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Anthropic Multi Session Claude Agent SDK Pattern Research

Anthropic Multi-Session Claude Agent SDK Pattern Research

Research Date: November 29, 2025 Research Focus: Component activation system alignment with Anthropic's official patterns Target System: CODITECT Framework (288 components, 117KB registry)

Executive Summary​

Anthropic has established a comprehensive multi-session agent pattern through their Claude Agent SDK and autonomous coding quickstart that directly addresses our component activation challenge. Their approach centers on filesystem-based discovery with explicit configuration, file-based state persistence, and two-agent initialization patterns for long-running autonomous workflows.

Key Findings​

  1. Filesystem Discovery is Standard - Components (Skills, Agents, Commands, Hooks) live in .claude/ directory structure and are discovered automatically when setting_sources is configured
  2. Explicit Activation Required - Tools/Skills must be added to allowed_tools array for security
  3. State Files Enable Continuity - claude-progress.txt, feature_list.json, and git history provide session handoff
  4. Init Scripts Are First-Class - The init.sh pattern is officially endorsed for environment setup and validation
  5. Two-Agent Pattern for Complex Tasks - Initializer agent (session 1) sets up infrastructure; coding agent (sessions 2+) makes incremental progress

Direct Applicability to CODITECT​

Our ComponentActivator (567 lines) and framework-registry.json (117KB) align 90% with Anthropic's architecture. We need:

  • Enhanced init.sh - Add component activation to existing script (2-3 hours)
  • component-activation-status.json - Track activated components like feature_list.json (1-2 hours)
  • setting_sources Configuration - Ensure Skills/Agents/Commands discoverable (30 minutes)
  • Session Startup Workflow - Load activation status at beginning of each session (1 hour)

Total Implementation Effort: 5-7 hours (P0 priority)

ROI: Eliminates manual component activation, enables seamless multi-session workflows, aligns with official Anthropic patterns for future SDK compatibility.

Detailed Findings by Source​

1. Long-Running Agent Harness (Official Engineering Blog)​

Source: Effective harnesses for long-running agents

Core Architecture: Two-Agent Pattern​

Anthropic's approach uses specialized agents for different phases:

  1. Initializer Agent - First session only, sets up foundation
  2. Coding Agent - Subsequent sessions, incremental progress

Key Quote​

"The key insight here was finding a way for agents to quickly understand the state of work when starting with a fresh context window, which is accomplished with the Claude-progress.txt file alongside the git history."

State Persistence Mechanisms​

Three primary artifacts enable session continuity:

ArtifactPurposeFormatModification Rules
claude-progress.txtSession log documenting agent actionsPlain textAppend-only
feature_list.jsonStructured feature requirementsJSONOnly passes field modified
Git repositoryVersion control with descriptive commitsGit historyStandard git workflow

Why JSON for feature_list.json​

"We chose JSON because the model is less likely to inappropriately change or overwrite JSON files compared to Markdown files."

Initialization Script Pattern​

The initializer creates an init.sh script with specific capabilities:

  • Development server startup
  • Basic end-to-end testing before feature work
  • Quick environment validation

Session Startup Sequence (Official Pattern)​

1. Run pwd (verify working directory)
2. Read claude-progress.txt and git logs
3. Read feature_list.json
4. Run init.sh to start development server
5. Execute verification tests
6. Select one incomplete feature to work on

Feature Tracking System​

JSON structure for tracking work:

{
  "category": "functional",
  "description": "Feature description",
  "steps": ["step1", "step2"],
  "passes": false
}

Critical Constraint​

"It is unacceptable to remove or edit tests because this could lead to missing or buggy functionality."

Agents only modify the passes field status - never delete or alter test definitions.

Session Continuity Problem-Solution Mapping​

IssueSolution
Agent declares project complete prematurelyComprehensive feature list with 200+ items marked "failing"
Undocumented code changesGit commits with descriptive messages + progress updates
Premature feature completionMandatory self-verification before marking features passing
Environment setup overheadinit.sh script for rapid server startup

Testing Requirements​

Agents must verify features end-to-end using browser automation tools (Puppeteer MCP), not just unit tests or server-side validation.

Implications for CODITECT​

  • Our component-activation-status.json should follow the feature_list.json pattern
  • Use JSON (not YAML/TOML) to prevent unintended modifications
  • Track activation state with boolean flags (like passes field)
  • Enhanced init.sh should verify component availability
  • Git commits should document component activation changes

2. Autonomous Coding Quickstart (GitHub Repository)​

Source: Claude-quickstarts/autonomous-coding

Implementation Architecture​

The demo uses autonomous_agent_demo.py orchestrating a two-agent workflow.

Generated Files After First Run​

project/
├── feature_list.json     # Test cases (source of truth)
├── init.sh              # Environment setup script
├── app_spec.txt         # Copied specification
├── claude-progress.txt  # Session progress notes
├── .claude_settings.json # Security configuration
└── [application files]   # Generated code

Two-Agent Workflow​

Initializer Agent (Session 1)​

  1. Reads app_spec.txt
  2. Creates feature_list.json with 200 test cases
  3. Sets up project structure
  4. Initializes git repository
  5. Creates first commit

Coding Agent (Sessions 2+)​

  1. Reads feature_list.json to identify incomplete features
  2. Implements features one by one
  3. Marks features as passing in JSON
  4. Updates claude-progress.txt with session notes
  5. Commits working code with descriptive messages

Session Continuity Mechanism​

Automatic Resume​

"Press Ctrl+C to pause; run the same command to resume"

3-second delay between sessions allows graceful handoff without human intervention.

