### Coordinator System Prompt Example

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04h-multi-agent.md

Illustrates the system prompt for the coordinator agent, defining its role as an orchestrator and outlining operational rules for worker management.

```plaintext
You are Claude Code, an AI assistant that orchestrates software engineering tasks across multiple workers.

Use `Agent` to spawn workers
Use `SendMessage` to continue an existing worker
Use `TaskStop` to stop a worker
Don't have one worker check on another worker
Launch independent workers in parallel
Serialize write operations by file set, research tasks can be parallel
```

--------------------------------

### Example Static Segment: Intro Section

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04g-prompt-management.md

An example of a static segment returned by `getSimpleIntroSection()`, defining the agent's identity and critical instructions.

```typescript
return `
You are an interactive agent that helps users ...

${CYBER_RISK_INSTRUCTION}
IMPORTANT: You must NEVER generate or guess URLs for the user unless ...
`
```

--------------------------------

### Runtime Environment Initialization in `setup.ts`

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/01-architecture-overview.md

This pseudo-code shows the structure of `setup.ts`, responsible for initializing the runtime environment, such as setting the working directory and starting watchers for configuration changes.

```typescript
// src/setup.ts structure pseudo-code
export async function setup(argv, permissionContext) {
  setCwd(resolvedWorkingDir)         // Set working directory
  startHooksWatcher()                // Listen for hooks config changes
  initWorktreeSnapshot()             // tmux/worktree snapshot
  initSessionMemory()                // Initialize session memory system
  startTeamMemoryWatcher()           // Start team memory file watcher
}
```

--------------------------------

### Facet Extraction Prompt Example

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/06b-negative-keyword-analysis.md

An example provided in a facet extraction prompt to illustrate how user input maps to the 'frustrated' label. This demonstrates the formal classification of user sentiment.

```text
"this is broken", "I give up" → frustrated
```

--------------------------------

### Session Memory File Setup with Strict Permissions

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04-agent-memory.md

Sets up the session memory directory and file with strict permissions (0o700 for directory, 0o600 for file), ensuring only the owner can read, write, or execute. The file is created only if it does not exist.

```typescript
async function setupSessionMemoryFile(ctx) {
 const sessionMemoryDir = getSessionMemoryDir()
 await fs.mkdir(sessionMemoryDir, { mode: 0o700 }) // Directory: owner only can read/write/execute

 const memoryPath = getSessionMemoryPath()
 await writeFile(memoryPath, '', {
 mode: 0o600, // File: owner only can read/write
 flag: 'wx', // O_CREAT|O_EXCL: create only if file does not exist, prevent overwriting existing memory
 })
}
```

--------------------------------

### Example Frustrated User Input Keywords

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/06b-negative-keyword-analysis.md

A list of keywords and phrases that indicate user frustration or dissatisfaction with the product. These are useful for immediate feedback and identifying problematic interactions.

```text
wtf
wth
this sucks
so frustrating
damn it
piece of shit
```

--------------------------------

### Append Proactive Mode Prompt

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04g-prompt-management.md

This example shows how to append a proactive mode prompt to the existing system prompt, ensuring it's added even if no user prompt is initially provided.

```typescript
const proactivePrompt = `
# Proactive Mode

You are in proactive mode. Take initiative — explore, act, and make progress without waiting for instructions.

Start by briefly greeting the user.
...
`
appendSystemPrompt = appendSystemPrompt
  ? `${appendSystemPrompt}\n\n${proactivePrompt}`
  : proactivePrompt
```

--------------------------------

### Get Main Transcript Path

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04i-session-storage-resume.md

Resolves the path for the main session transcript file. It constructs the path using the project directory and the session ID.

```typescript
export function getTranscriptPath(): string {
  const projectDir = getSessionProjectDir() ?? getProjectDir(getOriginalCwd())
  return join(projectDir, `${getSessionId()}.jsonl`)
}
```

--------------------------------

### REPL Launcher Function Signature

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/01-architecture-overview.md

This snippet provides the function signature for `launchRepl` in `replLauncher.tsx`, which is responsible for loading and starting the Ink rendering loop for the App and REPL components.

```typescript
// src/replLauncher.tsx
export async function launchRepl(
  root: Root,
  appProps: AppWrapperProps,
  replProps: REPLProps,
  renderAndRun: (root: Root, element: React.ReactNode) => Promise<void>
): Promise<void>
```

