refactor(logging): inject logger via context, drop package globals

cmd/entire/cli/agent/agent.go

@@ -68,7 +68,7 @@ type Agent interface {
 	ResolveSessionFile(sessionDir, agentSessionID string) string
 
 	// ReadSession reads session data from agent's storage.
-	ReadSession(input *HookInput) (*AgentSession, error)
+	ReadSession(ctx context.Context, input *HookInput) (*AgentSession, error)
 
 	// WriteSession writes session data for resumption.
 	WriteSession(ctx context.Context, session *AgentSession) error
@@ -184,7 +184,7 @@ type TokenCalculator interface {
 	Agent
 
 	// CalculateTokenUsage computes token usage from the transcript starting at the given offset.
-	CalculateTokenUsage(transcriptData []byte, fromOffset int) (*TokenUsage, error)
+	CalculateTokenUsage(ctx context.Context, transcriptData []byte, fromOffset int) (*TokenUsage, error)
 }
 
 // TextGenerator is an optional interface for agents whose CLI supports

cmd/entire/cli/agent/agent_test.go

@@ -42,7 +42,9 @@ func (m *mockAgent) ResolveSessionFile(sessionDir, agentSessionID string) string
 }
 
 //nolint:nilnil // Mock implementation
-func (m *mockAgent) ReadSession(_ *HookInput) (*AgentSession, error)       { return nil, nil }
+func (m *mockAgent) ReadSession(_ context.Context, _ *HookInput) (*AgentSession, error) {
+	return nil, nil
+}
 func (m *mockAgent) WriteSession(_ context.Context, _ *AgentSession) error { return nil }
 func (m *mockAgent) FormatResumeCommand(_ string) string                   { return "" }
 

cmd/entire/cli/agent/capabilities_test.go

@@ -23,11 +23,13 @@ func (m *mockBaseAgent) ReadTranscript(string) ([]byte, error)        { return n
 func (m *mockBaseAgent) ChunkTranscript(context.Context, []byte, int) ([][]byte, error) {
 	return nil, nil
 }
-func (m *mockBaseAgent) ReassembleTranscript([][]byte) ([]byte, error)     { return nil, nil }
-func (m *mockBaseAgent) GetSessionID(*HookInput) string                    { return "" }
-func (m *mockBaseAgent) GetSessionDir(string) (string, error)              { return "", nil }
-func (m *mockBaseAgent) ResolveSessionFile(string, string) string          { return "" }
-func (m *mockBaseAgent) ReadSession(*HookInput) (*AgentSession, error)     { return nil, nil } //nolint:nilnil // test mock
+func (m *mockBaseAgent) ReassembleTranscript([][]byte) ([]byte, error) { return nil, nil }
+func (m *mockBaseAgent) GetSessionID(*HookInput) string                { return "" }
+func (m *mockBaseAgent) GetSessionDir(string) (string, error)          { return "", nil }
+func (m *mockBaseAgent) ResolveSessionFile(string, string) string      { return "" }
+func (m *mockBaseAgent) ReadSession(context.Context, *HookInput) (*AgentSession, error) {
+	return nil, nil //nolint:nilnil // test mock
+}
 func (m *mockBaseAgent) WriteSession(context.Context, *AgentSession) error { return nil }
 func (m *mockBaseAgent) FormatResumeCommand(string) string                 { return "" }
 
@@ -76,7 +78,9 @@ func (m *mockFullAgent) ExtractSummary(string) (string, error)        { return "
 func (m *mockFullAgent) PrepareTranscript(context.Context, string) error { return nil }
 
 // TokenCalculator
-func (m *mockFullAgent) CalculateTokenUsage([]byte, int) (*TokenUsage, error) { return nil, nil } //nolint:nilnil // test mock
+func (m *mockFullAgent) CalculateTokenUsage(context.Context, []byte, int) (*TokenUsage, error) {
+	return nil, nil //nolint:nilnil // test mock
+}
 
 // TextGenerator
 func (m *mockFullAgent) GenerateText(context.Context, string, string) (string, error) {

cmd/entire/cli/agent/claudecode/claude.go

@@ -121,7 +121,7 @@ func (c *ClaudeCodeAgent) GetSessionBaseDir() (string, error) {
 // ReadSession reads a session from Claude's storage (JSONL transcript file).
 // The session data is stored in NativeData as raw JSONL bytes.
 // ModifiedFiles is computed by parsing the transcript.
-func (c *ClaudeCodeAgent) ReadSession(input *agent.HookInput) (*agent.AgentSession, error) {
+func (c *ClaudeCodeAgent) ReadSession(_ context.Context, input *agent.HookInput) (*agent.AgentSession, error) {
 	if input.SessionRef == "" {
 		return nil, errors.New("session reference (transcript path) is required")
 	}
@@ -251,8 +251,8 @@ func (c *ClaudeCodeAgent) FindCheckpointUUID(session *agent.AgentSession, toolUs
 
