fix(precedence): env vars now correctly override config file values

The documented precedence is Set > env > file > defaults, but collapse()
was using maps.Copy(ccm, mapConfig) which let file values (and Set values,
stored in the same map) unconditionally overwrite env values.

Split mapConfig into fileConfig (from ReadInConfig) and overrideConfig
(from Set/SetString/SetBool). collapse() now applies layers in correct
order: defaults, then file, then env (for known keys), then overrides.

Added TestPrecedenceChain to verify the full layering.

getters.go

@@ -12,7 +12,7 @@ func (c *ConfigManager) Get(key string) any {
 	defer c.mutex.RUnlock()
 	v, ok := c.combinedConfig[strings.ToLower(key)]
 	if !ok {
-		v, ok = c.envConfig[strings.ToLower(c.envPrefix+key)]
+		v, ok = c.envConfig[strings.ToLower(key)]
 		if !ok {
 			return nil
 		}
@@ -25,7 +25,7 @@ func (c *ConfigManager) GetBool(key string) bool {
 	defer c.mutex.RUnlock()
 	v, ok := c.combinedConfig[strings.ToLower(key)]
 	if !ok {
-		v, ok = c.envConfig[strings.ToLower(c.envPrefix+key)]
+		v, ok = c.envConfig[strings.ToLower(key)]
 		if !ok {
 			return false
 		}
@@ -56,7 +56,7 @@ func (c *ConfigManager) GetDuration(key string) time.Duration {
 	defer c.mutex.RUnlock()
 	v, ok := c.combinedConfig[strings.ToLower(key)]
 	if !ok {
-		v, ok = c.envConfig[strings.ToLower(c.envPrefix+key)]
+		v, ok = c.envConfig[strings.ToLower(key)]
 		if !ok {
 			return 0
 		}
@@ -91,7 +91,7 @@ func (c *ConfigManager) GetString(key string) string {
 	defer c.mutex.RUnlock()
 	v, ok := c.combinedConfig[strings.ToLower(key)]
 	if !ok {
-		v, ok = c.envConfig[strings.ToLower(c.envPrefix+key)]
+		v, ok = c.envConfig[strings.ToLower(key)]
 		if !ok {
 			return ""
 		}
@@ -110,7 +110,7 @@ func (c *ConfigManager) GetStringMap(key string) map[string]any {
 	defer c.mutex.RUnlock()
 	v, ok := c.combinedConfig[strings.ToLower(key)]
 	if !ok {
-		v, ok = c.envConfig[strings.ToLower(c.envPrefix+key)]
+		v, ok = c.envConfig[strings.ToLower(key)]
 		if !ok {
 			return nil
 		}
@@ -128,7 +128,7 @@ func (c *ConfigManager) GetStringSlice(key string) []string {
 	defer c.mutex.RUnlock()
 	v, ok := c.combinedConfig[strings.ToLower(key)]
 	if !ok {
-		v, ok = c.envConfig[strings.ToLower(c.envPrefix+key)]
+		v, ok = c.envConfig[strings.ToLower(key)]
 		if !ok {
 			return nil
 		}
@@ -157,7 +157,7 @@ func (c *ConfigManager) GetInt(key string) int {
 	defer c.mutex.RUnlock()
 	v, ok := c.combinedConfig[strings.ToLower(key)]
 	if !ok {
-		v, ok = c.envConfig[strings.ToLower(c.envPrefix+key)]
+		v, ok = c.envConfig[strings.ToLower(key)]
 		if !ok {
 			return 0
 		}
@@ -189,7 +189,7 @@ func (c *ConfigManager) GetIntSlice(key string) []int {
 	defer c.mutex.RUnlock()
 	v, ok := c.combinedConfig[strings.ToLower(key)]
 	if !ok {
-		v, ok = c.envConfig[strings.ToLower(c.envPrefix+key)]
+		v, ok = c.envConfig[strings.ToLower(key)]
 		if !ok {
 			return nil
 		}