--------------------------------

### MCP Server Startup Function (MCP Server Mode)

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/01-architecture-overview.md

This pseudo-code illustrates the `startMcpServer` function, which initializes an MCP server. It registers internal tools with their respective schemas and connects the server using StdioServerTransport.

```typescript
// src/entrypoints/mcp.ts structure pseudo-code
async function startMcpServer() {
  const server = new McpServer({ name: 'claude-code', version })
  // Wrap internal Tools (FileEdit, FileRead, Bash...) as MCP tool schemas
  for (const tool of getInternalTools()) {
    server.registerTool(tool.name, tool.inputSchema, wrapToolAsMcpHandler(tool))
  }
  await server.connect(new StdioServerTransport())
}
```

--------------------------------

### Get Session Memory Compaction Configuration

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04-agent-memory.md

Retrieves the configuration for session memory compaction, which includes the default retention token count.

```typescript
getSessionMemoryCompactConfig(
  workspace
);
```

--------------------------------

### Prompt Generation and Override Flow

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04g-prompt-management.md

Outlines the general flow for generating the system prompt, including startup parameters, default prompt assembly, and priority overrides with user and system context injection.

```text
Startup parameters / mode / agent / mcp / settings
                |
                v
getSystemPrompt() generates default system prompt array
                |
                v
buildEffectiveSystemPrompt() handles priority overrides
                |
                +---- userContext
                |       - CLAUDE.md
                |       - currentDate
                |
                +---- systemContext
                        - git status
                        - cacheBreaker
                |
                v
Query / REPL / Compact / Subagent call API
```

--------------------------------

### Get Agent Transcript Path

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04i-session-storage-resume.md

Resolves the path for a specific agent's transcript file within a session. Handles subdirectories for agents if configured.

```typescript
export function getAgentTranscriptPath(agentId: AgentId): string {
  const projectDir = getSessionProjectDir() ?? getProjectDir(getOriginalCwd())
  const sessionId = getSessionId()
  const subdir = agentTranscriptSubdirs.get(agentId)
  const base = subdir
    ? join(projectDir, sessionId, 'subagents', subdir)
    : join(projectDir, sessionId, 'subagents')
  return join(base, `agent-${agentId}.jsonl`)
}
```

--------------------------------

### Initializing Sandbox Runtime Configuration

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04e-sandbox-implementation.md

The beginning of the `convertToSandboxRuntimeConfig` function, showing initial default values for filesystem permissions.

```typescript
export function convertToSandboxRuntimeConfig(
  settings: SettingsJson,
): SandboxRuntimeConfig {
  const permissions = settings.permissions || {}

  const allowedDomains: string[] = []
  const deniedDomains: string[] = []

  const allowWrite: string[] = ['.', getClaudeTempDir()]
  const denyWrite: string[] = []
  const denyRead: string[] = []
  const allowRead: string[] = []
```

--------------------------------

### Get Deferred Tools Delta Attachment

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04-agent-memory.md

Appends the re-declared external capabilities back into the new queue after compaction, ensuring the model has its skill blueprint loaded.

```typescript
getDeferredToolsDeltaAttachment(
  workspace,
  compactedMessages
);
```

--------------------------------

### REPL Main Path Prompt Construction

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04g-prompt-management.md

Fetches default system prompt, user context, and system context in parallel, then builds the effective system prompt. The final system prompt is attached to toolUseContext.renderedSystemPrompt for persistent reference.

```typescript
const [defaultSystemPrompt, userContext, systemContext] = await Promise.all([
  getSystemPrompt(...),
  getUserContext(),
  getSystemContext(),
])
const systemPrompt = buildEffectiveSystemPrompt({
  mainThreadAgentDefinition,
  toolUseContext,
  customSystemPrompt,
  defaultSystemPrompt,
  appendSystemPrompt
})
toolUseContext.renderedSystemPrompt = systemPrompt;
```

