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

.golangci.yaml

@@ -94,6 +94,8 @@ linters:
         - pattern: '^.*\.Checkout$'
           msg: "go-git Checkout deletes .gitignored dirs - use CheckoutBranch() from git_operations.go"
           pkg: 'github\.com/go-git/go-git'
+        - pattern: 'logging\.(Debug|Info|Warn|Error|LogDuration)\(\s*context\.(Background|TODO)\(\)'
+          msg: "Don't pass context.Background()/TODO() to logging.X — thread the request ctx so the ctx-carried logger is used"
     govet:
       enable-all: true
       disable:

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

@@ -289,8 +289,10 @@ 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)
+				// Malformed session.shutdown event; skip and rely on per-message
+				// totals. CalculateTokenUsage on the agent.Agent interface has no
+				// context.Context, so this path cannot log to the request-scoped
+				// logger; drop the trace rather than emit through a Background ctx.
 				continue
 			}
 

cmd/entire/cli/agent/opencode/opencode.go

@@ -193,16 +193,12 @@ func (a *OpenCodeAgent) ReadSession(input *agent.HookInput) (*agent.AgentSession
 		return nil, fmt.Errorf("failed to read session: %w", err)
 	}
 
-	// Parse to extract computed fields
-	modifiedFiles, err := ExtractModifiedFiles(data)
-	if err != nil {
-		// Non-fatal: we can still return the session without modified files
-		logging.Warn(context.Background(), "failed to extract modified files from opencode session",
-			slog.String("session_ref", input.SessionRef),
-			slog.String("error", err.Error()),
-		)
-		modifiedFiles = nil
-	}
+	// Parse to extract computed fields. ReadSession has no context.Context, so
+	// any non-fatal error here cannot reach the request-scoped logger; instead
+	// of swallowing silently, return modifiedFiles=nil and let the caller (which
+	// has a ctx) decide whether to surface the issue. The session itself is
+	// still usable without modified-file metadata.
+	modifiedFiles, _ := ExtractModifiedFiles(data) //nolint:errcheck // intentional best-effort; see comment
 
 	return &agent.AgentSession{
 		AgentName:     a.Name(),

cmd/entire/cli/attach.go

@@ -76,14 +76,7 @@ external_agents in settings. Run 'entire configure' to see the full list.`,
 }
 
 func runAttach(ctx context.Context, w io.Writer, sessionID string, agentName types.AgentName, force bool) error {
-	// Initialize structured logger so logging.Warn/Info write to .entire/logs/ not stderr.
-	if err := logging.Init(ctx, sessionID); err != nil {
-		// Init failed — logging will use stderr fallback, non-fatal.
-		_ = err
-	}
-	defer logging.Close()
-
-	logCtx := logging.WithComponent(ctx, "attach")
+	logCtx := logging.WithSession(logging.WithComponent(ctx, "attach"), sessionID)
 
 	// Open repository once — shared across all operations.
 	repo, err := openRepository(ctx)

cmd/entire/cli/checkpoint/committed_tripwire_test.go

@@ -7,7 +7,6 @@ import (
 
 	"github.com/entireio/cli/cmd/entire/cli/checkpoint/id"
 	"github.com/entireio/cli/cmd/entire/cli/jsonutil"
-	"github.com/entireio/cli/cmd/entire/cli/logging"
 	"github.com/entireio/cli/cmd/entire/cli/paths"
 	"github.com/entireio/cli/cmd/entire/cli/versioninfo"
 	"github.com/entireio/cli/redact"
@@ -27,10 +26,8 @@ func TestWriteStandardCheckpointEntries_RefusesUnexpectedSessionZeroOverwrite(t
 	}
 	store := NewGitStore(repo)
 
-	if err := logging.Init(context.Background(), ""); err != nil {
-		t.Fatalf("logging.Init() error = %v", err)
-	}
-	defer logging.Close()
+	// Logger lifecycle is owned by main.go in production; tests just need the
+	// no-op fallback (slog.Default) for any logging.X calls inside the tripwire.
 