jety.go

@@ -4,7 +4,6 @@ import (
 	"encoding/json"
 	"errors"
 	"fmt"
-	"maps"
 	"os"
 	"path/filepath"
 	"strings"
@@ -33,8 +32,8 @@ type (
 		configPath       string
 		configFileUsed   string
 		configType       configType
-		envPrefix        string
-		mapConfig        map[string]ConfigMap
+		overrideConfig   map[string]ConfigMap
+		fileConfig       map[string]ConfigMap
 		defaultConfig    map[string]ConfigMap
 		envConfig        map[string]ConfigMap
 		combinedConfig   map[string]ConfigMap
@@ -51,10 +50,10 @@ var (
 func NewConfigManager() *ConfigManager {
 	cm := ConfigManager{}
 	cm.envConfig = make(map[string]ConfigMap)
-	cm.mapConfig = make(map[string]ConfigMap)
+	cm.overrideConfig = make(map[string]ConfigMap)
+	cm.fileConfig = make(map[string]ConfigMap)
 	cm.defaultConfig = make(map[string]ConfigMap)
 	cm.combinedConfig = make(map[string]ConfigMap)
-	cm.envPrefix = ""
 	envSet := os.Environ()
 	for _, env := range envSet {
 		key, value, found := strings.Cut(env, "=")
@@ -82,8 +81,6 @@ func (c *ConfigManager) WithEnvPrefix(prefix string) *ConfigManager {
 			c.envConfig[lower] = ConfigMap{Key: withoutPrefix, Value: value}
 		}
 	}
-	// Don't set envPrefix since keys are already stripped of prefix
-	c.envPrefix = ""
 	return c
 }
 
@@ -103,13 +100,21 @@ func (c *ConfigManager) collapse() {
 	c.mutex.Lock()
 	defer c.mutex.Unlock()
 	ccm := make(map[string]ConfigMap)
+	// Precedence (highest to lowest): overrides (Set) > env > file > defaults
 	for k, v := range c.defaultConfig {
 		ccm[k] = v
-		if _, ok := c.envConfig[k]; ok {
-			ccm[k] = c.envConfig[k]
+	}
+	for k, v := range c.fileConfig {
+		ccm[k] = v
+	}
+	for k := range c.defaultConfig {
+		if v, ok := c.envConfig[k]; ok {
+			ccm[k] = v
 		}
 	}
-	maps.Copy(ccm, c.mapConfig)
+	for k, v := range c.overrideConfig {
+		ccm[k] = v
+	}
 	c.combinedConfig = ccm
 }
 
@@ -171,7 +176,21 @@ func (c *ConfigManager) SetConfigType(configType string) error {
 func (c *ConfigManager) SetEnvPrefix(prefix string) {
 	c.mutex.Lock()
 	defer c.mutex.Unlock()
-	c.envPrefix = prefix
+	// Re-read environment variables, stripping the prefix from matching keys.
+	// This mirrors WithEnvPrefix behavior so that prefixed env vars are
+	// accessible by their unprefixed key name.
+	envSet := os.Environ()
+	c.envConfig = make(map[string]ConfigMap)
+	for _, env := range envSet {
+		key, value, found := strings.Cut(env, "=")
+		if !found {
+			continue
+		}
+		if withoutPrefix, ok := strings.CutPrefix(key, prefix); ok {
+			lower := strings.ToLower(withoutPrefix)
+			c.envConfig[lower] = ConfigMap{Key: withoutPrefix, Value: value}
+		}
+	}
 }
 
 func (c *ConfigManager) ReadInConfig() error {
@@ -206,7 +225,7 @@ func (c *ConfigManager) ReadInConfig() error {
 		conf[lower] = ConfigMap{Key: k, Value: v}
 	}
 	c.mutex.Lock()
-	c.mapConfig = conf
+	c.fileConfig = conf
 	c.configFileUsed = configFile
 	c.mutex.Unlock()
 	c.collapse()

jety_test.go

@@ -1,7 +1,9 @@
 package jety
 
 import (
+	"fmt"
 	"os"
+	"os/exec"
 	"path/filepath"
 	"sync"
 	"testing"
@@ -64,7 +66,7 @@ func TestNewConfigManager(t *testing.T) {
 	if cm.envConfig == nil {
 		t.Error("envConfig not initialized")
 	}
-	if cm.mapConfig == nil {
+	if cm.overrideConfig == nil {
 		t.Error("mapConfig not initialized")
 	}
 	if cm.defaultConfig == nil {
@@ -552,7 +554,7 @@ func TestEnvOverridesDefault(t *testing.T) {
 	}
 }
 
-func TestConfigFileOverridesEnv(t *testing.T) {
+func TestEnvOverridesConfigFile(t *testing.T) {
 	os.Setenv("PORT", "5000")
 	defer os.Unsetenv("PORT")
 
@@ -573,9 +575,9 @@ func TestConfigFileOverridesEnv(t *testing.T) {
 		t.Fatal(err)
 	}
 
-	// Config file should override env and default
-	if got := cm.GetInt("port"); got != 9000 {
-		t.Errorf("GetInt(port) = %d, want 9000 (from file)", got)
+	// Env should override config file (env > file > defaults)
+	if got := cm.GetInt("port"); got != 5000 {
+		t.Errorf("GetInt(port) = %d, want 5000 (env overrides file)", got)
 	}
 }
 
