File Index Handbook - Claude Code Source Code Quick Reference

After 28 chapters of in-depth analysis, you should have a comprehensive understanding of Claude Code’s architecture. But if you want to look at a specific feature’s implementation in the source code, where should you go?

This index handbook organizes Claude Code’s core source files by functional module, helping you quickly locate what you want to see.

Core Architecture Modules

Agent Loop Core

File Path	Core Class/Function	Description
`src/core/agent.ts`	`Agent` class	Agent Loop main loop, query-response-handling flow
`src/core/loop.ts`	`runLoop()`	Message loop executor, processes user input and tool results
`src/core/query.ts`	`processQuery()`	Single query processing, tool calls and response generation

Tool System

File Path	Core Class/Function	Description
`src/tools/base.ts`	`BaseTool` abstract class	Base class for all tools, defines common interface
`src/tools/registry.ts`	`ToolRegistry`	Tool registry, manages available tool list
`src/tools/loader.ts`	`loadTools()`	Dynamic tool module loading

Specific Tool Implementations

File Path	Core Class/Function	Description
`src/tools/FileReadTool.ts`	`FileReadTool`	File reading, supports offset/limit pagination
`src/tools/FileEditTool.ts`	`FileEditTool`	File editing, enforces read before edit
`src/tools/BashTool.ts`	`BashTool`	Bash command execution, includes Git safety protocol
`src/tools/GrepTool.ts`	`GrepTool`	Code search, based on ripgrep
`src/tools/AgentTool.ts`	`AgentTool`	Spawn sub-agents, supports fork mode
`src/tools/SkillTool.ts`	`SkillTool`	Skill system, budget constraint management

Context Management

Auto Compaction

File Path	Core Class/Function	Description
`src/services/compact/compact.ts`	`compact()`	Manual compaction, summary generation
`src/services/compact/autoCompact.ts`	`autoCompact()`	Auto compaction, threshold triggered
`src/services/compact/prompt.ts`	Compression prompt template	Defines compression behavior and summary format

Microcompaction

File Path	Core Class/Function	Description
`src/services/compact/microcompact.ts`	`microcompact()`	Microcompaction implementation, three-mechanism coordination
`src/services/compact/timeCleaner.ts`	`timeCleaner()`	Timestamp cleaner
`src/services/compact/cacheCleaner.ts`	`cacheCleaner()`	Cache-aware cleaner

Token Budget

File Path	Core Class/Function	Description
`src/constants/toolLimits.ts`	`DEFAULT_MAX_RESULT_SIZE_CHARS`	Tool result size limit (50K)
`src/constants/toolLimits.ts`	`MAX_TOOL_RESULTS_PER_MESSAGE_CHARS`	Single message tool result limit (200K)
`src/utils/tokenEstimator.ts`	`estimateTokens()`	Token estimator, conservative strategy

Prompt Engineering

System Prompts

File Path	Core Class/Function	Description
`src/constants/prompts.ts`	`getSystemPrompt()`	System prompt assembly
`src/constants/prompts.ts`	`getSimpleDoingTasksSection()`	Minimalist instruction group
`src/constants/prompts.ts`	`getGitSafetyProtocol()`	Git safety protocol

Dynamic Boundary

File Path	Core Class/Function	Description
`src/services/prompt/dynamicBoundary.ts`	`SYSTEM_PROMPT_DYNAMIC_BOUNDARY`	Dynamic boundary marker
`src/services/prompt/promptBuilder.ts`	`buildPrompt()`	Prompt builder

Cache System

Cache Break Detection

File Path	Core Class/Function	Description
`src/services/api/promptCacheBreakDetection.ts`	`recordPromptState()`	Record prompt state
`src/services/api/promptCacheBreakDetection.ts`	`checkResponseForCacheBreak()`	Detect cache breaks
`src/services/api/promptCacheBreakDetection.ts`	`perToolHashes`	Per-tool independent hashes

Cache Optimization

File Path	Core Class/Function	Description
`src/services/cache/dateMemoization.ts`	`getMemoizedDate()`	Date memoization, avoid midnight cache breaks
`src/services/cache/schemaCache.ts`	`schemaCache`	Tool Schema cache
`src/services/cache/betaHeaderLatch.ts`	`afkModeHeaderLatched`	Beta Header latch

Permissions and Security

Permission System

File Path	Core Class/Function	Description
`src/utils/permissions/types.ts`	`PermissionMode` enum	Permission mode type definitions
`src/utils/permissions/modeResolver.ts`	`resolvePermissionMode()`	Permission mode resolution
`src/utils/permissions/denialTracking.ts`	`DENIAL_LIMITS`	Denial tracking thresholds (3/20)
`src/utils/permissions/denialTracking.ts`	`shouldFallbackToPrompting()`	Fallback determination