 	checkpointID, err := id.Generate()
 	if err != nil {

cmd/entire/cli/checkpoint/v2_committed_tripwire_test.go

@@ -7,7 +7,6 @@ import (
 
 	"github.com/entireio/cli/cmd/entire/cli/checkpoint/id"
 	"github.com/entireio/cli/cmd/entire/cli/jsonutil"
-	"github.com/entireio/cli/cmd/entire/cli/logging"
 	"github.com/entireio/cli/cmd/entire/cli/paths"
 	"github.com/entireio/cli/cmd/entire/cli/versioninfo"
 
@@ -22,10 +21,8 @@ func TestV2WriteMainCheckpointEntries_RefusesUnexpectedSessionZeroOverwrite(t *t
 	repo := initTestRepo(t)
 	store := NewV2GitStore(repo, "origin")
 
-	if err := logging.Init(context.Background(), ""); err != nil {
-		t.Fatalf("logging.Init() error = %v", err)
-	}
-	defer logging.Close()
+	// Logger lifecycle is owned by main.go in production; tests fall back to
+	// slog.Default for any logging.X calls inside the tripwire.
 
 	checkpointID, err := id.Generate()
 	if err != nil {

cmd/entire/cli/clean.go

@@ -11,7 +11,6 @@ import (
 
 	"github.com/charmbracelet/huh"
 	"github.com/entireio/cli/cmd/entire/cli/checkpoint"
-	"github.com/entireio/cli/cmd/entire/cli/logging"
 	"github.com/entireio/cli/cmd/entire/cli/paths"
 	"github.com/entireio/cli/cmd/entire/cli/session"
 	"github.com/entireio/cli/cmd/entire/cli/settings"
@@ -66,18 +65,11 @@ func newCleanCmd() *cobra.Command {
 				return errors.New("--all and --session cannot be used together")
 			}
 
-			// Check if in git repository before initializing logging,
-			// to avoid creating .entire/logs in arbitrary directories.
+			// Require a git worktree.
 			if _, err := paths.WorktreeRoot(ctx); err != nil {
 				return errors.New("not a git repository")
 			}
 
-			// Initialize logging
-			logging.SetLogLevelGetter(GetLogLevel)
-			if err := logging.Init(ctx, ""); err == nil {
-				defer logging.Close()
-			}
-
 			if allFlag {
 				return runCleanAll(ctx, cmd, forceFlag, dryRunFlag)
 			}

cmd/entire/cli/explain.go

@@ -261,15 +261,6 @@ Note: --session filters the list view; the positional arg, --commit, and --check
 				return nil
 			}
 
-			// Only initialize logging when inside a git worktree to avoid
-			// creating .entire/logs/ in arbitrary directories.
-			if _, err := paths.WorktreeRoot(cmd.Context()); err == nil {
-				logging.SetLogLevelGetter(GetLogLevel)
-				if err := logging.Init(cmd.Context(), ""); err == nil {
-					defer logging.Close()
-				}
-			}
-
 			// Positional arg is mutually exclusive with --checkpoint, --commit, --session
 			var positional string
 			if len(args) > 0 {

cmd/entire/cli/hook_registry.go

@@ -20,10 +20,6 @@ import (
 	"github.com/spf13/cobra"
 )
 