 // ReadSessionFromPath is a convenience method that reads a session directly from a file path.
 // This is useful when you have the path but not a HookInput.
-func (c *ClaudeCodeAgent) ReadSessionFromPath(transcriptPath, sessionID string) (*agent.AgentSession, error) {
-	return c.ReadSession(&agent.HookInput{
+func (c *ClaudeCodeAgent) ReadSessionFromPath(ctx context.Context, transcriptPath, sessionID string) (*agent.AgentSession, error) {
+	return c.ReadSession(ctx, &agent.HookInput{
 		SessionID:  sessionID,
 		SessionRef: transcriptPath,
 	})

cmd/entire/cli/agent/claudecode/lifecycle.go

@@ -90,7 +90,7 @@ func (c *ClaudeCodeAgent) PrepareTranscript(ctx context.Context, sessionRef stri
 }
 
 // CalculateTokenUsage computes token usage from the transcript starting at the given line offset.
-func (c *ClaudeCodeAgent) CalculateTokenUsage(transcriptData []byte, fromOffset int) (*agent.TokenUsage, error) {
+func (c *ClaudeCodeAgent) CalculateTokenUsage(_ context.Context, transcriptData []byte, fromOffset int) (*agent.TokenUsage, error) {
 	return c.CalculateTotalTokenUsage(transcriptData, fromOffset, "")
 }
 

cmd/entire/cli/agent/codex/codex.go

@@ -119,7 +119,7 @@ func (c *CodexAgent) ResolveRestoredSessionFile(sessionDir, agentSessionID strin
 func (c *CodexAgent) ProtectedDirs() []string { return []string{".codex"} }
 
 // ReadSession reads a session from Codex's storage (JSONL rollout file).
-func (c *CodexAgent) ReadSession(input *agent.HookInput) (*agent.AgentSession, error) {
+func (c *CodexAgent) ReadSession(_ context.Context, input *agent.HookInput) (*agent.AgentSession, error) {
 	if input.SessionRef == "" {
 		return nil, errors.New("session reference (transcript path) is required")
 	}

cmd/entire/cli/agent/codex/codex_test.go

@@ -125,7 +125,7 @@ func TestCodexAgent_ReadSession(t *testing.T) {
 	ag := &CodexAgent{}
 	path := writeSampleRollout(t)
 
-	session, err := ag.ReadSession(&agent.HookInput{
+	session, err := ag.ReadSession(t.Context(), &agent.HookInput{
 		SessionID:  "codex-session-1",
 		SessionRef: path,
 	})
@@ -145,7 +145,7 @@ func TestCodexAgent_ReadSession_InvalidSessionMeta(t *testing.T) {
 	path := filepath.Join(dir, "rollout.jsonl")
 	require.NoError(t, os.WriteFile(path, []byte(`{"timestamp":"2026-03-25T11:31:11.754Z","type":"response_item","payload":{"type":"message"}}`), 0o600))
 
-	_, err := ag.ReadSession(&agent.HookInput{
+	_, err := ag.ReadSession(t.Context(), &agent.HookInput{
 		SessionID:  "codex-session-1",
 		SessionRef: path,
 	})

cmd/entire/cli/agent/codex/transcript.go

@@ -3,6 +3,7 @@ package codex
 import (
 	"bufio"
 	"bytes"
+	"context"
 	"encoding/json"
 	"errors"
 	"fmt"
@@ -197,7 +198,7 @@ func extractFilesFromApplyPatch(input string) []string {
 // CalculateTokenUsage computes token usage from the transcript starting at the given line offset.
 // Codex reports cumulative total_token_usage, so we compute the delta between the last
 // token_count at/before the offset and the last token_count after the offset.
-func (c *CodexAgent) CalculateTokenUsage(transcriptData []byte, fromOffset int) (*agent.TokenUsage, error) {
+func (c *CodexAgent) CalculateTokenUsage(_ context.Context, transcriptData []byte, fromOffset int) (*agent.TokenUsage, error) {
 	var baselineUsage *tokenUsageData // last token_count at or before offset
 	var lastUsage *tokenUsageData     // last token_count after offset
 	apiCalls := 0

cmd/entire/cli/agent/codex/transcript_test.go

@@ -98,7 +98,7 @@ func TestCalculateTokenUsage(t *testing.T) {
 	ag := &CodexAgent{}
 