--------------------------------

### Whitelist IDE Tools for MCP

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04d-mcp-implementation.md

Defines a whitelist of allowed IDE-specific tools to be processed by MCP. Only tools starting with 'mcp__ide__' and present in the ALLOWED_IDE_TOOLS array are permitted.

```typescript
// src/services/mcp/client.ts:569
const ALLOWED_IDE_TOOLS = [
  'mcp__ide__getDiagnostics',
  'mcp__ide__getOpenEditorFiles',
  // ... only a few high-privilege tools pass through the whitelist
]

function isIncludedMcpTool(tool: Tool): boolean {
  // non-IDE tools are all allowed; IDE tools are only allowed if on the whitelist
  return !tool.name.startsWith('mcp__ide__') || ALLOWED_IDE_TOOLS.includes(tool.name)
}
```

--------------------------------

### Initialize Agent Memory from Snapshot

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04-agent-memory.md

Logic for copying snapshot files to initialize local agent memory.

```text
Snapshot directory
 -> Copy all files except snapshot.json
 -> Write to local agent memory directory
 -> Save.snapshot-synced.json
```

--------------------------------

### Skill Loading Process Flow

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04c-skills-implementation.md

Illustrates the sequence of operations for discovering, parsing, and loading skills, culminating in command instantiation.

```text
User directory / Project directory /.claude/skills/<skill-name>/SKILL.md
        │
        ▼
getSkillDirCommands(cwd)           ← Scan all skill directories in parallel, results memoized
        │
        ▼
loadSkillsFromSkillsDir(basePath)  ← Read directory, filter SKILL.md files
        │
        ▼
parseFrontmatter(content)          ← Parse YAML metadata
parseSkillFrontmatterFields(fm)    ← Extract name/paths/model/effort/...
        │
        ▼
createSkillCommand(fields)         ← Instantiate as Command object, plug into command system
        │
        ▼  (User invokes /<skill-name> or model selects autonomously)
getPromptForCommand(args, ctx)
  ├── substituteArguments()        ← Expand CLI parameters
  ├── Expand ${CLAUDE_SKILL_DIR}   ← Built-in variable substitution
  └── executeShellCommandsInPrompt() ← Execute embedded Shell (trusted sources only)
        │
        ▼
Final Prompt returned to the model (with real-time system state)
```

--------------------------------

### Get All Base Tools Function

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04b-tool-call-implementation.md

Retrieves a list of all built-in tools available in the system. This list can include tools conditionally enabled by environment variables or specific modes.

```typescript
export function getAllBaseTools(): Tools {
  return [
    AgentTool,
    TaskOutputTool,
    BashTool,
    ...
    FileEditTool,
    WebFetchTool,
    ...(isEnvTruthy(process.env.ENABLE_LSP_TOOL) ? [LSPTool] : []),
    ...(isWorktreeModeEnabled() ? [EnterWorktreeTool, ExitWorktreeTool] : []),
    ...(isToolSearchEnabledOptimistic() ? [ToolSearchTool] : []),
  ]
}
```

--------------------------------

### Handle System Prompt Options

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04g-prompt-management.md

This snippet demonstrates how to handle CLI options for system prompts, including reading from files and preventing conflicting options.

```typescript
let appendSystemPrompt = options.appendSystemPrompt;
if (options.appendSystemPromptFile) {
  if (options.appendSystemPrompt) {
    process.stderr.write(chalk.red('Error: Cannot use both ...'));
    process.exit(1);
  }
  const filePath = resolve(options.appendSystemPromptFile);
  appendSystemPrompt = readFileSync(filePath, 'utf8');
}
```

--------------------------------

### Typical Agent Memory Runtime Flow

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04-agent-memory.md

Outlines the sequence of events from agent definition loading to subsequent invocations, showing how memory rules, directory location, and current index content are integrated into the agent's system prompt.

```text
Load agent definition
 -> agent.memory = user / project / local
 -> Automatically add FileRead / FileWrite / FileEdit
 -> getSystemPrompt() appends Agent Memory prompt

Spawn agent
 -> Prompt already contains:
 1. Memory usage rules
 2. Memory directory location
 3. Current MEMORY.md index content

Agent discovers information worth remembering during work
 -> First read MEMORY.md or existing memory files
 -> Add or update a memory entry
 -> Then maintain the MEMORY.md index

Subsequent invocation of the same agent
 -> Re-read the same directory's MEMORY.md
 -> Get the long-term memory (accumulated) from last time
```

