return "pnpm", []string{"install", "--prod", "--ignore-scripts", "--silent"}, nil
+	case "bun":
+		return "bun", []string{"install", "--production", "--ignore-scripts", "--no-progress", "--no-summary", "--silent"}, nil
+	case "yarn":
+		return "yarn", []string{"install", "--frozen-lockfile"}, nil
+	case "npm":
+		return "npm", []string{"install", "--no-audit", "--no-fund", "--omit=dev", "--ignore-scripts"}, nil
+	default:
+		return "npm", []string{"install", "--no-audit", "--no-fund", "--omit=dev", "--ignore-scripts"}, nil
+	}
+}
+
 func generateBunLockfile(ctx BundleContext, logger logger.Logger, dir string) error {
 	args := []string{"install", "--lockfile-only"}
 	install := exec.CommandContext(ctx.Context, "bun", args...)
@@ -153,29 +185,69 @@ func generateBunLockfile(ctx BundleContext, logger logger.Logger, dir string) er
 	return nil
 }
 
-func bundleJavascript(ctx BundleContext, dir string, outdir string, theproject *project.Project) error {
+// applyCIModifications applies CI-specific modifications to install command arguments
+func applyCIModifications(ctx BundleContext, cmd, runtime string, args []string) []string {
+	if !ctx.CI {
+		return args
+	}
 
-	if ctx.Install || !util.Exists(filepath.Join(dir, "node_modules")) {
-		var install *exec.Cmd
-		switch theproject.Bundler.Runtime {
-		case "nodejs":
-			install = exec.CommandContext(ctx.Context, "npm", "install", "--no-audit", "--no-fund", "--include=prod", "--ignore-scripts")
-		case "bunjs":
-			// for bun, we need to ensure the lockfile is up to date before we can run the install below
-			// otherwise we'll get an error about the lockfile being out of date
-			if err := generateBunLockfile(ctx, ctx.Logger, dir); err != nil {
-				return err
+	if cmd == "bun" {
+		// Drop quiet flags for CI using a filtered copy
+		filtered := make([]string, 0, len(args))
+		for _, arg := range args {
+			if arg == "--no-progress" || arg == "--no-summary" || arg == "--silent" {
+				continue
 			}
-			args := []string{"install", "--production", "--ignore-scripts"}
-			if ctx.CI {
-				args = append(args, "--verbose", "--no-cache")
-			} else {
-				args = append(args, "--no-progress", "--no-summary", "--silent")
+			filtered = append(filtered, arg)
+		}
+		return filtered
+	} else if cmd == "pnpm" {
+		// Remove silent flag and add CI-specific flags
+		filtered := make([]string, 0, len(args)+2)
+		for _, arg := range args {
+			if arg == "--silent" {
+				continue
 			}
-			install = exec.CommandContext(ctx.Context, "bun", args...)
-		default:
-			return fmt.Errorf("unsupported runtime: %s", theproject.Bundler.Runtime)
+			filtered = append(filtered, arg)
 		}
+		filtered = append(filtered, "--reporter=append-only", "--frozen-lockfile")
+		return filtered
+	}
+
+	return args
+}
+
+// getJSInstallCommand returns the complete install command with CI modifications applied
+func getJSInstallCommand(ctx BundleContext, projectDir, runtime string) (string, []string, error) {
+	// For bun, we need to ensure the lockfile is up to date before we can run the install
+	// otherwise we'll get an error about the lockfile being out of date
+	// Only do this if we have a logger (i.e., not in tests)
+	if runtime == "bunjs" && ctx.Logger != nil {
+		if err := generateBunLockfile(ctx, ctx.Logger, projectDir); err != nil {
+			return "", nil, err
+		}
+	}
+
+	cmd, args, err := jsInstallCommandSpec(projectDir)
+	if err != nil {
+		return "", nil, err
+	}
+
+	// Apply CI-specific modifications
+	args = applyCIModifications(ctx, cmd, runtime, args)
+
+	return cmd, args, nil
+}
+
+func bundleJavascript(ctx BundleContext, dir string, outdir string, theproject *project.Project) error {
+
+	if ctx.Install || !util.Exists(filepath.Join(dir, "node_modules")) {
+		cmd, args, err := getJSInstallCommand(ctx, dir, theproject.Bundler.Runtime)
+		if err != nil {
+			return err
+		}
+
+		install := exec.CommandContext(ctx.Context, cmd, args...)
 		util.ProcessSetup(install)
 		install.Dir = dir
 		out, err := install.CombinedOutput()
diff --git a/internal/bundler/bundler_test.go b/internal/bundler/bundler_test.go
index ae9c4f13..b2e0a546 100644
--- a/internal/bundler/bundler_test.go
+++ b/internal/bundler/bundler_test.go
@@ -1,9 +1,13 @@
 package bundler
 
 import (
+	"context"
+	"os"
+	"path/filepath"
 	"testing"
 