@@ -804,11 +806,6 @@ func TestWriteConfigUnsupportedType(t *testing.T) {
 func TestSetEnvPrefix(t *testing.T) {
 	cm := NewConfigManager()
 	cm.SetEnvPrefix("PREFIX_")
-
-	// Verify it doesn't panic
-	if cm.envPrefix != "PREFIX_" {
-		t.Errorf("envPrefix = %q, want %q", cm.envPrefix, "PREFIX_")
-	}
 }
 
 func TestDeeplyNestedConfig(t *testing.T) {
@@ -1095,9 +1092,6 @@ func TestPackageLevelSetConfigName(t *testing.T) {
 func TestPackageLevelSetEnvPrefix(t *testing.T) {
 	defaultConfigManager = NewConfigManager()
 	SetEnvPrefix("JETY_TEST_")
-	if defaultConfigManager.envPrefix != "JETY_TEST_" {
-		t.Errorf("envPrefix = %q, want %q", defaultConfigManager.envPrefix, "JETY_TEST_")
-	}
 }
 
 func TestPackageLevelWriteConfig(t *testing.T) {
@@ -1266,3 +1260,140 @@ func TestDeeplyNestedWriteConfig(t *testing.T) {
 		})
 	}
 }
+
+func TestSetEnvPrefixOverridesDefault(t *testing.T) {
+	// Subprocess test: env vars must exist before NewConfigManager is called.
+	if os.Getenv("TEST_SET_ENV_PREFIX") == "1" {
+		cm := NewConfigManager()
+		cm.SetEnvPrefix("MYAPP_")
+		cm.SetDefault("port", 8080)
+
+		if got := cm.GetInt("port"); got != 9999 {
+			fmt.Fprintf(os.Stderr, "GetInt(port) = %d, want 9999\n", got)
+			os.Exit(1)
+		}
+		if got := cm.GetString("host"); got != "envhost" {
+			fmt.Fprintf(os.Stderr, "GetString(host) = %q, want %q\n", got, "envhost")
+			os.Exit(1)
+		}
+		// Unprefixed var should not be visible.
+		if got := cm.GetString("other"); got != "" {
+			fmt.Fprintf(os.Stderr, "GetString(other) = %q, want empty\n", got)
+			os.Exit(1)
+		}
+		os.Exit(0)
+	}
+
+	cmd := exec.Command(os.Args[0], "-test.run=^TestSetEnvPrefixOverridesDefault$")
+	cmd.Env = append(os.Environ(),
+		"TEST_SET_ENV_PREFIX=1",
+		"MYAPP_PORT=9999",
+		"MYAPP_HOST=envhost",
+		"OTHER=should_not_see",
+	)
+	out, err := cmd.CombinedOutput()
+	if err != nil {
+		t.Fatalf("subprocess failed: %v\n%s", err, out)
+	}
+}
+
+func TestSetEnvPrefixWithSetDefault(t *testing.T) {
+	// SetDefault should pick up prefixed env vars after SetEnvPrefix.
+	if os.Getenv("TEST_SET_ENV_PREFIX_DEFAULT") == "1" {
+		cm := NewConfigManager()
+		cm.SetEnvPrefix("APP_")
+		cm.SetDefault("database_host", "localhost")
+
+		if got := cm.GetString("database_host"); got != "db.example.com" {
+			fmt.Fprintf(os.Stderr, "GetString(database_host) = %q, want %q\n", got, "db.example.com")
+			os.Exit(1)
+		}
+		os.Exit(0)
+	}
+
+	cmd := exec.Command(os.Args[0], "-test.run=^TestSetEnvPrefixWithSetDefault$")
+	cmd.Env = append(os.Environ(),
+		"TEST_SET_ENV_PREFIX_DEFAULT=1",
+		"APP_DATABASE_HOST=db.example.com",
+	)
+	out, err := cmd.CombinedOutput()
+	if err != nil {
+		t.Fatalf("subprocess failed: %v\n%s", err, out)
+	}
+}
+
+func TestPackageLevelSetEnvPrefixOverrides(t *testing.T) {
+	// Package-level SetEnvPrefix should work the same way.
+	if os.Getenv("TEST_PKG_SET_ENV_PREFIX") == "1" {
+		// Reset the default manager to pick up our env vars.
+		defaultConfigManager = NewConfigManager()
+		SetEnvPrefix("PKG_")
+		SetDefault("val", "default")
+
+		if got := GetString("val"); got != "from_env" {
+			fmt.Fprintf(os.Stderr, "GetString(val) = %q, want %q\n", got, "from_env")
+			os.Exit(1)
+		}
+		os.Exit(0)
+	}
+
+	cmd := exec.Command(os.Args[0], "-test.run=^TestPackageLevelSetEnvPrefixOverrides$")
+	cmd.Env = append(os.Environ(),
+		"TEST_PKG_SET_ENV_PREFIX=1",
+		"PKG_VAL=from_env",
+	)
+	out, err := cmd.CombinedOutput()
+	if err != nil {
+		t.Fatalf("subprocess failed: %v\n%s", err, out)
+	}
+}
+
+func TestPrecedenceChain(t *testing.T) {
+	// Verify: Set > env > file > defaults
+	os.Setenv("PORT", "5000")
+	os.Setenv("HOST", "envhost")
+	os.Setenv("LOG", "envlog")
+	defer os.Unsetenv("PORT")
+	defer os.Unsetenv("HOST")
+	defer os.Unsetenv("LOG")
+
+	dir := t.TempDir()
+	configFile := filepath.Join(dir, "config.yaml")
+	if err := os.WriteFile(configFile, []byte("port: 9000\nhost: filehost\nlog: filelog\nname: filename"), 0o644); err != nil {
+		t.Fatal(err)
+	}
+
+	cm := NewConfigManager()
+	cm.SetDefault("port", 8080)
+	cm.SetDefault("host", "defaulthost")
+	cm.SetDefault("log", "defaultlog")
+	cm.SetDefault("name", "defaultname")
+	cm.SetDefault("extra", "defaultextra")
+
+	cm.SetConfigFile(configFile)
+	if err := cm.SetConfigType("yaml"); err != nil {
+		t.Fatal(err)
+	}
+	if err := cm.ReadInConfig(); err != nil {
+		t.Fatal(err)
+	}
+
+	cm.Set("port", 1111) // Set overrides everything
+
+	// port: Set(1111) > env(5000) > file(9000) > default(8080) → 1111
+	if got := cm.GetInt("port"); got != 1111 {
+		t.Errorf("port: got %d, want 1111 (Set overrides all)", got)
+	}
+	// host: env(envhost) > file(filehost) > default(defaulthost) → envhost
+	if got := cm.GetString("host"); got != "envhost" {
+		t.Errorf("host: got %q, want envhost (env overrides file)", got)
+	}
+	// name: file(filename) > default(defaultname) → filename
+	if got := cm.GetString("name"); got != "filename" {
+		t.Errorf("name: got %q, want filename (file overrides default)", got)
+	}
+	// extra: only default → defaultextra
+	if got := cm.GetString("extra"); got != "defaultextra" {
+		t.Errorf("extra: got %q, want defaultextra (default)", got)
+	}
+}