--------------------------------

### Main Structure of System Prompt

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04g-prompt-management.md

Illustrates the assembly of the system prompt, combining static backbone segments with dynamic sections, separated by a dynamic boundary.

```typescript
return [
  getSimpleIntroSection(outputStyleConfig),
  getSimpleSystemSection(),
  outputStyleConfig === null ||
  outputStyleConfig.keepCodingInstructions === true
    ? getSimpleDoingTasksSection()
    : null,
  getActionsSection(),
  getUsingYourToolsSection(enabledTools),
  getSimpleToneAndStyleSection(),
  getOutputEfficiencySection(),
  ...(shouldUseGlobalCacheScope() ? [SYSTEM_PROMPT_DYNAMIC_BOUNDARY] : []),
  ...resolvedDynamicSections,
].filter(s => s !== null)
```

--------------------------------

### Sandbox Runtime Configuration Logic

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/02-security-analysis.md

This pseudo-code illustrates the core logic for converting user-defined permissions into a sandbox runtime configuration. It specifies allowed and denied paths for file system access and lists allowed and denied network domains.

```typescript
// sandbox-adapter.ts core conversion logic (pseudo-code)
function convertToSandboxRuntimeConfig(permissions) {
  return {
    filesystem: {
      allowWrite: [...paths explicitly allowed by user for writing],
      denyWrite:  [...system core paths, e.g. ~/.claude/settings.json],
      allowRead:  [...paths explicitly allowed by user for reading],
      denyRead:   [...sensitive config paths]
    },
    network: {
      allowedDomains:  [...allowed domains extracted from WebFetchTool rules],
      deniedDomains:   [...denied domains],
      allowManagedOnly: [...enterprise managed mode — only managed domains allowed]
    }
  }
}
```

--------------------------------

### Get App State Setter

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/components/05-function-level-core-walkthrough.md

Provides direct access to the store's `setState` function for updating the application state. Components using this hook will not re-render due to state changes they do not subscribe to.

```typescript
return store.setState;
```

--------------------------------

### Spawn Teammate using Backend Registry

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/01-architecture-overview.md

Spawns a teammate instance by looking up the appropriate backend in a registry. Uses a configuration object to determine the backend type.

```typescript
const BACKEND_REGISTRY: Record<string, TeammateBackend> = {
  'in-process': InProcessBackend,
  'tmux':       TmuxBackend,
  'iterm2':     ITerm2PaneBackend,
}

export function spawnTeammate(config: TeammateConfig): TeammateHandle {
  const Backend = BACKEND_REGISTRY[config.backendType]
  return new Backend(config).spawn()
}
```

--------------------------------

### Get App State Store Instance

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/components/05-function-level-core-walkthrough.md

Provides direct access to the application state store instance. This is useful for components that need to interact with the store's methods beyond just subscribing or setting state.

```typescript
return store;
```

--------------------------------

### Extracting Network Domains from WebFetch Permission Rules

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04e-sandbox-implementation.md

Extracts allowed network domains from permission rules that specify the WEB_FETCH_TOOL_NAME and start with 'domain:'. This integrates application-layer rules into the sandbox's network allowlist.

```typescript
for (const ruleString of permissions.allow || []) {
  const rule = permissionRuleValueFromString(ruleString)
  if (
    rule.toolName === WEB_FETCH_TOOL_NAME &&
    rule.ruleContent?.startsWith('domain:')
  ) {
    allowedDomains.push(rule.ruleContent.substring('domain:'.length))
  }
}
```

--------------------------------

### Build Memory Prompt with Truncated Entrypoint Content

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/01-architecture-overview.md

Constructs a memory prompt by reading and truncating an entrypoint file. Uses synchronous file reading.

```typescript
export const ENTRYPOINT_NAME    = 'MEMORY.md'
export const MAX_ENTRYPOINT_LINES = 200
export const MAX_ENTRYPOINT_BYTES = 25_000

export function buildMemoryPrompt(params: {
  displayName: string
  memoryDir:   string
  extraGuidelines?: string[]
}): string {
  const entrypoint = params.memoryDir + ENTRYPOINT_NAME
  const raw = fs.readFileSync(entrypoint, { encoding: 'utf-8' })  // Sync read
  const t   = truncateEntrypointContent(raw)                       // Hard truncation protection

  const lines = buildMemoryLines(params.displayName, params.memoryDir, ...)
  lines.push(`## ${ENTRYPOINT_NAME}`, '', t.content)
  return lines.join('
')
}
```

