Claude Code Multi-Agent System — Implementation Details
A deep dive into the architecture, spawn flow, context passing, and collaboration mechanisms of multi-agent orchestration.
Architecture · Spawn Flow · Tool Pool · Context Passing · Teams Internals · Task Engine · DreamTask · Worktree Isolation · Permission Sync · Lifecycle Data Flow · Source Index · Feature Flags

1. Architecture Overview
Claude Code's multi-agent system consists of the following core modules:
5 Core Modules
| Module | Responsibility | Key Files |
|---|---|---|
| Agent Tool | Primary entry point, routing & dispatch, parameter parsing | src/tools/AgentTool/AgentTool.tsx |
| Execution Engine | Agent lifecycle management, query loop | src/tools/AgentTool/runAgent.ts |
| Context Manager | System prompt construction, cache-safe parameters | src/utils/forkedAgent.ts |
| Task System | State tracking, progress updates, notification queue | src/tasks/LocalAgentTask/ |
| Swarm Infrastructure | Team management, mailbox communication, permission sync | src/utils/swarm/ |
5 Agent Categories
┌─────────────────────────────────────────────────┐
│ Agent Tool │
│ (Entry & Route Dispatch) │
├───────────┬───────────┬───────────┬─────────────┤
│ Subagent │ Fork │ Teammate │ Remote │
│ │ │ │ │
│ Standalone│ Inherited │ Team │ CCR │
│ context │ context │ collab │ environment │
│ Type-based│ Cache │ Mailbox │ Remote │
│ tool pool │ sharing │ comms │ execution │
│ │ Byte-level│ Permission│ Poll for │
│ │ consistent│ sync │ results │
└───────────┴───────────┴───────────┴─────────────┘
│
┌─────┴─────┐
│ DreamTask │
│ (Memory │
│ Consolidation) │
│ Scheduled │
│ background│
└───────────┘2. Agent Spawn Flow — Four Paths
Entry Point: AgentTool.call()
The call() function in src/tools/AgentTool/AgentTool.tsx is the entry point for all agent spawning. Based on input parameters, it routes to one of four spawn paths:
AgentTool.call(input)
│
├─ team_name + name? ──────→ Path 1: spawnTeammate()
│
├─ run_in_background? ────→ Path 2: registerAsyncAgent()
│ └─ agent.background?
│
├─ subagent_type omitted? ─→ Path 3: Fork (buildForkedMessages())
│ └─ fork experiment on?
│
└─ default ────────────────→ Path 4: runAgent() synchronous executionPath 1: Teammate Spawn
Trigger: Both team_name and name are present
Entry function: spawnTeammate() — src/tools/shared/spawnMultiAgent.ts
Flow:
- Detect execution backend (tmux / iTerm2 / in-process)
- Generate a unique
agentIdfor the teammate:formatAgentId(name, teamName) - Assign a color (from a predefined palette)
- Create the execution environment:
- in-process: Start in the same process via
spawnInProcessTeammate() - tmux: Create a new pane via
TmuxBackend - iTerm2: Create a new window via
ITerm2Backend
- in-process: Start in the same process via
- Write to the TeamFile member list
- Return
TeammateSpawnedOutput(including pane ID, agent ID, etc.)
In-Process Teammate Isolation:
// src/utils/swarm/spawnInProcess.ts
export async function spawnInProcessTeammate(config, context) {
// 1. Independent AbortController (not tied to leader's cancellation)
const abortController = new AbortController()
// 2. AsyncLocalStorage context isolation
runWithTeammateContext(teammateContext, async () => {
// 3. Independent task state
// 4. Independent message loop
// 5. Shared permission pipeline (via mailbox)
})
}Path 2: Async Subagent
Trigger: run_in_background=true or background: true in the agent definition
Flow:
registerAsyncAgent()
│
├─ Create LocalAgentTask (status: 'running')
├─ Register in agentNameRegistry (if named)
├─ Create output file symlink
├─ Create AbortController (linked to parent)
├─ Emit SDK event: task_started
│
└─ void runAsyncAgentLifecycle() ← fire-and-forget async
│
├─ Create ProgressTracker
├─ Iterate makeStream() generator
│ ├─ Append messages to agentMessages[]
│ ├─ Update progress (tokens, tools, activities)
│ └─ Emit SDK progress events
│
└─ On completion:
├─ finalizeAgentTool() (extract result)
├─ completeAgentTask() (mark complete)
├─ Clean up worktree (if isolated)
└─ enqueuePendingNotification() (notify primary agent)Key implementation: src/tools/AgentTool/agentToolUtils.ts — runAsyncAgentLifecycle()
Path 3: Fork Subagent
Trigger: subagent_type is omitted and the fork experiment is enabled
Core optimization: Achieves prompt cache hits through byte-level consistent API request prefixes.