 	// From offset 0 (no baseline), should return full cumulative total
-	usage, err := ag.CalculateTokenUsage([]byte(sampleRollout), 0)
+	usage, err := ag.CalculateTokenUsage(t.Context(), []byte(sampleRollout), 0)
 	require.NoError(t, err)
 	require.NotNil(t, usage)
 
@@ -115,7 +115,7 @@ func TestCalculateTokenUsage_WithOffset(t *testing.T) {
 
 	// Skip past first token_count (line 4) — baseline is {5000, 4000, 100}
 	// Last after offset is {15000, 12000, 300} → delta = {10000, 8000, 200}
-	usage, err := ag.CalculateTokenUsage([]byte(sampleRollout), 4)
+	usage, err := ag.CalculateTokenUsage(t.Context(), []byte(sampleRollout), 4)
 	require.NoError(t, err)
 	require.NotNil(t, usage)
 
@@ -130,7 +130,7 @@ func TestCalculateTokenUsage_NoData(t *testing.T) {
 	t.Parallel()
 	ag := &CodexAgent{}
 
-	usage, err := ag.CalculateTokenUsage([]byte(`{"timestamp":"t","type":"session_meta","payload":{}}`), 0)
+	usage, err := ag.CalculateTokenUsage(t.Context(), []byte(`{"timestamp":"t","type":"session_meta","payload":{}}`), 0)
 	require.NoError(t, err)
 	require.Nil(t, usage)
 }

cmd/entire/cli/agent/copilotcli/copilotcli.go

@@ -85,7 +85,7 @@ func (c *CopilotCLIAgent) ProtectedDirs() []string {
 }
 
 // ReadSession reads a session from Copilot CLI's storage (JSONL transcript file).
-func (c *CopilotCLIAgent) ReadSession(input *agent.HookInput) (*agent.AgentSession, error) {
+func (c *CopilotCLIAgent) ReadSession(_ context.Context, input *agent.HookInput) (*agent.AgentSession, error) {
 	if input.SessionRef == "" {
 		return nil, errors.New("session reference (transcript path) is required")
 	}

cmd/entire/cli/agent/copilotcli/copilotcli_test.go

@@ -156,7 +156,7 @@ func TestReadSession_Success(t *testing.T) {
 		SessionRef: transcriptPath,
 	}
 
-	session, err := ag.ReadSession(input)
+	session, err := ag.ReadSession(t.Context(), input)
 	if err != nil {
 		t.Fatalf("ReadSession() error = %v", err)
 	}
@@ -189,7 +189,7 @@ func TestReadSession_NativeDataMatchesFile(t *testing.T) {
 		SessionRef: transcriptPath,
 	}
 
-	session, err := ag.ReadSession(input)
+	session, err := ag.ReadSession(t.Context(), input)
 	if err != nil {
 		t.Fatalf("ReadSession() error = %v", err)
 	}
@@ -209,7 +209,7 @@ func TestReadSession_EmptySessionRef(t *testing.T) {
 	ag := &CopilotCLIAgent{}
 	input := &agent.HookInput{SessionID: "sess-no-ref"}
 
-	_, err := ag.ReadSession(input)
+	_, err := ag.ReadSession(t.Context(), input)
 	if err == nil {
 		t.Fatal("ReadSession() should error when SessionRef is empty")
 	}
@@ -223,7 +223,7 @@ func TestReadSession_MissingFile(t *testing.T) {
 		SessionRef: "/nonexistent/path/events.jsonl",
 	}
 
-	_, err := ag.ReadSession(input)
+	_, err := ag.ReadSession(t.Context(), input)
 	if err == nil {
 		t.Fatal("ReadSession() should error when transcript file doesn't exist")
 	}
@@ -271,7 +271,7 @@ func TestWriteSession_RoundTrip(t *testing.T) {
 		SessionID:  "roundtrip-session",
 		SessionRef: transcriptPath,
 	}
-	session, err := ag.ReadSession(input)
+	session, err := ag.ReadSession(t.Context(), input)
 	if err != nil {
 		t.Fatalf("ReadSession() error = %v", err)
 	}
@@ -562,7 +562,7 @@ func TestReadTranscript_MatchesReadSession(t *testing.T) {
 		t.Fatalf("ReadTranscript() error = %v", err)
 	}
 