--------------------------------

### Function Signature for Reading Transcript for Load

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04i-session-storage-resume.md

Defines the asynchronous function signature for reading a transcript file, returning the boundary start offset, the buffer after the boundary, and a flag indicating if a preserved segment was found.

```typescript
export async function readTranscriptForLoad(filePath, fileSize): Promise<{
  boundaryStartOffset: number
  postBoundaryBuf: Buffer
  hasPreservedSegment: boolean
}>
```

--------------------------------

### Initialize App State Store

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/components/05-function-level-core-walkthrough.md

Initializes the application state store with default or provided state and sets up change listeners. It also handles permission mode adjustments and mounts necessary providers.

```typescript
const store = createStore(initialState ?? getDefaultAppState(), onChangeAppState);

useEffect(() => {
  if (toolPermissionContext.isBypassPermissionsModeAvailable) {
    // ... permission logic ...
  }
  useSettingsChange(onSettingsChange);
  // ... mount providers ...
}, []);
```

--------------------------------

### Build Memory Prompt with Entrypoint Content

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04-agent-memory.md

Assembles the complete memory prompt for an agent, incorporating existing content from the MEMORY.md file. It handles synchronous file reading and includes hard truncation protection for the entrypoint content to prevent prompt explosion.

```typescript
export function buildMemoryPrompt(params: {
 displayName: string
 memoryDir: string
 extraGuidelines?: string[]
}): string {
 const entrypoint = params.memoryDir + ENTRYPOINT_NAME // <dir>/MEMORY.md

 // Synchronous read (some calls come from the React render path and cannot use await)
 let entrypointContent = ''
 try {
 entrypointContent = fs.readFileSync(entrypoint, { encoding: 'utf-8' })
 } catch { /* Silently ignore when file does not exist */ }

 const lines = buildMemoryLines(params.displayName, params.memoryDir, params.extraGuidelines)

 if (entrypointContent.trim()) {
 const t = truncateEntrypointContent(entrypointContent) // Hard truncation protection
 logMemoryDirCounts(params.memoryDir, {
 content_length: t.byteCount, line_count: t.lineCount,
 was_truncated: t.wasLineTruncated,
 // Type annotation prevents PII from being mistakenly reported
 memory_type: memoryType as AnalyticsMetadata_I_VERIFIED_THIS_IS_NOT_CODE_OR_FILEPATHS,
 })
 lines.push(`## ${ENTRYPOINT_NAME}`, '', t.content)
 } else {
 lines.push(
 `## ${ENTRYPOINT_NAME}`, '',
 `Your ${ENTRYPOINT_NAME} is currently empty. When you save new memories, they will appear here.`,
 )
 }
 return lines.join('
')
}
```

--------------------------------

### Load Conversation For Resume Pseudocode

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04i-session-storage-resume.md

This pseudocode outlines the comprehensive orchestration involved in loading a conversation for resume. It handles various sources, performs consistency checks, restores skill state, and processes session start hooks to ensure a continuable message stream.

```typescript
async function loadConversationForResume(source) {
  log = resolveSourceToLogOrJsonl(source)

  if (log is lite log) {
    log = loadFullLog(log)
  }

  sessionId = resolveSessionId(log)
  copyPlanForResume(log, sessionId)
  copyFileHistoryForResume(log)

  messages = log.messages
  checkResumeConsistency(messages)

  restoreSkillStateFromMessages(messages)

  deserialized = deserializeMessagesWithInterruptDetection(messages)
  messages = deserialized.messages

  hookMessages = processSessionStartHooks('resume', { sessionId })
  messages.push(...hookMessages)

  return {
    messages,
    turnInterruptionState,
    fileHistorySnapshots,
    attributionSnapshots,
    contentReplacements,
    contextCollapseCommits,
    session metadata...
  }
}
```

--------------------------------

### Initialization Logic in `init.ts`

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/01-architecture-overview.md