Flow:
buildForkedMessages(directive, assistantMessage)
│
├─ Preserve parent agent's complete assistant message (all tool_use blocks)
├─ Build user message:
│ ├─ Create placeholder tool_result for each tool_use (byte-consistent)
│ └─ Append per-child directive (the only divergent part)
│
└─ Result: byte-level consistent API prefix → prompt cache hit!Fork child behavioral constraints (injected via FORK_BOILERPLATE_TAG):
1. You are a forked worker process, not the primary agent
2. Do not converse, ask questions, or suggest next steps
3. Use tools directly (Bash, Read, Write, etc.)
4. If you modify files, commit changes before reporting
5. Do not output text between tool calls
6. Stay strictly within the scope of your directive
7. Keep your report under 500 words
8. Your response must begin with "Scope:"Anti-recursion protection: isInForkChild() detects whether execution is inside a fork child, preventing nested forks.
Path 4: Synchronous Subagent
Trigger: Default path (no team_name, no background, not a fork)
Flow:
runAgent(promptMessages, toolUseContext, options)
│
├─ Resolve agent definition (getSystemPrompt, tools, permissions)
├─ Build system prompt (buildEffectiveSystemPrompt)
├─ Create isolated ToolUseContext (createSubagentContext)
├─ Start query loop (query() async generator)
│ ├─ Send API request
│ ├─ Process streaming events
│ ├─ Execute tool calls
│ └─ Accumulate messages and usage
│
└─ Return AgentToolResult
├─ content: text from the last assistant message
├─ totalToolUseCount
├─ totalDurationMs
└─ totalTokens3. Tool Pool System — Three-Layer Filtering

Layer 1: Global Disallow List
ALL_AGENT_DISALLOWED_TOOLS — tools disallowed for all agents:
| Tool | Reason for Disallowing |
|---|---|
| TaskOutput | Only the primary agent may read task output |
| ExitPlanMode | Only the primary agent may exit plan mode |
| EnterPlanMode | Only the primary agent may enter plan mode |
| AskUserQuestion | Subagents should not directly ask the user |
| TaskStop | Only the primary agent may terminate tasks |
| Agent | Prevent recursive spawning (Anthropic internal exception) |
Layer 2: Agent Type Filtering
filterToolsForAgent() — tool filtering based on agent type:
// src/tools/AgentTool/agentToolUtils.ts
function filterToolsForAgent(tools, agentDef) {
// 1. Remove ALL_AGENT_DISALLOWED_TOOLS
// 2. If not a built-in agent, also remove CUSTOM_AGENT_DISALLOWED_TOOLS
// 3. If async agent, restrict to ASYNC_AGENT_ALLOWED_TOOLS
// 4. MCP tools are always allowed
}ASYNC_AGENT_ALLOWED_TOOLS (15 tools):
Read, WebSearch, TodoWrite, Grep, WebFetch, Glob,
Bash/PowerShell, FileEdit, FileWrite, NotebookEdit,
Skill, SyntheticOutput, ToolSearch, EnterWorktree, ExitWorktreeLayer 3: Agent Definition Filtering
resolveAgentTools() — tool resolution based on agent definition:
function resolveAgentTools(agentDef, availableTools) {
if (tools === ['*'] || undefined) → wildcard, allow all
if (tools === ['Read', 'Grep']) → allow only listed tools
if (disallowedTools === ['Agent']) → subtract from available tools
}Filtering Pipeline:
All available tools
│
├─ Subtract ALL_AGENT_DISALLOWED_TOOLS ──→ Global disallow
│
├─ Not built-in? Subtract CUSTOM_AGENT_DISALLOWED_TOOLS ──→ Custom restrictions
│
├─ Async? Restrict to ASYNC_AGENT_ALLOWED_TOOLS ──→ Async allowlist
│
├─ Has tools list? Intersect ──→ Agent allowlist
│
├─ Has disallowedTools? Subtract ──→ Agent denylist
│
└─ Final tool pool4. Context Passing Mechanism

CacheSafeParams — Cache-Safe Parameters
// src/utils/forkedAgent.ts
export type CacheSafeParams = {
systemPrompt: SystemPrompt // System prompt
userContext: { [k: string]: string } // Directory structure, CLAUDE.md, etc.