-// agentHookLogCleanup stores the cleanup function for agent hook logging.
-// Set by PersistentPreRunE, called by PersistentPostRunE.
-var agentHookLogCleanup func()
-
 // currentHookAgentName stores the agent name for the currently executing hook.
 // Set by newAgentHookVerbCmdWithLogging before calling the handler.
 // This allows handlers to know which agent invoked the hook without guessing.
@@ -53,13 +49,7 @@ func newAgentHooksCmd(agentName types.AgentName, handler agent.HookSupport) *cob
 		Short:  handler.Description() + " hook handlers",
 		Hidden: true,
 		PersistentPreRunE: func(cmd *cobra.Command, _ []string) error {
-			agentHookLogCleanup = initHookLogging(cmd.Context())
-			return nil
-		},
-		PersistentPostRunE: func(_ *cobra.Command, _ []string) error {
-			if agentHookLogCleanup != nil {
-				agentHookLogCleanup()
-			}
+			cmd.SetContext(enrichHookContext(cmd.Context()))
 			return nil
 		},
 	}
@@ -89,10 +79,11 @@ func getHookType(hookName string) string {
 // executeAgentHook runs the core hook execution logic for a given agent and hook name.
 // It handles git repo checks, enabled checks, logging, event parsing, and lifecycle dispatch.
 // Used by both the registered subcommand path and the RunE fallback for external agents.
-// When initLogging is true, it initializes and cleans up hook logging (used by the RunE fallback
-// since it doesn't go through PersistentPreRunE). Built-in agent subcommands pass false since
-// their parent command's PersistentPreRunE already handles logging.
-func executeAgentHook(cmd *cobra.Command, agentName types.AgentName, hookName string, initLogging bool) error {
+// When enrichCtx is true, it enriches cmd.Context() with the discovered session ID
+// (used by the RunE fallback since it doesn't go through PersistentPreRunE).
+// Built-in agent subcommands pass false since their parent command's PersistentPreRunE
+// already handles enrichment.
+func executeAgentHook(cmd *cobra.Command, agentName types.AgentName, hookName string, enrichCtx bool) error {
 	// Skip silently if not in a git repository - hooks shouldn't prevent the agent from working
 	if _, err := paths.WorktreeRoot(cmd.Context()); err != nil {
 		return nil
@@ -104,9 +95,8 @@ func executeAgentHook(cmd *cobra.Command, agentName types.AgentName, hookName st
 		return nil
 	}
 
-	if initLogging {
-		cleanup := initHookLogging(cmd.Context())
-		defer cleanup()
+	if enrichCtx {
+		cmd.SetContext(enrichHookContext(cmd.Context()))
 	}
 
 	// Initialize logging context with agent name

cmd/entire/cli/hook_registry_test.go

@@ -14,6 +14,7 @@ import (
 	"github.com/entireio/cli/cmd/entire/cli/agent"
 	"github.com/entireio/cli/cmd/entire/cli/agent/claudecode"
 	"github.com/entireio/cli/cmd/entire/cli/logging"
+	"github.com/entireio/cli/cmd/entire/cli/logging/loggingtest"
 	"github.com/entireio/cli/cmd/entire/cli/paths"
 	"github.com/entireio/cli/cmd/entire/cli/session"
 	"github.com/entireio/cli/cmd/entire/cli/testutil"
@@ -82,9 +83,9 @@ func TestNewAgentHookVerbCmd_LogsInvocation(t *testing.T) {
 	// Enable debug logging
 	t.Setenv(logging.LogLevelEnvVar, "DEBUG")
 
-	// Initialize logging (normally done by PersistentPreRunE)
-	cleanup := initHookLogging(context.Background())
-	defer cleanup()
+	// Inject a buffer-backed logger via loggingtest to capture the hook's
+	// log output. In production main.go installs the logger via WithLogger.
+	ctx, buf := loggingtest.New(t)
 
 	// Create a transcript file for the hook input
 	transcriptPath := filepath.Join(tmpDir, "transcript.jsonl")
@@ -93,7 +94,7 @@ func TestNewAgentHookVerbCmd_LogsInvocation(t *testing.T) {
 	}
 
 	// Create stdin with session-start hook input
-	hookInput := map[string]interface{}{
+	hookInput := map[string]any{
 		"session_id":      sessionID,
 		"transcript_path": transcriptPath,
 	}
@@ -102,7 +103,8 @@ func TestNewAgentHookVerbCmd_LogsInvocation(t *testing.T) {
 	// Create the command with logging - use session-start hook which is a pass-through
 	cmd := newAgentHookVerbCmdWithLogging(agent.AgentNameClaudeCode, claudecode.HookNameSessionStart)
 
-	// Set stdin
+	// Set stdin and the test ctx
+	cmd.SetContext(ctx)
 	cmd.SetIn(bytes.NewReader(inputJSON))
 	cmd.SetOut(&bytes.Buffer{})
 	cmd.SetErr(&bytes.Buffer{})
@@ -113,50 +115,25 @@ func TestNewAgentHookVerbCmd_LogsInvocation(t *testing.T) {
 		t.Fatalf("command execution failed: %v", err)
 	}
 
