diff --git a/agentbox/cmd/agentbox/run_command.go b/agentbox/cmd/agentbox/run_command.go
index 2c7d8b0..d0631be 100644
--- a/agentbox/cmd/agentbox/run_command.go
+++ b/agentbox/cmd/agentbox/run_command.go
@@ -67,7 +67,7 @@ func run(ctx context.Context, args []string) error {
 		fmt.Fprintf(os.Stderr, "Run artifacts: %s\n", traceStore.Directory())
 		return err
 	}
-	fmt.Printf("Replay written to:\n%s\n", traceStore.Directory())
+	fmt.Printf("Run artifacts written to:\n%s\n", traceStore.Directory())
 	return nil
 }
 
diff --git a/agentbox/internal/agent/deterministic.go b/agentbox/internal/agent/deterministic.go
index 2c2aa59..9ccafc3 100644
--- a/agentbox/internal/agent/deterministic.go
+++ b/agentbox/internal/agent/deterministic.go
@@ -76,6 +76,8 @@ func greenCentroidX(screenshot []byte) (float64, error) {
 	for y := bounds.Min.Y; y < bounds.Max.Y; y++ {
 		for x := bounds.Min.X; x < bounds.Max.X; x++ {
 			red, green, blue, _ := renderedImage.At(x, y).RGBA()
+			// Match the mover's #00ff66 square. Requiring 1,000 matching pixels
+			// prevents a small green UI detail from passing verification.
 			if green > 0xc000 && red < 0x4000 && blue < 0x8000 {
 				xCoordinateSum += uint64(x)
 				greenPixelCount++
diff --git a/agentbox/internal/agent/openai_protocol.go b/agentbox/internal/agent/openai_protocol.go
index 1ada81c..5e137d4 100644
--- a/agentbox/internal/agent/openai_protocol.go
+++ b/agentbox/internal/agent/openai_protocol.go
@@ -87,12 +87,14 @@ func modelPrompt(task string, history []Step, observation Observation) (string,
 		return "", err
 	}
 	return "You control an interactive Linux application from screenshots. " +
-		"Choose exactly one safe input action, or mark done when the task is complete. " +
+		"Choose exactly one allowed input action, or mark done when the task is complete. " +
 		"Use logical key names such as RIGHT, ENTER, or ESCAPE. Keep waits under 5000 ms.\n" +
 		string(data), nil
 }
 
 func decisionSchema() map[string]any {
+	// Strict structured output requires every action property to be present,
+	// even when a particular action ignores most of them.
 	actionProperties := map[string]any{
 		"type": map[string]any{
 			"type": "string",
diff --git a/agentbox/internal/appspec/appspec.go b/agentbox/internal/appspec/appspec.go
index b4f0f79..33bfaec 100644
--- a/agentbox/internal/appspec/appspec.go
+++ b/agentbox/internal/appspec/appspec.go
@@ -11,10 +11,10 @@ import (
 )
 
 type manifest struct {
-	Command     string            `json:"command"`
-	Args        []string          `json:"args"`
-	Env         map[string]string `json:"env"`
-	WindowTitle string            `json:"window_title"`
+	Command              string            `json:"command"`
+	Args                 []string          `json:"args"`
+	EnvironmentVariables map[string]string `json:"env"`
+	WindowTitle          string            `json:"window_title"`
 }
 
 // Resolve turns either an executable path or a directory containing
@@ -58,9 +58,9 @@ func Resolve(path string) (environment.Command, error) {
 		return environment.Command{}, errors.New("manifest command must be a regular executable file")
 	}
 	return environment.Command{
-		Path:        commandPath,
-		Args:        config.Args,
-		Env:         config.Env,
-		WindowTitle: config.WindowTitle,
+		Path:                 commandPath,
+		Args:                 config.Args,
+		EnvironmentVariables: config.EnvironmentVariables,
+		WindowTitle:          config.WindowTitle,
 	}, nil
 }
diff --git a/agentbox/internal/environment/dockerx11/application.go b/agentbox/internal/environment/dockerx11/application.go
index 357be43..1e79561 100644
--- a/agentbox/internal/environment/dockerx11/application.go
+++ b/agentbox/internal/environment/dockerx11/application.go
@@ -17,7 +17,7 @@ func (environmentBackend *Environment) Launch(
 	ctx context.Context,
 	application environment.Command,
 ) error {
-	fmt.Fprintln(environmentBackend.config.Output, "Uploading build...")
+	fmt.Fprintln(environmentBackend.config.Output, "Staging application...")
 	executable, err := os.Open(application.Path)
 	if err != nil {
 		return fmt.Errorf("open application: %w", err)
@@ -47,7 +47,7 @@ func (environmentBackend *Environment) Launch(
 