This pseudo-code outlines the structure of `init.ts`, detailing the steps for logic initialization, including applying safe environment variables and setting up telemetry before trust is established.

```typescript
// src/entrypoints/init.ts structure pseudo-code
export async function init(argv) {
  applySafeEnvironmentVariables()    // Only apply safe env vars (pre-trust)
  initializeCertificates()           // Certificates and HTTPS proxy
  initializeHttpAgent()              // HTTP agent configuration
  initTelemetrySkeleton()            // Register telemetry sink, but don't emit events
  // Note: initializeTelemetryAfterTrust() is called by main.tsx after trust is established
}

export async function initializeTelemetryAfterTrust() {
  applyFullEnvironmentVariables()    // Apply all env vars only after trust passes
  attachAnalyticsSink()              // Start processing telemetry event queue
}
```

--------------------------------

### Effective System Prompt Assembly Priority

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04g-prompt-management.md

The comment in `buildEffectiveSystemPrompt` outlines the priority order for assembling the final system prompt, including overrides and default segments.

```typescript
/**
 * 0. Override system prompt
 * 1. Coordinator system prompt
 * 2. Agent system prompt
 * 3. Custom system prompt
 * 4. Default system prompt
 * Plus appendSystemPrompt is always added at the end
 */
```

--------------------------------

### Pseudocode for System Prompt Override Logic

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04g-prompt-management.md

Illustrates the decision tree for constructing the final system prompt based on various conditions like override, coordinator mode, and proactive mode.

```pseudocode
if overrideSystemPrompt:
    final = [overrideSystemPrompt]
else if coordinator mode:
    final = [coordinatorPrompt] + [appendPrompt?]
else:
    base =
      agentPrompt
      or customSystemPrompt
      or defaultSystemPrompt

    if proactive mode and agentPrompt exists:
        final = defaultSystemPrompt + ["# Custom Agent Instructions" + agentPrompt]
    else:
        final = [base]

    if appendSystemPrompt:
        final += [appendSystemPrompt]
```

--------------------------------

### Main Launcher Key Imports

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/01-architecture-overview.md

This snippet shows key imports in `main.tsx`, reflecting its broad responsibility for system orchestration and initialization.

```typescript
// src/main.tsx —— key imports reflecting scope of responsibility
import { init, initializeTelemetryAfterTrust } from './entrypoints/init.js'
import { launchRepl } from './replLauncher.js'
import { fetchBootstrapData } from './services/api/bootstrap.js'
import { getMcpToolsCommandsAndResources } from './services/mcp/client.js'
import { getTools } from './tools.js'
import { getAgentDefinitionsWithOverrides } from './tools/AgentTool/loadAgentsDir.js'
import { initBundledSkills } from './skills/bundled/index.js'
import { showSetupScreens, exitWithError } from './interactiveHelpers.js'
import { settingsChangeDetector } from './utils/settings/changeDetector.js'
// ... and about 80 more imports
```

--------------------------------

### Agent Memory Prompt Generation Steps

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04-agent-memory.md

Illustrates the sequence of operations within the loadAgentMemoryPrompt function, including scope note generation, memory directory computation, asynchronous directory creation, and building the final memory prompt.

```typescript
loadAgentMemoryPrompt()
 -> Generates scopeNote based on scope
 -> Computes memoryDir
 -> fire-and-forget ensureMemoryDirExists(memoryDir)
 -> buildMemoryPrompt({
 displayName: 'Persistent Agent Memory',
 memoryDir,
 extraGuidelines: [scopeNote,...possible additional environment rules]
 })
```

--------------------------------

### Agent Runtime Components

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04-agent-memory.md

Illustrates the components that constitute the agent runtime when memory is considered. This is a conceptual representation.

```text
agent runtime
 = agent definition
 + system prompt
 + tool set
 + permission context
 + memory directory
 + snapshot state
```

--------------------------------

### QueryEngine Class Structure (Headless/SDK Mode)

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/01-architecture-overview.md

This pseudo-code outlines the structure of the QueryEngine class, responsible for managing multi-turn session state in headless mode. It handles message assembly, API calls, and tool use management.

```typescript
// src/QueryEngine.ts structure pseudo-code
export class QueryEngine {
  async query(userInput: string): AsyncGenerator<StreamEvent> {
    // 1. Assemble messages + system prompt
    // 2. Call claude.ts API
    // 3. Handle tool_use / tool_result
    // 4. yield events to caller
  }
}
```

