Appendix A: Key File Index

This appendix lists the key files in the Claude Code v2.1.88 source code and their responsibilities, grouped by subsystem. File paths are relative to restored-src/src/.

Entry Points and Core Loop

File	Responsibility	Related Chapters
main.tsx	CLI entry point, parallel prefetch, lazy import, Feature Flag gating	Chapter 1
query.ts	Agent Loop main loop, queryLoop state machine	Chapter 3
query/transitions.ts	Loop transition types: Continue, Terminal	Chapter 3

Tool System

File	Responsibility	Related Chapters
Tool.ts	Tool interface contract, TOOL_DEFAULTS fail-closed defaults	Chapters 2, 25
tools.ts	Tool registration, Feature Flag conditional loading	Chapter 2
services/tools/toolOrchestration.ts	Tool execution orchestration, partitionToolCalls concurrency partitioning	Chapter 4
services/tools/toolExecution.ts	Single-tool execution lifecycle	Chapter 4
services/tools/StreamingToolExecutor.ts	Streaming tool executor	Chapter 4
tools/BashTool/	Bash tool implementation, including Git safety protocol	Chapters 8, 27
tools/FileEditTool/	File edit tool, "read before edit" enforcement	Chapters 8, 27
tools/FileReadTool/	File read tool, default 2000 lines	Chapter 8
tools/GrepTool/	ripgrep-based search tool	Chapter 8
tools/AgentTool/	Sub-Agent spawning tool	Chapters 8, 20
tools/SkillTool/	Skill invocation tool	Chapters 8, 22
tools/SkillTool/prompt.ts	Skill list budget: 1% of context window	Chapters 12, 26

System Prompts

File	Responsibility	Related Chapters
constants/prompts.ts	System prompt construction, SYSTEM_PROMPT_DYNAMIC_BOUNDARY	Chapters 5, 6, 25
constants/systemPromptSections.ts	Section registry with cache control scope	Chapter 5
constants/toolLimits.ts	Tool result budget constants	Chapters 12, 26

API and Caching

File	Responsibility	Related Chapters
services/api/claude.ts	API call construction, cache breakpoint placement	Chapter 13
services/api/promptCacheBreakDetection.ts	Cache break detection, PreviousState tracking	Chapters 14, 25
utils/api.ts	splitSysPromptPrefix() three-way cache splitting	Chapters 5, 13

Context Compaction

File	Responsibility	Related Chapters
services/compact/compact.ts	Compaction orchestration, POST_COMPACT_MAX_FILES_TO_RESTORE	Chapters 9, 10
services/compact/autoCompact.ts	Auto-compaction threshold and circuit breaker	Chapters 9, 25, 26
services/compact/prompt.ts	Compaction prompt template	Chapters 9, 28
services/compact/microCompact.ts	Time-based micro-compaction	Chapter 11
services/compact/apiMicrocompact.ts	API-native cached micro-compaction	Chapter 11

Permissions and Security

File	Responsibility	Related Chapters
utils/permissions/yoloClassifier.ts	YOLO auto-mode classifier	Chapter 17
utils/permissions/denialTracking.ts	Denial tracking, DENIAL_LIMITS	Chapters 17, 27
tools/BashTool/bashPermissions.ts	Bash command permission checks	Chapter 16

CLAUDE.md and Skills

File	Responsibility	Related Chapters
utils/claudemd.ts	CLAUDE.md loading and injection, 4-layer priority	Chapter 19
skills/bundled/	Built-in skills directory	Chapter 22
skills/loadSkillsDir.ts	User-defined skill discovery	Chapter 22
skills/mcpSkillBuilders.ts	MCP-to-skill bridge	Chapter 22

Multi-Agent Orchestration

File	Responsibility	Related Chapters
coordinator/coordinatorMode.ts	Coordinator mode implementation	Chapter 20
utils/teammate.ts	Teammate Agent tools	Chapter 20
utils/swarm/teammatePromptAddendum.ts	Teammate prompt addendum content	Chapter 20

Tool Results and Storage

File	Responsibility	Related Chapters
utils/toolResultStorage.ts	Large result persistence, truncation previews	Chapters 12, 28
utils/toolSchemaCache.ts	Tool Schema caching	Chapter 15

Cross-Session Memory

File	Responsibility	Related Chapters
memdir/memdir.ts	MEMORY.md index and topic file loading, system prompt injection	Chapter 24
memdir/paths.ts	Memory directory path resolution, three-level priority chain	Chapter 24
services/extractMemories/extractMemories.ts	Fork agent automatic memory extraction	Chapter 24
services/SessionMemory/sessionMemory.ts	Rolling session summary for compaction	Chapter 24
utils/sessionStorage.ts	JSONL session record storage and recovery	Chapter 24
tools/AgentTool/agentMemory.ts	Sub-Agent persistence and VCS snapshots	Chapter 24
services/autoDream/autoDream.ts	Overnight memory consolidation and pruning	Chapter 24

Telemetry and Observability

File	Responsibility	Related Chapters
services/analytics/index.ts	Event entry point, queue-attach pattern, PII tag types	Chapter 29
services/analytics/sink.ts	Dual-path dispatch (Datadog + 1P), sampling	Chapter 29
services/analytics/firstPartyEventLogger.ts	OTel BatchLogRecordProcessor integration	Chapter 29
services/analytics/firstPartyEventLoggingExporter.ts	Custom Exporter, disk-persistent retry	Chapter 29
services/analytics/metadata.ts	Event metadata, tool name sanitization, PII grading	Chapter 29
services/analytics/datadog.ts	Datadog allow-list, batch flushing	Chapter 29
services/analytics/sinkKillswitch.ts	Remote circuit breaker (tengu_frond_boric)	Chapter 29
services/api/logging.ts	API three-event model (query/success/error)	Chapter 29
services/api/withRetry.ts	Retry telemetry, gateway fingerprint detection	Chapter 29
utils/debug.ts	Debug logging, --debug flag	Chapter 29
utils/diagLogs.ts	PII-free container diagnostics	Chapter 29
utils/errorLogSink.ts	Error file logging	Chapter 29
utils/telemetry/sessionTracing.ts	OTel spans, three-level tracing	Chapter 29
utils/telemetry/perfettoTracing.ts	Perfetto visualization tracing	Chapter 29
utils/gracefulShutdown.ts	Cascading timeout graceful shutdown	Chapter 29
cost-tracker.ts	Cost tracking, cross-session persistence	Chapter 29

Configuration and State

File	Responsibility	Related Chapters
utils/effort.ts	Effort level parsing	Chapter 21
utils/fastMode.ts	Fast Mode management	Chapter 21
utils/managedEnvConstants.ts	Managed environment variable allowlist	Appendix B
screens/REPL.tsx	Main interactive interface (5000+ line React component)	Chapter 1