 	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
 )
 
 func TestPyProject(t *testing.T) {
@@ -32,3 +36,124 @@ func TestPyProject(t *testing.T) {
 	assert.Equal(t, "1.0.0-alpha", pyProjectVersionRegex.FindStringSubmatch(`version = "1.0.0-alpha"`)[1])
 	assert.Equal(t, "1.0.0-beta", pyProjectVersionRegex.FindStringSubmatch(`version = "1.0.0-beta"`)[1])
 }
+
+// Helper function to test package manager detection logic
+func testPackageManagerCommand(t *testing.T, tempDir string, runtime string, isCI bool, expectedCmd string, expectedArgs []string) {
+	ctx := BundleContext{
+		Context: context.Background(),
+		Logger:  nil, // nil logger will skip bun lockfile generation in tests
+		CI:      isCI,
+	}
+	
+	actualCmd, actualArgs, err := getJSInstallCommand(ctx, tempDir, runtime)
+	require.NoError(t, err)
+	
+	assert.Equal(t, expectedCmd, actualCmd)
+	assert.Equal(t, expectedArgs, actualArgs)
+}
+
+func TestJavaScriptPackageManagerDetection(t *testing.T) {
+	tests := []struct {
+		name         string
+		runtime      string
+		lockFiles    []string
+		expectedCmd  string
+		expectedArgs []string
+	}{
+		{
+			name:         "nodejs with yarn.lock should use yarn",
+			runtime:      "nodejs",
+			lockFiles:    []string{"yarn.lock"},
+			expectedCmd:  "yarn",
+			expectedArgs: []string{"install", "--frozen-lockfile"},
+		},
+		{
+			name:         "nodejs without yarn.lock should use npm",
+			runtime:      "nodejs",
+			lockFiles:    []string{},
+			expectedCmd:  "npm",
+			expectedArgs: []string{"install", "--no-audit", "--no-fund", "--omit=dev", "--ignore-scripts"},
+		},
+		{
+			name:         "nodejs with package-lock.json should use npm",
+			runtime:      "nodejs",
+			lockFiles:    []string{"package-lock.json"},
+			expectedCmd:  "npm",
+			expectedArgs: []string{"install", "--no-audit", "--no-fund", "--omit=dev", "--ignore-scripts"},
+		},
+		{
+			name:         "nodejs with both yarn.lock and package-lock.json should prefer yarn",
+			runtime:      "nodejs",
+			lockFiles:    []string{"yarn.lock", "package-lock.json"},
+			expectedCmd:  "yarn",
+			expectedArgs: []string{"install", "--frozen-lockfile"},
+		},
+		{
+			name:         "pnpm runtime should use pnpm",
+			runtime:      "pnpm",
+			lockFiles:    []string{"pnpm-lock.yaml"},
+			expectedCmd:  "pnpm",
+			expectedArgs: []string{"install", "--prod", "--ignore-scripts", "--silent"},
+		},
+		{
+			name:         "bunjs runtime should use bun with bun.lockb",
+			runtime:      "bunjs",
+			lockFiles:    []string{"bun.lockb", "package.json"},
+			expectedCmd:  "bun",
+			expectedArgs: []string{"install", "--production", "--ignore-scripts", "--no-progress", "--no-summary", "--silent"},
+		},
+		{
+			name:         "bunjs runtime should use bun with bun.lock",
+			runtime:      "bunjs",
+			lockFiles:    []string{"bun.lock", "package.json"},
+			expectedCmd:  "bun",
+			expectedArgs: []string{"install", "--production", "--ignore-scripts", "--no-progress", "--no-summary", "--silent"},
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			// Create temporary directory
+			tempDir := t.TempDir()
+
+			// Create lock files and package.json
+			for _, lockFile := range tt.lockFiles {
+				filePath := filepath.Join(tempDir, lockFile)
+				var content []byte
+				if lockFile == "package.json" {
+					content = []byte(`{"name": "test-package", "version": "1.0.0"}`)
+				} else {
+					content = []byte("")
+				}
+				err := os.WriteFile(filePath, content, 0644)
+				require.NoError(t, err)
+			}
+
+			// Test the logic with CI=false
+			testPackageManagerCommand(t, tempDir, tt.runtime, false, tt.expectedCmd, tt.expectedArgs)
+		})
+	}
+}
+
+func TestPnpmCIFlags(t *testing.T) {
+	tempDir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(tempDir, "pnpm-lock.yaml"), []byte(""), 0644))
+	// CI=true
+	testPackageManagerCommand(
+		t,
+		tempDir,
+		"pnpm",
+		true,
+		"pnpm",
+		[]string{"install", "--prod", "--ignore-scripts", "--reporter=append-only", "--frozen-lockfile"},
+	)
+	// CI=false
+	testPackageManagerCommand(
+		t,
+		tempDir,
+		"pnpm",
+		false,
+		"pnpm",
+		[]string{"install", "--prod", "--ignore-scripts", "--silent"},
+	)
+}
diff --git a/internal/dev/dev.go b/internal/dev/dev.go
index 335c1f2e..d7d999f0 100644
--- a/internal/dev/dev.go
+++ b/internal/dev/dev.go
@@ -125,7 +125,7 @@ func CreateRunProjectCmd(ctx context.Context, log logger.Logger, theproject proj
 		projectServerCmd.Env = append(projectServerCmd.Env, "NODE_ENV=development")
 	}
 