-	session, err := ag.ReadSession(&agent.HookInput{
+	session, err := ag.ReadSession(t.Context(), &agent.HookInput{
 		SessionID:  "compare-session",
 		SessionRef: transcriptPath,
 	})

cmd/entire/cli/agent/copilotcli/transcript.go

@@ -7,6 +7,7 @@ import (
 	"encoding/json"
 	"fmt"
 	"io"
+	"log/slog"
 	"os"
 
 	"github.com/entireio/cli/cmd/entire/cli/agent"
@@ -267,19 +268,19 @@ const eventTypeSessionShutdown = "session.shutdown"
 // contains session-wide aggregates. For sliced transcripts, session.shutdown
 // would overcount because it is not checkpoint-scoped, so we fall back to
 // summing assistant.message outputTokens within the slice.
-func (c *CopilotCLIAgent) CalculateTokenUsage(transcriptData []byte, fromOffset int) (*agent.TokenUsage, error) {
+func (c *CopilotCLIAgent) CalculateTokenUsage(ctx context.Context, transcriptData []byte, fromOffset int) (*agent.TokenUsage, error) {
 	events, err := parseEventsFromOffset(transcriptData, fromOffset)
 	if err != nil {
 		return nil, fmt.Errorf("failed to parse transcript for token usage: %w", err)
 	}
 
-	return extractTokenUsageFromEvents(events, fromOffset == 0), nil
+	return extractTokenUsageFromEvents(ctx, events, fromOffset == 0), nil
 }
 
 // extractTokenUsageFromEvents extracts token usage from parsed events.
 // Prefers session.shutdown aggregate only when the caller is looking at the
 // full transcript; otherwise falls back to per-message outputTokens.
-func extractTokenUsageFromEvents(events []copilotEvent, preferSessionShutdown bool) *agent.TokenUsage {
+func extractTokenUsageFromEvents(ctx context.Context, events []copilotEvent, preferSessionShutdown bool) *agent.TokenUsage {
 	if preferSessionShutdown {
 		// session.shutdown is authoritative, but only for full-session totals.
 		for i := len(events) - 1; i >= 0; i-- {
@@ -289,8 +290,8 @@ func extractTokenUsageFromEvents(events []copilotEvent, preferSessionShutdown bo
 
 			var data sessionShutdownData
 			if err := json.Unmarshal(events[i].Data, &data); err != nil {
-				logging.Debug(context.Background(), "copilot-cli: session.shutdown data unmarshal failed",
-					"err", err)
+				logging.Debug(ctx, "copilot-cli: session.shutdown data unmarshal failed",
+					slog.String("err", err.Error()))
 				continue
 			}
 

cmd/entire/cli/agent/copilotcli/transcript_test.go

@@ -382,7 +382,7 @@ func TestCalculateTokenUsage_SessionShutdown(t *testing.T) {
 	)
 	content := []byte(strings.Join(lines, "\n") + "\n")
 
-	usage, err := ag.CalculateTokenUsage(content, 0)
+	usage, err := ag.CalculateTokenUsage(t.Context(), content, 0)
 	if err != nil {
 		t.Fatalf("unexpected error: %v", err)
 	}
@@ -412,7 +412,7 @@ func TestCalculateTokenUsage_MultiModel(t *testing.T) {
 	}
 	content := []byte(strings.Join(lines, "\n") + "\n")
 
-	usage, err := ag.CalculateTokenUsage(content, 0)
+	usage, err := ag.CalculateTokenUsage(t.Context(), content, 0)
 	if err != nil {
 		t.Fatalf("unexpected error: %v", err)
 	}
@@ -445,7 +445,7 @@ func TestCalculateTokenUsage_EmptyModelMetrics(t *testing.T) {
 	}
 	content := []byte(strings.Join(lines, "\n") + "\n")
 
-	usage, err := ag.CalculateTokenUsage(content, 0)
+	usage, err := ag.CalculateTokenUsage(t.Context(), content, 0)
 	if err != nil {
 		t.Fatalf("unexpected error: %v", err)
 	}
@@ -468,7 +468,7 @@ func TestCalculateTokenUsage_FallbackToAssistantMessages(t *testing.T) {
 	}
 	content := []byte(strings.Join(lines, "\n") + "\n")
 
