Preserve subagent token totals during condensation

Condensation was recalculating Claude Code token usage without the session subagent transcript directory, so metadata written on user commits dropped Task-spawned token totals even though live session state could see them. The fix reuses the transcript-dir/session-id convention already used by lifecycle hooks and locks the behavior with a focused condensation regression.

Constraint: Checkpoint metadata pushes for this branch must route through stale2000/cli, so the committed Entire settings point checkpoint_remote at the fork.

Rejected: Rework token parsing or checkpoint storage | the loss was caused by a missing subagent transcript directory argument, not the parser or metadata schema.

Confidence: high

Scope-risk: narrow

Directive: Keep condensation subagent path derivation aligned with lifecycle hook path derivation when changing transcript layouts.

Tested: go test ./cmd/entire/cli/strategy -run 'TestCondenseSession' -count=1

Tested: go test ./cmd/entire/cli/agent/claudecode -run 'TestCalculateTotalTokenUsage|TestExtractAllModifiedFiles' -count=1

Not-tested: Full mise run check because unrelated local uiform work currently trips lint before this branch is isolated.
Entire-Checkpoint: 36286545221f

Author: stale2000

.entire/settings.json

@@ -4,7 +4,7 @@
   "strategy_options": {
     "checkpoint_remote": {
       "provider": "github",
-      "repo": "entireio/cli-checkpoints"
+      "repo": "stale2000/cli"
     },
     "filtered_fetches": true
   },

cmd/entire/cli/strategy/manual_commit_condensation.go

@@ -462,6 +462,13 @@ func (s *ManualCommitStrategy) extractOrCreateSessionData(ctx context.Context, r
 	}
 }
 
+func subagentsDirForTranscript(transcriptPath, sessionID string) string {
+	if transcriptPath == "" || sessionID == "" {
+		return ""
+	}
+	return filepath.Join(filepath.Dir(transcriptPath), sessionID, "subagents")
+}
+
 // generateSummary produces an LLM-generated summary of the session transcript.
 // The transcript must be pre-redacted to avoid sending secrets to the LLM.
 // Returns nil if the scoped transcript is empty or generation fails.
@@ -898,7 +905,8 @@ func (s *ManualCommitStrategy) extractSessionData(ctx context.Context, repo *git
 	// extract them from offset 0; consumers can filter by checkpoint_transcript_start
 	// if they only render the checkpoint-scoped slice.
 	if len(data.Transcript) > 0 {
-		data.TokenUsage = agent.CalculateTokenUsage(ctx, ag, data.Transcript, checkpointTranscriptStart, "") //TODO: why do we not use here subagents dir?
+		subagentsDir := subagentsDirForTranscript(liveTranscriptPath, sessionID)
+		data.TokenUsage = agent.CalculateTokenUsage(ctx, ag, data.Transcript, checkpointTranscriptStart, subagentsDir)
 		data.SkillEvents = agent.ExtractSkillEvents(ctx, ag, data.Transcript, 0)
 	}
 
@@ -940,7 +948,8 @@ func (s *ManualCommitStrategy) extractSessionDataFromLiveTranscript(ctx context.
 	// extract them from offset 0; consumers can filter by checkpoint_transcript_start
 	// if they only render the checkpoint-scoped slice.
 	if len(data.Transcript) > 0 {
-		data.TokenUsage = agent.CalculateTokenUsage(ctx, ag, data.Transcript, state.CheckpointTranscriptStart, "") //TODO: why do we not use here subagents dir?
+		subagentsDir := subagentsDirForTranscript(transcriptPath, state.SessionID)
+		data.TokenUsage = agent.CalculateTokenUsage(ctx, ag, data.Transcript, state.CheckpointTranscriptStart, subagentsDir)
 		data.SkillEvents = agent.ExtractSkillEvents(ctx, ag, data.Transcript, 0)
 	}
 

cmd/entire/cli/strategy/manual_commit_test.go

@@ -23,6 +23,8 @@ import (
 	"github.com/go-git/go-git/v6/plumbing/object"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
+
+	_ "github.com/entireio/cli/cmd/entire/cli/agent/claudecode" // Register Claude Code agent for condensation token tests
 )
 
 const testTrailerCheckpointID id.CheckpointID = "a1b2c3d4e5f6"
@@ -3323,6 +3325,65 @@ func TestCondenseSession_TranscriptRelocatedMidSession(t *testing.T) {
 	}
 }
 