YOLO Classifier

File Path	Core Class/Function	Description
`src/services/classifier/yoloClassifier.ts`	`YOLOClassifier` class	YOLO classifier main class
`src/services/classifier/stage1Fast.ts`	`stage1Fast()`	Stage 1 fast filtering
`src/services/classifier/stage2Deep.ts`	`stage2Deep()`	Stage 2 deep reasoning
`src/services/classifier/whitelist.ts`	`isWhitelisted()`	Whitelist check

Agent System

Sub-Agents

File Path	Core Class/Function	Description
`src/agents/base.ts`	`BaseAgent` class	Agent base class
`src/agents/subAgent.ts`	`SubAgent` class	Standard sub-agent implementation
`src/agents/fork.ts`	`forkAgent()`	Fork mode, inherits context

Coordinator Mode

File Path	Core Class/Function	Description
`src/agents/coordinator.ts`	`CoordinatorAgent` class	Coordinator Agent
`src/agents/coordinatorPrompt.ts`	Coordinator prompt	“Never delegate understanding”
`src/agents/worker.ts`	`WorkerAgent` class	Worker Agent

Agent Lifecycle

File Path	Core Class/Function	Description
`src/agents/lifecycle.ts`	`registerAsyncAgent()`	Register background Agent
`src/agents/lifecycle.ts`	`completeAsyncAgent()`	Mark Agent complete
`src/agents/lifecycle.ts`	`enqueueAgentNotification()`	Result notification injection

Memory System

Memdir Core

File Path	Core Class/Function	Description
`src/memory/memdir.ts`	`Memdir` class	Memory directory management
`src/memory/memdir.ts`	`MEMORY_FILENAME`	MEMORY.md index file

Auto Extraction

File Path	Core Class/Function	Description
`src/memory/extractMemories.ts`	`extractMemories()`	Automatic memory extraction
`src/memory/extractAgent.ts`	`ExtractAgent`	Extraction-specific Agent

Auto-Dream

File Path	Core Class/Function	Description
`src/memory/autoDream.ts`	`autoDream()`	Automatic overnight consolidation
`src/memory/consolidator.ts`	`ConsolidatorAgent`	Consolidator Agent
`src/memory/lock.ts`	`acquireConsolidateLock()`	PID lock mechanism

Session Memory

File Path	Core Class/Function	Description
`src/memory/sessionMemory.ts`	`SessionMemory` class	Session summary management
`src/memory/sessionMemory.ts`	`summarizeSession()`	Session summary generation

Hooks System

Hooks Core

File Path	Core Class/Function	Description
`src/hooks/registry.ts`	`HookRegistry`	Hook registry
`src/hooks/dispatcher.ts`	`dispatchHook()`	Hook dispatcher
`src/hooks/types.ts`	`HookType` enum	Hook type definitions

Specific Hook Implementations

File Path	Event Name	Trigger Timing
`src/hooks/commandHooks.ts`	`before:command`	Before command execution
`src/hooks/commandHooks.ts`	`after:command`	After command execution
`src/hooks/agentHooks.ts`	`before:agent`	Before Agent call
`src/hooks/agentHooks.ts`	`after:agent`	After Agent call
`src/hooks/httpHooks.ts`	`before:http`	Before HTTP request
`src/hooks/httpHooks.ts`	`after:http`	After HTTP response

Skills System

Skills Core

File Path	Core Class/Function	Description
`src/skills/registry.ts`	`SkillRegistry`	Skills registry
`src/skills/loader.ts`	`loadSkill()`	Skills loader
`src/skills/types.ts`	`Skill` interface	Skill type definitions

Skills Storage

File Path	Core Class/Function	Description
`src/skills/storage.ts`	`getSkillStoragePath()`	Get skill storage path
`src/skills/storage.ts`	`loadSkillManifest()`	Load skill manifest

Feature Flags

Flag Definitions

File Path	Core Class/Function	Description
`src/featureFlags/flags.ts`	`feature()` function	Build-time Flag check
`src/featureFlags/flags.ts`	`KAIROS`	KAIROS mode Flag
`src/featureFlags/flags.ts`	`TRANSCRIPT_CLASSIFIER`	Classifier Flag

Remote Configuration

File Path	Core Class/Function	Description
`src/featureFlags/remote.ts`	`getRemoteFlag()`	Get remote Flag value
`src/featureFlags/growthbook.ts`	`GrowthBookClient`	GrowthBook client