 	fmt.Fprintln(environmentBackend.config.Output, "Launching application...")
 	dockerArguments := []string{"exec", "-d"}
-	for variableName, variableValue := range application.Env {
+	for variableName, variableValue := range application.EnvironmentVariables {
 		dockerArguments = append(
 			dockerArguments,
 			"-e",
diff --git a/agentbox/internal/environment/dockerx11/lifecycle.go b/agentbox/internal/environment/dockerx11/lifecycle.go
index a378d7d..fe8fd0a 100644
--- a/agentbox/internal/environment/dockerx11/lifecycle.go
+++ b/agentbox/internal/environment/dockerx11/lifecycle.go
@@ -69,6 +69,8 @@ func (environmentBackend *Environment) Start(ctx context.Context) error {
 	); err != nil {
 		return fmt.Errorf("start environment: %w", err)
 	}
+	// entrypoint.sh creates this file only after both Xvfb and Openbox accept
+	// requests. It is the readiness handshake between host and container.
 	if err := waitFor(ctx, 10*time.Second, func() bool {
 		_, readyErr := environmentBackend.runDocker(
 			ctx,
diff --git a/agentbox/internal/environment/environment.go b/agentbox/internal/environment/environment.go
index c7667e3..66d9b4c 100644
--- a/agentbox/internal/environment/environment.go
+++ b/agentbox/internal/environment/environment.go
@@ -8,10 +8,10 @@ import (
 // Command describes a host executable and how it should start in an
 // environment. Environment implementations decide how to stage the file.
 type Command struct {
-	Path        string
-	Args        []string
-	Env         map[string]string
-	WindowTitle string
+	Path                 string
+	Args                 []string
+	EnvironmentVariables map[string]string
+	WindowTitle          string
 }
 
 // InputType identifies one backend-neutral keyboard, mouse, or timing action.
@@ -36,7 +36,8 @@ type InputAction struct {
 	DurationMS int       `json:"duration_ms,omitempty"`
 }
 
-// LogEntry is a snapshot of one application output stream.
+// LogEntry is a cumulative snapshot of one application output stream. Time is
+// when Agentbox captured the snapshot, not when the application emitted it.
 type LogEntry struct {
 	Stream  string    `json:"stream"`
 	Message string    `json:"message"`
diff --git a/agentbox/internal/phase1/run.go b/agentbox/internal/phase1/run.go
index b072d5d..39cdd7d 100644
--- a/agentbox/internal/phase1/run.go
+++ b/agentbox/internal/phase1/run.go
@@ -117,7 +117,7 @@ func Run(ctx context.Context) (runErr error) {
 		return fmt.Errorf("build environment image: %w", err)
 	}
 
-	fmt.Println("Creating isolated graphical environment...")
+	fmt.Println("Creating restricted graphical environment...")
 	_, err = r.docker(ctx,
 		"create",
 		"--name", r.containerName,
@@ -327,6 +327,8 @@ func squareCentroid(path string) (point, error) {
 	for y := bounds.Min.Y; y < bounds.Max.Y; y++ {
 		for x := bounds.Min.X; x < bounds.Max.X; x++ {
 			red, green, blue, _ := img.At(x, y).RGBA()
+			// Match the demo square's #00ff66 color with enough tolerance for
+			// image conversion while rejecting the black background.
 			if green > 0xc000 && red < 0x4000 && blue < 0x8000 {
 				sumX += uint64(x)
 				sumY += uint64(y)
diff --git a/agentbox/internal/runtime/runtime.go b/agentbox/internal/runtime/runtime.go
index dd561f8..c82b632 100644
--- a/agentbox/internal/runtime/runtime.go
+++ b/agentbox/internal/runtime/runtime.go
@@ -45,7 +45,7 @@ func Run(ctx context.Context, config Config) (runErr error) {
 	if err := config.Environment.Launch(ctx, config.Command); err != nil {
 		return err
 	}
-	fmt.Fprintln(config.Output, "Agent attached.")
+	fmt.Fprintln(config.Output, "Agent loop started.")
 
 	var stepHistory []agent.Step
 	var actionHistory []environment.InputAction
diff --git a/agentbox/internal/trace/doc.go b/agentbox/internal/trace/doc.go
new file mode 100644
index 0000000..97f90ec
--- /dev/null
+++ b/agentbox/internal/trace/doc.go
@@ -0,0 +1,4 @@
+// Package trace stores durable run records. steps.jsonl contains complete
+// observations and decisions, actions.jsonl is an action-only view, and PNG
+// screenshots remain separate files referenced by relative paths.
+package trace
diff --git a/agentbox/internal/trace/reader.go b/agentbox/internal/trace/reader.go
index 2ceb3ca..833b9fe 100644
--- a/agentbox/internal/trace/reader.go
+++ b/agentbox/internal/trace/reader.go
@@ -25,6 +25,8 @@ func List(projectRoot string) ([]Run, error) {
 			continue
 		}
 		run, err := Read(projectRoot, entry.Name())
+		// Old or malformed trace directories are intentionally hidden rather
+		// than making the entire run listing fail.
 		if err == nil && run.SchemaVersion == SchemaVersion {
 			runs = append(runs, run)
 		}
@@ -87,6 +89,7 @@ func ReadSteps(projectRoot, runID string) ([]StepRecord, error) {
 }
 
 func validateRunID(runID string) error {
+	// Run IDs become path components, so reject separators and traversal.
 	if filepath.Base(runID) != runID {
 		return errors.New("invalid run ID")
 	}