+func TestCondenseSession_ClaudeSubagentTokenUsage(t *testing.T) {
+	dir := t.TempDir()
+	testutil.InitRepo(t, dir)
+	testutil.WriteFile(t, dir, "README.md", "initial\n")
+	testutil.GitAdd(t, dir, "README.md")
+	testutil.GitCommit(t, dir, "initial")
+	t.Chdir(dir)
+
+	sessionID := "2026-06-09-claude-subagent-token"
+	transcriptDir := filepath.Join(dir, ".claude", "transcripts")
+	transcriptPath := filepath.Join(transcriptDir, "main.jsonl")
+	subagentsDir := filepath.Join(transcriptDir, sessionID, "subagents")
+	require.NoError(t, os.MkdirAll(subagentsDir, 0o755))
+
+	mainTranscript := strings.Join([]string{
+		`{"type":"assistant","uuid":"a-main","message":{"id":"msg_main","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_task1","name":"Task","input":{"description":"write helper","prompt":"write helper"}}],"usage":{"input_tokens":100,"cache_creation_input_tokens":0,"cache_read_input_tokens":0,"output_tokens":10}}}`,
+		`{"type":"user","uuid":"u-main","message":{"content":[{"type":"tool_result","tool_use_id":"toolu_task1","content":"agentId: sub1"}]}}`,
+	}, "\n") + "\n"
+	require.NoError(t, os.WriteFile(transcriptPath, []byte(mainTranscript), 0o644))
+
+	subagentTranscript := `{"type":"assistant","uuid":"a-sub","message":{"id":"msg_sub","type":"message","role":"assistant","content":[{"type":"text","text":"wrote helper"}],"usage":{"input_tokens":200,"cache_creation_input_tokens":0,"cache_read_input_tokens":0,"output_tokens":20}}}` + "\n"
+	require.NoError(t, os.WriteFile(filepath.Join(subagentsDir, "agent-sub1.jsonl"), []byte(subagentTranscript), 0o644))
+
+	repo, err := git.PlainOpen(dir)
+	require.NoError(t, err)
+	head, err := repo.Head()
+	require.NoError(t, err)
+	initialHash := head.Hash().String()
+
+	state := &SessionState{
+		SessionID:                 sessionID,
+		BaseCommit:                initialHash,
+		AttributionBaseCommit:     initialHash,
+		WorktreePath:              dir,
+		TranscriptPath:            transcriptPath,
+		FilesTouched:              []string{"helper.go"},
+		AgentType:                 agent.AgentTypeClaudeCode,
+		ModelName:                 "claude-sonnet-repro",
+		CheckpointTranscriptStart: 0,
+	}
+
+	s := &ManualCommitStrategy{}
+	checkpointID := id.MustCheckpointID("dd11cc22bb33")
+	_, err = s.CondenseSession(context.Background(), repo, checkpointID, state, nil)
+	require.NoError(t, err)
+
+	store := checkpoint.NewGitStore(repo, checkpoint.DefaultV1Refs())
+	content, err := store.ReadLatestSessionContent(t.Context(), checkpointID)
+	require.NoError(t, err)
+
+	require.NotNil(t, content.Metadata.TokenUsage, "TokenUsage should be persisted")
+	assert.Equal(t, 100, content.Metadata.TokenUsage.InputTokens)
+	assert.Equal(t, 10, content.Metadata.TokenUsage.OutputTokens)
+	require.NotNil(t, content.Metadata.TokenUsage.SubagentTokens, "SubagentTokens should survive condensation")
+	assert.Equal(t, 200, content.Metadata.TokenUsage.SubagentTokens.InputTokens)
+	assert.Equal(t, 20, content.Metadata.TokenUsage.SubagentTokens.OutputTokens)
+	assert.Equal(t, 1, content.Metadata.TokenUsage.SubagentTokens.APICallCount)
+}
+
 // TestCondenseSession_GeminiTranscript verifies that CondenseSession works correctly
 // with Gemini JSON format transcripts, including prompt extraction and format detection.
 func TestCondenseSession_GeminiTranscript(t *testing.T) {