setters.go

@@ -8,7 +8,7 @@ func (c *ConfigManager) SetBool(key string, value bool) {
 	c.mutex.Lock()
 	defer c.mutex.Unlock()
 	lower := strings.ToLower(key)
-	c.mapConfig[lower] = ConfigMap{Key: key, Value: value}
+	c.overrideConfig[lower] = ConfigMap{Key: key, Value: value}
 	c.combinedConfig[lower] = ConfigMap{Key: key, Value: value}
 }
 
@@ -16,7 +16,7 @@ func (c *ConfigManager) SetString(key string, value string) {
 	c.mutex.Lock()
 	defer c.mutex.Unlock()
 	lower := strings.ToLower(key)
-	c.mapConfig[lower] = ConfigMap{Key: key, Value: value}
+	c.overrideConfig[lower] = ConfigMap{Key: key, Value: value}
 	c.combinedConfig[lower] = ConfigMap{Key: key, Value: value}
 }
 
@@ -24,7 +24,7 @@ func (c *ConfigManager) Set(key string, value any) {
 	c.mutex.Lock()
 	defer c.mutex.Unlock()
 	lower := strings.ToLower(key)
-	c.mapConfig[lower] = ConfigMap{Key: key, Value: value}
+	c.overrideConfig[lower] = ConfigMap{Key: key, Value: value}
 	c.combinedConfig[lower] = ConfigMap{Key: key, Value: value}
 }
 
@@ -33,14 +33,14 @@ func (c *ConfigManager) SetDefault(key string, value any) {
 	defer c.mutex.Unlock()
 	lower := strings.ToLower(key)
 	c.defaultConfig[lower] = ConfigMap{Key: key, Value: value}
-	if _, ok := c.mapConfig[lower]; !ok {
+	if _, ok := c.overrideConfig[lower]; !ok {
 		if envVal, ok := c.envConfig[lower]; ok {
-			c.mapConfig[lower] = ConfigMap{Key: key, Value: envVal.Value}
+			c.overrideConfig[lower] = ConfigMap{Key: key, Value: envVal.Value}
 			c.combinedConfig[lower] = ConfigMap{Key: key, Value: envVal.Value}
 		} else {
 			c.combinedConfig[lower] = ConfigMap{Key: key, Value: value}
 		}
 	} else {
-		c.combinedConfig[lower] = c.mapConfig[lower]
+		c.combinedConfig[lower] = c.overrideConfig[lower]
 	}
 }