systemContext: { [k: string]: string } // Git status, environment info
toolUseContext: ToolUseContext // Tool configuration, model, options
forkContextMessages: Message[] // Fork context messages (for cache sharing)
}Cache Sharing Principle:
Fork agents reuse prompt cache by keeping API request prefixes byte-level consistent:
┌─────────────────────────────────────────┐
│ Shared Prefix (byte-consistent) │
│ ┌──────────────────────────────────┐ │
│ │ System Prompt │ │
│ │ User Context │ │
│ │ System Context │ │
│ │ Tool Use Context │ │
│ │ Conversation History Messages │ │
│ │ Assistant Message (all tool_use) │ │
│ │ User Message (placeholder results│) │
│ └──────────────────────────────────┘ │
├─────────────────────────────────────────┤
│ Only divergence: per-child directive │
└─────────────────────────────────────────┘System Prompt Construction
buildEffectiveSystemPrompt() — src/utils/systemPrompt.ts
Priority chain (highest to lowest):
Override System Prompt ← Highest priority, full replacement
↓
Coordinator System Prompt ← Coordinator mode only
↓
Agent System Prompt ← agentDefinition.getSystemPrompt()
↓ - proactive mode: appended to default
↓ - otherwise: replaces default
Custom System Prompt ← --system-prompt argument
↓
Default System Prompt ← Standard Claude Code prompt
↓
Append System Prompt ← Appended to the endAgent-specific system prompt enhancement:
// src/tools/AgentTool/runAgent.ts
function getAgentSystemPrompt(agentDef, toolUseContext) {
let prompt = agentDef.getSystemPrompt({ toolUseContext })
prompt = enhanceSystemPromptWithEnvDetails(prompt)
// Adds: working directory, enabled tools list, model info, environment variables
return prompt
}SubagentContext — Subagent Context Isolation
// src/utils/forkedAgent.ts
export type SubagentContextOverrides = {
options?: ToolUseContext['options'] // Custom tools, model
agentId?: AgentId // Subagent ID
agentType?: string // Agent type
messages?: Message[] // Custom message history
readFileState?: ToolUseContext['readFileState'] // File read cache
abortController?: AbortController // Abort controller
// Explicit opt-in sharing (isolated by default)
shareSetAppState?: boolean // Share AppState writes
shareSetResponseLength?: boolean // Share response length metrics
shareAbortController?: boolean // Share abort controller
// Experimental injection
criticalSystemReminder_EXPERIMENTAL?: string // Re-injected each turn
contentReplacementState?: ContentReplacementState
}Isolation vs. Sharing:
| Resource | Default | Description |
|---|---|---|
| readFileState | Cloned | File read cache is independent |
| messages | New | Message history is independent |
| abortController | New (linked to parent) | Child is cancelled when parent cancels |
| setAppState | No-op | Does not affect parent state by default |
| contentReplacementState | Cloned | Content replacement state is independent |
Model Resolution
getAgentModel() — src/utils/model/agent.ts
Priority chain:
CLAUDE_CODE_SUBAGENT_MODEL env var ← Highest
↓
Agent({ model: 'opus' }) parameter ← Specified via tool
↓
agentDefinition.model ← Agent definition
↓
'inherit' ← Inherit parent model5. Agent Teams Internals
TeamFile Structure
// Storage path: ~/.claude/teams/{team_name}/config.json
{
name: string // Team name
description?: string // Team description
createdAt: number // Creation timestamp
leadAgentId: string // Team Lead's Agent ID
leadSessionId?: string // Lead's session UUID
hiddenPaneIds?: string[] // Panes hidden in UI
teamAllowedPaths?: TeamAllowedPath[] // Team-level shared permissions
members: Array<{
agentId: string // Member Agent ID
name: string // Display name
agentType?: string // Role type
model?: string // Model used
prompt?: string // Initial task
color?: string // UI color
planModeRequired?: boolean // Whether plan approval is required
joinedAt: number // Join timestamp
tmuxPaneId: string // Terminal pane ID
cwd: string // Working directory
worktreePath?: string // Worktree path
sessionId?: string // Session ID
subscriptions: string[] // Message subscriptions
backendType?: 'tmux'|'iterm2'|'in-process'
isActive?: boolean // false=idle, true/undefined=active
mode?: PermissionMode // Current permission mode
}>
}Mailbox System

Storage path: ~/.claude/teams/{team_name}/inboxes/{agent_name}.json
// src/utils/teammateMailbox.ts
type TeammateMessage = {
from: string // Sender name
text: string // Message content (plain text or JSON)
timestamp: string // ISO timestamp
read: boolean // Whether the message has been read
color?: string // Sender's color
summary?: string // 5-10 word summary
}Concurrency safety: Uses proper-lockfile file locks with 10 retries and 5-100ms exponential backoff.