-	// for nodejs, we need to enable source maps directly in the environment.
+	// for nodejs and pnpm, we need to enable source maps directly in the environment.
 	// for bun, we need to inject a shim helper to parse the source maps
 	if theproject.Project.Bundler.Runtime == "nodejs" {
 		nodeOptions := os.Getenv("NODE_OPTIONS")
diff --git a/internal/mcp/project.go b/internal/mcp/project.go
index 93e71724..2a9459aa 100644
--- a/internal/mcp/project.go
+++ b/internal/mcp/project.go
@@ -23,7 +23,7 @@ type CreateProjectArguments struct {
 }
 
 type ListTemplatesArguments struct {
-	Provider string `json:"provider" jsonschema:"required,description=The provider to use for the project which can be either 'bunjs' for BunJS, 'nodejs' for NodeJS or 'python-uv' for Python with UV"`
+	Provider string `json:"provider" jsonschema:"required,description=The provider to use for the project which can be either 'bunjs' for BunJS, 'nodejs' for NodeJS, or 'uv' for Python with UV"`
 }
 
 func init() {
diff --git a/internal/project/project.go b/internal/project/project.go
index 94752b2f..37740d49 100644
--- a/internal/project/project.go
+++ b/internal/project/project.go
@@ -193,12 +193,12 @@ func (p *Project) Load(dir string) error {
 	}
 	switch p.Bundler.Language {
 	case "js", "javascript", "typescript":
-		if p.Bundler.Runtime != "bunjs" && p.Bundler.Runtime != "nodejs" && p.Bundler.Runtime != "deno" {
-			return fmt.Errorf("invalid bundler.runtime value: %s. only bunjs, nodejs, and deno are supported", p.Bundler.Runtime)
+		if p.Bundler.Runtime != "bunjs" && p.Bundler.Runtime != "nodejs" {
+			return fmt.Errorf("invalid bundler.runtime value: %s. only bunjs and nodejs are supported", p.Bundler.Runtime)
 		}
 	case "py", "python":
-		if p.Bundler.Runtime != "uv" && p.Bundler.Runtime != "python" && p.Bundler.Runtime != "" {
-			return fmt.Errorf("invalid bundler.runtime value: %s. only uv or python is supported", p.Bundler.Runtime)
+		if p.Bundler.Runtime != "uv" {
+			return fmt.Errorf("invalid bundler.runtime value: %s. only uv is supported", p.Bundler.Runtime)
 		}
 	default:
 		return fmt.Errorf("invalid bundler.language value: %s. only js or py are supported", p.Bundler.Language)