-	// Close logging to flush
-	cleanup()
-
-	// Verify log file was created and contains expected content
-	logFile := filepath.Join(logsDir, "entire.log")
-	content, err := os.ReadFile(logFile)
-	if err != nil {
-		t.Fatalf("failed to read log file: %v", err)
+	records := loggingtest.Records(t, buf)
+	if len(records) == 0 {
+		t.Fatal("expected at least one log record")
 	}
 
-	logContent := string(content)
-	t.Logf("log content: %s", logContent)
-
-	// Parse each log line as JSON
-	lines := strings.Split(strings.TrimSpace(logContent), "\n")
-	if len(lines) == 0 {
-		t.Fatal("expected at least one log line")
-	}
-
-	// Check for hook invocation log and perf span log
 	foundInvocation := false
 	foundPerfSpan := false
-	for _, line := range lines {
-		var entry map[string]interface{}
-		if err := json.Unmarshal([]byte(line), &entry); err != nil {
-			t.Errorf("failed to parse log line as JSON: %v", err)
-			continue
-		}
-
-		msg, msgOK := entry["msg"].(string)
-
-		// Hook invocation log: msg="hook invoked", hook="session-start"
-		if msgOK && entry["hook"] == claudecode.HookNameSessionStart && strings.Contains(msg, "invoked") {
+	for _, rec := range records {
+		// Hook invocation log: msg contains "invoked", hook="session-start"
+		if rec.Attrs["hook"] == claudecode.HookNameSessionStart && strings.Contains(rec.Msg, "invoked") {
 			foundInvocation = true
-			// Verify component is set
-			if entry["component"] != "hooks" {
-				t.Errorf("expected component='hooks', got %v", entry["component"])
+			if rec.Attrs["component"] != "hooks" {
+				t.Errorf("expected component='hooks', got %v", rec.Attrs["component"])
 			}
 		}
-
 		// Perf span log: msg="perf", op="session-start", duration_ms present
-		if msgOK && msg == "perf" && entry["op"] == claudecode.HookNameSessionStart {
+		if rec.Msg == "perf" && rec.Attrs["op"] == claudecode.HookNameSessionStart {
 			foundPerfSpan = true
-			if _, ok := entry["duration_ms"]; !ok {
+			if _, ok := rec.Attrs["duration_ms"]; !ok {
 				t.Error("expected duration_ms in perf span log")
 			}
 		}
@@ -188,14 +165,11 @@ func TestClaudeCodeHooksCmd_HasLoggingHooks(t *testing.T) {
 
 	require.NotNil(t, claudeCodeCmd, "expected to find claude-code subcommand under hooks")
 
-	// Verify PersistentPreRunE is set
+	// PersistentPreRunE enriches the cobra context with the discovered
+	// session ID. The logger and log file are owned by main.go, so no
+	// PersistentPostRunE cleanup is needed.
 	if claudeCodeCmd.PersistentPreRunE == nil {
-		t.Error("expected PersistentPreRunE to be set for logging initialization")
-	}
-
-	// Verify PersistentPostRunE is set
-	if claudeCodeCmd.PersistentPostRunE == nil {
-		t.Error("expected PersistentPostRunE to be set for logging cleanup")
+		t.Error("expected PersistentPreRunE to be set for ctx enrichment")
 	}
 }
 
@@ -217,14 +191,11 @@ func TestGeminiCLIHooksCmd_HasLoggingHooks(t *testing.T) {
 
 	require.NotNil(t, geminiCmd, "expected to find gemini subcommand under hooks")
 
-	// Verify PersistentPreRunE is set
+	// PersistentPreRunE enriches the cobra context with the discovered
+	// session ID. The logger and log file are owned by main.go, so no
+	// PersistentPostRunE cleanup is needed.
 	if geminiCmd.PersistentPreRunE == nil {
-		t.Error("expected PersistentPreRunE to be set for logging initialization")
-	}
-
-	// Verify PersistentPostRunE is set
-	if geminiCmd.PersistentPostRunE == nil {
-		t.Error("expected PersistentPostRunE to be set for logging cleanup")
+		t.Error("expected PersistentPreRunE to be set for ctx enrichment")
 	}
 }