Message Types:
| Message | Format | Purpose |
|---|---|---|
| Plain text | string | Regular conversation messages |
| shutdown_request | { type, reason } | Request a teammate to shut down |
| shutdown_response | { type, request_id, approve } | Approve/reject shutdown |
| plan_approval_response | { type, request_id, approve } | Approve a plan |
| permission_request | { type, toolName, path } | Permission request |
| idle_notification | Special format | Idle notification |
Inbox Polling
// src/hooks/useInboxPoller.ts
// Poll interval: 1000ms
useEffect(() => {
const interval = setInterval(async () => {
const messages = await readUnreadMessages(agentName, teamName)
for (const msg of messages) {
if (isShutdownRequest(msg.text)) {
// Handle shutdown request
} else if (isPlanApprovalResponse(msg.text)) {
// Handle plan approval
} else if (isPermissionRequest(msg.text)) {
// Route to permission system
} else {
// Plain text message → submit as new conversation turn
onSubmitMessage(formatted)
}
}
}, INBOX_POLL_INTERVAL_MS)
}, [])Message Processing States:
| State | Description |
|---|---|
pending | Newly received, awaiting processing |
processing | Currently being processed (e.g., permission requests) |
processed | Processing complete |
Message Routing
SendMessage({ to, message })
│
├─ to === "*" → Broadcast
│ └─ Iterate all teammates, write to each mailbox
│
├─ agentNameRegistry.has(to) → In-process subagent
│ └─ Route via AppState pending messages queue
│
├─ teamFile.members.find(to) → Process-level teammate
│ └─ writeToMailbox(to, message, teamName)
│
├─ to.startsWith("bridge:") → Remote session
│ └─ postInterClaudeMessage(sessionId, message)
│
└─ to.startsWith("uds:") → Unix Domain Socket
└─ sendToUdsSocket(socketPath, message)6. Background Task Engine

LocalAgentTask State Machine
// src/tasks/LocalAgentTask/LocalAgentTask.tsx
type LocalAgentTaskState = {
type: 'local_agent'
agentId: AgentId // Unique identifier
status: 'running' | 'completed' | 'failed' | 'killed'
isBackgrounded: boolean // Foreground vs. background
progress: {
latestInputTokens: number // Latest input tokens
cumulativeOutputTokens: number // Cumulative output tokens
toolUseCount: number // Tool invocation count
recentActivities: ToolActivity[] // Last 5 activities
lastActivity: number // Last activity timestamp
}
result?: AgentToolResult // Final result
abortController: AbortController // Abort controller
retain: boolean // UI retention flag
evictAfter?: number // Delayed eviction timestamp
}State Transitions:
┌──────────────────────────┐
│ │
register │ ┌──── killed ←── abort()
│ │ │
▼ │ │
running ─────┼────┼──── completed ← finalizeAgentTool()
│ │
│ └──── failed ← error / timeout
│
└──── evict ← notified && endTime > graceProgress Tracking
// ProgressTracker
function updateProgressFromMessage(tracker, message) {
// 1. Track input tokens (take latest value)
tracker.latestInputTokens = message.usage?.input_tokens
// 2. Accumulate output tokens
tracker.cumulativeOutputTokens += message.usage?.output_tokens
// 3. Count tool invocations
tracker.toolUseCount += countToolUses(message)
// 4. Maintain recent activities (circular buffer, max 5)
tracker.recentActivities = [...activities].slice(-5)
}Notification System
// src/utils/messageQueueManager.ts
function enqueuePendingNotification(taskId, result) {
// 1. Atomically set notified flag (prevent duplicates)
if (task.notified) return
task.notified = true
// 2. Format XML notification
const notification = `
<task-notification>
<task-id>${taskId}</task-id>
<status>${status}</status>
<summary>${summary}</summary>
<output-file>${outputPath}</output-file>
</task-notification>
`
// 3. Enqueue for primary agent consumption
pendingNotifications.push(notification)
}Output Management
Storage path: ~/.claude/temp/{sessionId}/tasks/{taskId}.output
| Parameter | Value |
|---|---|
| Max capacity | 5GB / file |
| Circular buffer | 1000 lines |
| Poll interval | 1 second |
| Terminal state retention | 3 seconds (30 seconds for task panel) |
| Write method | Asynchronous queue writes to prevent memory buildup |
| Safety measure | O_NOFOLLOW to prevent symlink attacks |
7. DreamTask — Automatic Memory Consolidation
DreamTask is a special background agent used for cross-session memory consolidation.
