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.

jety.go

@@ -4,7 +4,6 @@ import (
 	"encoding/json"
 	"errors"
 	"fmt"
-	"maps"
 	"os"
 	"path/filepath"
 	"strings"
@@ -33,7 +32,8 @@ type (
 		configPath       string
 		configFileUsed   string
 		configType       configType
-		mapConfig        map[string]ConfigMap
+		overrideConfig   map[string]ConfigMap
+		fileConfig       map[string]ConfigMap
 		defaultConfig    map[string]ConfigMap
 		envConfig        map[string]ConfigMap
 		combinedConfig   map[string]ConfigMap
@@ -50,7 +50,8 @@ 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)
 	envSet := os.Environ()
@@ -99,13 +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
 }
 
@@ -216,7 +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

@@ -66,7 +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 {
@@ -554,7 +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")
 
@@ -575,9 +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)
 	}
 }
 
@@ -1347,3 +1347,53 @@ func TestPackageLevelSetEnvPrefixOverrides(t *testing.T) {
 		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]
 	}
 }