--------------------------------

### Feature Toggle to Command Mapping

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/11-hidden-features-and-easter-eggs.md

Demonstrates how feature toggles map to specific commands. This shows the integration of experimental features into the command-line interface.

```javascript
VOICE_MODE introduces /voice
```

```javascript
ULTRAPLAN introduces ultraplan
```

```javascript
BUDDY introduces buddy
```

```javascript
BRIDGE_MODE introduces bridge capabilities
```

--------------------------------

### CLI Entrypoint Routing Logic

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/01-architecture-overview.md

This pseudo-code illustrates the early routing logic in `cli.tsx`. It handles fast-path commands like version checking or system prompt dumping, exiting early to avoid full application startup.

```typescript
// src/entrypoints/cli.tsx structure pseudo-code
async function main() {
  const argv = parseArgs(process.argv)

  // Fast path routing — if matched, execute and exit, don't enter main.tsx
  if (argv['--version']) {
    console.log(version); process.exit(0)
  }
  if (argv['--dump-system-prompt']) {
    await dumpSystemPrompt(); process.exit(0)
  }
  if (argv['remote-control']) {
    return runRemoteControl(argv)
  }
  if (argv['daemon'] || argv['bg'] || argv['runner']) {
    return runDaemonOrBackground(argv)
  }

  // Default: enter full main launcher
  await import('./main.tsx').then(m => m.main(argv))
}
```

--------------------------------

### Enable SIMPLE Mode

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/03-privacy-avoidance.md

Use the --bare or SIMPLE mode flag to disable auto memory and other features.

```bash
--bare
```

--------------------------------

### Main Flow of `main.tsx`

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/01-architecture-overview.md

This pseudo-code illustrates the main execution flow within `main.tsx`, covering early initialization, argument parsing, conditional branching for different runtime modes, and the default path leading to the REPL.

```typescript
// src/main.tsx main flow (pseudo-code)
export async function main(argv: ParsedArgs) {
  // 1. Early initialization (doesn't depend on trust)
  await init(argv)

  // 2. Parse CLI args -> determine permission mode, model, tools, etc.
  const permissionMode = initialPermissionModeFromCLI(argv)
  const model = resolveModel(argv)

  // 3. Conditional branches: select execution path
  if (argv['--print'] || argv['--sdk']) {
    return runHeadless(argv, model, permissionMode)
  }
  if (argv['bridge']) {
    return runBridge(argv)
  }
  if (argv['remote']) {
    return runRemote(argv)
  }

  // 4. Default path: initialize full runtime then enter REPL
  const bootstrap = await fetchBootstrapData()          // Fetch remote config
  const mcpTools  = await getMcpToolsCommandsAndResources() // Connect MCP
  const tools     = getTools(permissionContext)          // Assemble tool pool
  const skills    = initBundledSkills()                  // Load built-in skills
  const agents    = getAgentDefinitionsWithOverrides()   // Load agent definitions

  await initializeTelemetryAfterTrust()                 // Start telemetry only after trust

  settingsChangeDetector.start()                        // Listen for config hot-reload

  // 5. Enter REPL
  await launchRepl(root, appProps, replProps, renderAndRun)
}
```

--------------------------------

### Memory Directory Structure and Indexing

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04-agent-memory.md

Illustrates the hierarchical structure of memory storage, with MEMORY.md acting as an index for topic-specific markdown files. This approach separates content from its index, preventing prompt explosion and update conflicts.

```text
Session transcript / current query
 ├─> Auto Memory extraction
 │ ├─> MEMORY.md index
 │ ├─> topic memories/*.md
 │ └─> relevant recall selects a few files to inject back into the current context
 │
 ├─> Session Memory
 │ └─> Current session summary markdown
 │
 ├─> Agent Memory
 │ ├─> user scope
 │ ├─> project scope
 │ └─> local scope
 │ └─> Injected directly into the agent system prompt
 │
 └─> Team Memory
 └─> Team-synchronized shared memory

Additionally:
 └─> Agent Memory Snapshot
 ├─> Initialize local agent memory
 └─> Notify that a new version of local memory snapshot is available for sync
```