Trigger Conditions
// src/services/autoDream/autoDream.ts
function executeAutoDream() {
// Four gates:
if (hoursSinceLastConsolidation < minHours) return // Time gate: default 24h
if (sessionsSinceLastConsolidation < minSessions) return // Session gate: default 5
if (otherProcessConsolidating) return // Lock gate: mutual exclusion
if (timeSinceLastScan < 10min) return // Scan throttle: 10 minutes
}DreamTask State
type DreamTaskState = {
type: 'dream'
phase: 'starting' | 'updating' // updating = has started editing files
sessionsReviewing: number // Number of sessions being reviewed
filesTouched: string[] // File paths that have been edited
turns: DreamTurn[] // Conversation turn records
}8. Worktree Isolation Implementation
Creation Flow
// src/utils/worktree.ts
async function createAgentWorktree(slug) {
// 1. Validate slug (prevent directory traversal attacks)
validateWorktreeSlug(slug)
// 2. Create git worktree
git worktree add {path} -b {branch}
// 3. Symlink large directories (save disk space)
symlink(node_modules, worktree/node_modules)
// 4. Apply sparse-checkout (if configured)
if (sparseCheckoutPaths) {
git sparse-checkout set {paths}
}
// 5. Return WorktreeSession
return { worktreePath, worktreeBranch, headCommit }
}Cleanup Mechanism
- After agent completion, automatically checks for changes (
hasWorktreeChanges()) - If changes exist: returns the worktree path and branch name to the user
- If no changes: automatically deletes the worktree (
removeAgentWorktree()) - On abnormal exit: cleanup is ensured via
registerTeamForSessionCleanup()
9. Permission Synchronization
Team-Level Permissions
type TeamAllowedPath = {
path: string // Absolute directory path
toolName: string // Applicable tool (e.g., "Edit", "Write")
addedBy: string // Who added it
addedAt: number // When it was added
}Teammates automatically inherit team-level permission rules on startup.