Configuration and Settings

Configuration Files

File Path	Purpose	Description
`CLAUDE.md`	Project-level config	Coding standards, architecture constraints
`.claude/settings.json`	User settings	Personal preferences, feature toggles
`.claude/settings.local.json`	Local settings	Machine-specific configuration

Settings Management

File Path	Core Class/Function	Description
`src/settings/loader.ts`	`loadSettings()`	Settings loader
`src/settings/validator.ts`	`validateSettings()`	Settings validator
`src/settings/types.ts`	`Settings` interface	Settings type definitions

Utility Modules

Git Operations

File Path	Core Class/Function	Description
`src/utils/git/status.ts`	`getGitStatus()`	Get Git status
`src/utils/git/diff.ts`	`getGitDiff()`	Get Git diff
`src/utils/git/worktree.ts`	`createWorktree()`	Create git worktree

File Operations

File Path	Core Class/Function	Description
`src/utils/file/reader.ts`	`readFile()`	File reading, pagination support
`src/utils/file/writer.ts`	`writeFile()`	File writing
`src/utils/file/watcher.ts`	`FileWatcher`	File change listener

Network Requests

File Path	Core Class/Function	Description
`src/utils/http/client.ts`	`HttpClient`	HTTP client
`src/utils/http/retry.ts`	`retryRequest()`	Request retry logic

Quick Lookup Index

Lookup by Function

You want to understand…	Start here
How Agent Loop works	`src/core/agent.ts`, `src/core/loop.ts`
How tools are defined	`src/tools/base.ts`, tool files
How context is compressed	`src/services/compact/` directory
How token budget is calculated	`src/constants/toolLimits.ts`
How system prompts are assembled	`src/constants/prompts.ts`
How cache is optimized	`src/services/cache/` directory
How permissions are judged	`src/utils/permissions/` directory
How YOLO classifier works	`src/services/classifier/` directory
How sub-agents are spawned	`src/agents/subAgent.ts`
How Fork mode is implemented	`src/agents/fork.ts`
How memory is stored	`src/memory/memdir.ts`
How auto extraction works	`src/memory/extractMemories.ts`
How Auto-Dream is triggered	`src/memory/autoDream.ts`
How Hooks are used	`src/hooks/` directory
How skills are loaded	`src/skills/` directory
How Feature Flags are defined	`src/featureFlags/flags.ts`
How settings are read	`src/settings/loader.ts`

Lookup by Problem

You have this problem…	Check these files
Why read before edit	`src/tools/FileEditTool.ts`
Why Git operations have safety limits	`src/tools/BashTool.ts` prompts
How to restore files after compaction	`src/services/compact/compact.ts`
Why token estimation is conservative	`src/utils/tokenEstimator.ts`
Why cache breaks	`src/services/api/promptCacheBreakDetection.ts`
Why classifier denies	`src/services/classifier/yoloClassifier.ts`
Why coordinator doesn’t code	`src/agents/coordinatorPrompt.ts`
Why memory doesn’t work	`src/memory/memdir.ts`, `src/memory/extractMemories.ts`
Why Hooks don’t trigger	`src/hooks/dispatcher.ts`

Usage Suggestions

Debugging Tips

Environment variables: CLAUDE_CODE_DEBUG=1 to enable debug logging
Log location: ~/.claude/logs/ for detailed logs
API logs: CLAUDE_CODE_DUMP_AUTO_MODE=1 to export classifier input/output

Contributing Code

Coding standards: Refer to project standards in CLAUDE.md
Test requirements: Core module changes require accompanying tests
Documentation sync: Code changes sync related documentation updates

This index handbook covers Claude Code’s main source files. As versions iterate, file paths may change, but core architecture and design philosophy remain stable. Recommend bookmarking for quick reference when needed.

Core Architecture Modules#

Agent Loop Core#

Tool System#

Specific Tool Implementations#

Context Management#

Auto Compaction#

Microcompaction#

Token Budget#

Prompt Engineering#

System Prompts#

Dynamic Boundary#

Cache System#

Cache Break Detection#

Cache Optimization#

Permissions and Security#

Permission System#

YOLO Classifier#

Agent System#

Sub-Agents#

Coordinator Mode#

Agent Lifecycle#

Memory System#

Memdir Core#

Auto Extraction#

Auto-Dream#

Session Memory#

Hooks System#

Hooks Core#

Specific Hook Implementations#

Skills System#

Skills Core#

Skills Storage#

Feature Flags#

Flag Definitions#

Remote Configuration#

Configuration and Settings#

Configuration Files#

Settings Management#

Utility Modules#

Git Operations#

File Operations#

Network Requests#

Quick Lookup Index#

Lookup by Function#

Lookup by Problem#

Usage Suggestions#

Recommended Order for Reading Source Code#

Debugging Tips#

Contributing Code#