--------------------------------

### Face Rendering Logic for Different Buddy Species

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/11-hidden-features-and-easter-eggs.md

Illustrates how different buddy species have unique face designs for narrow terminal mode. This highlights the detailed customization applied to each character.

```string
duck / goose is (${eye}>
cat is =${eye}ω${eye}=
dragon is <${eye}~${eye}>
octopus is ~(${eye}${eye})~
axolotl is }${eye}.${eye}{
robot is [${eye}${eye}]
```

--------------------------------

### Platform Control Plane Diagram

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/components/03-platform-components.md

Illustrates the hierarchical structure of the platform's control plane components and their dependencies.

```text
PromptInput / slash command / footer
 ├─> permissions
 ├─> tasks
 ├─> agents
 ├─> mcp
 ├─> teams
 ├─> Settings
 └─> memory / skills / hooks / sandbox

The above control planes uniformly depend downward on:
 -> AppState / Context / hooks
 -> services / tools / swarm / mcp / permissions / fs
```

--------------------------------

### Discover Skills from Filesystem Directories

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04c-skills-implementation.md

This function discovers and loads skills from multiple filesystem locations, including user-defined, managed, and project-specific directories. It supports parallel loading and deduplicates skills based on their real paths to prevent duplicates from symlinks.

```typescript
export const getSkillDirCommands = memoize(
  async (cwd: string): Promise<Command[]> => {
    const userSkillsDir    = join(getClaudeConfigHomeDir(), 'skills')  // ~/.claude/skills
    const managedSkillsDir = join(getManagedFilePath(), '.claude', 'skills')  // Policy-managed directory
    const projectSkillsDirs = getProjectDirsUpToHome('skills', cwd)   // Crawl up from project directory

    // --bare mode: skip auto-discovery, only load paths explicitly specified with --add-dir
    if (isBareMode()) {
      return additionalDirs.flatMap(dir =>
        loadSkillsFromSkillsDir(join(dir, '.claude', 'skills'), 'projectSettings')
      )
    }

    // Normal mode: load all sources in parallel
    const [managedSkills, userSkills, projectSkillsNested, additionalSkillsNested, legacyCommands] = 
      await Promise.all([
        loadSkillsFromSkillsDir(managedSkillsDir, 'policySettings'),    // Policy-level skills
        loadSkillsFromSkillsDir(userSkillsDir,    'userSettings'),      // User-level skills
        Promise.all(projectSkillsDirs.map(dir =>
          loadSkillsFromSkillsDir(dir, 'projectSettings'))),            // Project-level skills (multi-directory)
        Promise.all(additionalDirs.map(dir =>
          loadSkillsFromSkillsDir(join(dir, '.claude', 'skills'), 'projectSettings'))), // --add-dir
        loadSkillsFromCommandsDir(cwd),                                 // Legacy /commands/ directory
      ])

    // Merge + deduplicate (inode level, prevent symlink duplicates)
    return deduplicateByRealpath([
      ...managedSkills, ...userSkills,
      ...projectSkillsNested.flat(),
      ...additionalSkillsNested.flat(),
      ...legacyCommands,
    ])
  }
)
```

--------------------------------

### Component Backbone Diagram

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/components/01-component-architecture-overview.md

Illustrates the hierarchical structure and dependencies of the main components in the application, showing the flow from the App component down to various layers and services.

```text
App
 -> REPL / FullscreenLayout
 -> Messages
 | -> VirtualMessageList
 | -> MessageRow / Message / messages/*
 |
 -> PromptInput
 -> Footer / Suggestions / Notifications
 -> QuickOpen / Search / Tasks / Teams / Bridge / ModelPicker

Messages and PromptInput both depend downward on:
 -> AppState
 -> hooks
 -> services
```

--------------------------------

### Spawn Teammate Entry Point

Source: https://github.com/alankatanoisi/claude-code-analysis-mine/blob/main/analysis/04h-multi-agent.md

The main entry point for creating a teammate agent, abstracting the spawning logic into a shared module. This function is callable by various tools, including dedicated team tools and the AgentTool.

```typescript
export async function spawnTeammate(
  config: SpawnTeammateConfig,
  context: ToolUseContext,
): Promise<{ data: SpawnOutput }> {
  return handleSpawn(config, context)
}
```