Bubble Mode
Fork agents use the bubble permission mode — permission prompts bubble up to the parent agent's terminal:
Fork Agent needs permission
│
└─ bubble mode → Permission request sent to parent agent
│
└─ Parent agent's ToolUseConfirm dialog is displayed
│
├─ User approves → Result relayed back to Fork Agent
└─ User denies → Fork Agent receives denialIn-Process Teammate Permissions
Teammate needs permission
│
├─ Has UI bridge → Displayed directly in Leader's confirmation dialog
│ └─ With worker badge indicating source
│
└─ No UI bridge → Queued via mailbox
└─ Handled by Leader's useSwarmPermissionPoller10. Agent Lifecycle End-to-End Data Flow
1. User triggers Agent Tool
│
2. AgentTool.call() routes and dispatches
│
3. Resolve agent definition
├─ Look up agent type (built-in > plugin > user > project)
├─ Load system prompt
├─ Resolve tool pool (three-layer filtering)
└─ Determine permission mode and model
│
4. Create isolated context
├─ createSubagentContext() (clone readFileState)
├─ Generate agentId
├─ Create AbortController
└─ Optional: create worktree
│
5. Register task state
├─ registerAsyncAgent() or registerAgentForeground()
├─ Emit SDK event: task_started
└─ Register Perfetto trace
│
6. Execute query loop
├─ query() async generator
│ ├─ Build API request (with CacheSafeParams)
│ ├─ Process streaming response
│ ├─ Execute tool calls
│ └─ Accumulate usage metrics
├─ Update progress (ProgressTracker)
└─ Record transcript
│
7. Completion handling
├─ finalizeAgentTool() (extract result text)
├─ completeAgentTask() (mark complete)
├─ Clean up resources
│ ├─ Release file state cache
│ ├─ Close MCP connections
│ └─ Delete worktree (if applicable)
├─ enqueuePendingNotification() (notify primary agent)
└─ Emit SDK event: task_completed
│
8. Primary agent consumes result
├─ Synchronous: directly receives AgentToolResult
└─ Asynchronous: processes after receiving <task-notification>11. Key Source File Index
Agent Tool Core
| File | Responsibility |
|---|---|
src/tools/AgentTool/AgentTool.tsx | Main tool implementation, routing & dispatch |
src/tools/AgentTool/runAgent.ts | Execution engine, query loop |
src/tools/AgentTool/agentToolUtils.ts | Tool pool resolution, result finalization |
src/tools/AgentTool/forkSubagent.ts | Fork semantics, message inheritance |
src/tools/AgentTool/loadAgentsDir.ts | Agent definition types, parsing & loading |
src/tools/AgentTool/builtInAgents.ts | Built-in agent registry |
src/tools/AgentTool/prompt.ts | Agent tool schema and documentation |
src/tools/AgentTool/agentMemory.ts | Agent persistent memory |
Swarm Infrastructure
| File | Responsibility |
|---|---|
src/tools/TeamCreateTool/TeamCreateTool.ts | Team creation |
src/tools/TeamDeleteTool/TeamDeleteTool.ts | Team cleanup |
src/tools/SendMessageTool/SendMessageTool.ts | Inter-agent communication |
src/tools/shared/spawnMultiAgent.ts | Teammate spawn entry point |
src/utils/swarm/spawnInProcess.ts | In-process teammate spawning |
src/utils/swarm/teamHelpers.ts | Team file read/write |
src/utils/swarm/constants.ts | Constant definitions |
src/utils/swarm/teammateInit.ts | Teammate initialization |
src/utils/swarm/permissionSync.ts | Permission synchronization |
src/utils/teammate.ts | Teammate identity resolution |
src/utils/teammateMailbox.ts | Mailbox message queue |
src/utils/teamDiscovery.ts | Team discovery |
src/hooks/useInboxPoller.ts | Inbox polling |
Context Management
| File | Responsibility |
|---|---|
src/utils/forkedAgent.ts | Cache-safe parameters, subagent context |
src/utils/systemPrompt.ts | System prompt priority construction |
src/utils/model/agent.ts | Agent model resolution |
src/utils/worktree.ts | Git worktree isolation |
Task System
| File | Responsibility |
|---|---|
src/tasks/LocalAgentTask/LocalAgentTask.tsx | Local agent task |
src/tasks/RemoteAgentTask/RemoteAgentTask.tsx | Remote agent task |
src/tasks/InProcessTeammateTask/ | In-process teammate task |
src/tasks/DreamTask/DreamTask.ts | Memory consolidation task |
src/utils/task/framework.ts | Task registration, state updates |
src/utils/task/diskOutput.ts | Task output file management |
src/utils/messageQueueManager.ts | Notification queue |
Coordinator
| File | Responsibility |
|---|---|
src/coordinator/coordinatorMode.ts | Coordinator mode configuration |
12. Feature Flags
| Flag | Controls |
|---|---|
FORK_SUBAGENT | Enable fork path (when subagent_type is omitted) |
BUILTIN_EXPLORE_PLAN_AGENTS | Enable Explore/Plan agents |
VERIFICATION_AGENT | Enable verification agent |
COORDINATOR_MODE | Enable coordinator mode |
KAIROS | Enable cwd parameter |
tengu_auto_background_agents | Auto-background after 120 seconds |
tengu_slim_subagent_claudemd | Omit CLAUDE.md for read-only agents |
tengu_agent_list_attach | Inject agent list via attachment |