-	usage, err := ag.CalculateTokenUsage(content, 0)
+	usage, err := ag.CalculateTokenUsage(t.Context(), content, 0)
 	if err != nil {
 		t.Fatalf("unexpected error: %v", err)
 	}
@@ -487,7 +487,7 @@ func TestCalculateTokenUsage_EmptyTranscript(t *testing.T) {
 	t.Parallel()
 	ag := &CopilotCLIAgent{}
 
-	usage, err := ag.CalculateTokenUsage([]byte{}, 0)
+	usage, err := ag.CalculateTokenUsage(t.Context(), []byte{}, 0)
 	if err != nil {
 		t.Fatalf("unexpected error: %v", err)
 	}
@@ -509,7 +509,7 @@ func TestCalculateTokenUsage_WithOffset(t *testing.T) {
 	}
 	content := []byte(strings.Join(lines, "\n") + "\n")
 
-	usage, err := ag.CalculateTokenUsage(content, 1)
+	usage, err := ag.CalculateTokenUsage(t.Context(), content, 1)
 	if err != nil {
 		t.Fatalf("unexpected error: %v", err)
 	}

cmd/entire/cli/agent/cursor/cursor.go

@@ -125,7 +125,7 @@ func (c *CursorAgent) GetSessionBaseDir() (string, error) {
 // Note: ModifiedFiles is left empty because Cursor's transcript does not contain
 // tool_use blocks for file detection. TranscriptAnalyzer extracts prompts and
 // summaries; file detection relies on git status.
-func (c *CursorAgent) ReadSession(input *agent.HookInput) (*agent.AgentSession, error) {
+func (c *CursorAgent) ReadSession(_ context.Context, input *agent.HookInput) (*agent.AgentSession, error) {
 	if input.SessionRef == "" {
 		return nil, errors.New("session reference (transcript path) is required")
 	}

cmd/entire/cli/agent/cursor/cursor_test.go

@@ -239,7 +239,7 @@ func TestReadSession_Success(t *testing.T) {
 		SessionRef: transcriptPath,
 	}
 
-	session, err := ag.ReadSession(input)
+	session, err := ag.ReadSession(t.Context(), input)
 	if err != nil {
 		t.Fatalf("ReadSession() error = %v", err)
 	}
@@ -272,7 +272,7 @@ func TestReadSession_NativeDataMatchesFile(t *testing.T) {
 		SessionRef: transcriptPath,
 	}
 
-	session, err := ag.ReadSession(input)
+	session, err := ag.ReadSession(t.Context(), input)
 	if err != nil {
 		t.Fatalf("ReadSession() error = %v", err)
 	}
@@ -298,7 +298,7 @@ func TestReadSession_ModifiedFilesEmpty(t *testing.T) {
 		SessionRef: transcriptPath,
 	}
 
-	session, err := ag.ReadSession(input)
+	session, err := ag.ReadSession(t.Context(), input)
 	if err != nil {
 		t.Fatalf("ReadSession() error = %v", err)
 	}
@@ -315,7 +315,7 @@ func TestReadSession_EmptySessionRef(t *testing.T) {
 	ag := &CursorAgent{}
 	input := &agent.HookInput{SessionID: "sess-no-ref"}
 
-	_, err := ag.ReadSession(input)
+	_, err := ag.ReadSession(t.Context(), input)
 	if err == nil {
 		t.Fatal("ReadSession() should error when SessionRef is empty")
 	}
@@ -329,7 +329,7 @@ func TestReadSession_MissingFile(t *testing.T) {
 		SessionRef: "/nonexistent/path/transcript.jsonl",
 	}
 
-	_, err := ag.ReadSession(input)
+	_, err := ag.ReadSession(t.Context(), input)
 	if err == nil {
 		t.Fatal("ReadSession() should error when transcript file doesn't exist")
 	}
@@ -377,7 +377,7 @@ func TestWriteSession_RoundTrip(t *testing.T) {
 		SessionID:  "roundtrip-session",
 		SessionRef: transcriptPath,
 	}
-	session, err := ag.ReadSession(input)
+	session, err := ag.ReadSession(t.Context(), input)
 	if err != nil {
 		t.Fatalf("ReadSession() error = %v", err)
 	}

cmd/entire/cli/agent/cursor/lifecycle_test.go

@@ -627,7 +627,7 @@ func TestReadTranscript_MatchesReadSession(t *testing.T) {
 	}
 
 	// ReadSession
-	session, err := ag.ReadSession(&agent.HookInput{
+	session, err := ag.ReadSession(t.Context(), &agent.HookInput{
 		SessionID:  "compare-session",
 		SessionRef: transcriptPath,
 	})