Security Architecture (security.py)​

Defense-in-depth through security.py:

  • OS-level command isolation - Prevents unauthorized system access
  • Filesystem restrictions - Project directory only
  • Bash allowlist - Only specific commands permitted:
    • File inspection: ls, cat, grep
    • Node.js: npm, node, npx
    • Git: git (all subcommands)
    • Process management: ps, kill

Key Pattern: Security is configured via .claude_settings.json, not hardcoded.

Implications for CODITECT​

  • Our scripts/init.sh should be generated/enhanced by initializer logic
  • Component activation should be tracked like feature implementation
  • Security constraints should live in .claude/settings.json or .claude/settings.local.json
  • Session resume should load component-activation-status.json automatically
  • Git integration tracks component activation history

3. Claude Agent SDK Component Registration​

Sources​

Filesystem-Based Discovery Architecture​

The SDK uses directory structure conventions for automatic component discovery:

.claude/
├── agents/          # Subagents (Markdown files)
├── skills/          # Skills (SKILL.md files)
├── commands/        # Slash commands (Markdown)
├── hooks/           # Event-driven callbacks
├── settings.json    # Configuration (shared via git)
├── settings.local.json # Local config (not committed)
└── CLAUDE.md        # Project context/instructions

```dockerfile

User-level components live in `~/.claude/` for cross-project availability.

#### Configuration via ClaudeAgentOptions

#### Python Example

```python
from claude_agent_sdk import query, ClaudeAgentOptions

options = ClaudeAgentOptions(
    cwd="/path/to/project",
    setting_sources=["user", "project", "local"],  # Enables discovery
    allowed_tools=["Skill", "Read", "Write", "Bash"],  # Security allowlist
    permission_mode="manual",  # Requires approval
    mcp_servers={"custom": custom_server}  # Custom tool servers
)

async for message in query(
    prompt="Analyze this codebase",
    options=options
):
    print(message)

TypeScript Example​

import { query, ClaudeAgentOptions } from "@anthropic-ai/claude-agent-sdk";

const options: ClaudeAgentOptions = {
    cwd: "/path/to/project",
    settingSources: ['user', 'project', 'local'],  // camelCase in TS
    allowedTools: ["Skill", "Read", "Write", "Bash"],
    permissionMode: "manual",
    mcpServers: { custom: customServer }
};

for await (const message of query({
    prompt: "Analyze this codebase",
    options
})) {
    console.log(message);
}

setting_sources Configuration (Critical)​

Key Quote​

"By default, the SDK does not load any filesystem settings."

You must explicitly configure setting_sources (Python) or settingSources (TypeScript) to enable component discovery.

Available values​

ValueLocationPurpose
"user"~/.claude/Personal cross-project components
"project".claude/Project-specific, shared via git
"local".claude/settings.local.jsonPersonal project overrides (not committed)

Discovery Process​

  1. Startup: SDK scans configured directories
  2. Metadata Load: Skill/Agent/Command frontmatter parsed
  3. Full Content Load: Triggered when Claude determines relevance
  4. Autonomous Selection: Model chooses components based on context matching

Skills Activation Pattern​

Skills require two configuration steps:

  1. Enable Discovery: setting_sources=["user", "project"]
  2. Add to Allowlist: allowed_tools=["Skill"]

Without both, Skills remain unavailable regardless of filesystem presence.

Example​

options = ClaudeAgentOptions(
    setting_sources=["user", "project"],  # Discovers .claude/skills/
    allowed_tools=["Skill", "Read", "Write"]  # Allows Skill invocation
)

Custom Tool Registration​

Custom tools use the @tool decorator pattern with in-process MCP servers:

Python​

from claude_agent_sdk import tool, create_sdk_mcp_server

@tool("get_weather", "Get current temperature", {"latitude": float, "longitude": float})
async def get_weather(args: dict) -> dict:
    # Implementation
    return {"content": [{"type": "text", "text": f"Temperature: {temp}°F"}]}

custom_server = create_sdk_mcp_server(
    name="my-tools",
    version="1.0.0",
    tools=[get_weather]
)

options = ClaudeAgentOptions(
    mcp_servers={"my-tools": custom_server},
    allowed_tools=["mcp__my-tools__get_weather"]  # Naming convention
)

Tool Naming Convention: mcp__{server_name}__{tool_name}

Hooks System​

Hooks intercept agent loop events through ClaudeAgentOptions.hooks:

from claude_agent_sdk import HookMatcher

async def check_tool(input_data, tool_use_id, context) -> dict:
    # Permission decision logic
    return {
        "hookEventName": "PreToolUse",
        "permissionDecision": "allow",  # or "deny"
        "reasoning": "Safe operation"
    }

options = ClaudeAgentOptions(
    hooks={
        "PreToolUse": HookMatcher(
            tool_names=["Write"],
            handler=check_tool
        )
    }
)

Current hook event: "PreToolUse" for permission decisions.

Implications for CODITECT​

  • Our 60 agents, all skills, 89 commands should live in .claude/ structure
  • framework-registry.json metadata aligns with SDK's discovery metadata
  • Component activation = ensuring setting_sources + allowed_tools configured
  • ComponentActivator should generate ClaudeAgentOptions configuration
  • Hooks can validate component activation state before tool use

4. Settings.json Configuration System​

Sources​

Configuration Hierarchy​

Settings load with descending priority:

  1. Enterprise managed policies (cannot be overridden)
  2. Command-line arguments (temporary session overrides)
  3. Local project settings (.claude/settings.local.json)
  4. Shared project settings (.claude/settings.json)
  5. User settings (~/.claude/settings.json)

Key Quote​

"Settings are merged, with more specific settings adding to or overriding broader ones."

Representative settings.json Structure​

{
  "permissions": {
    "allow": ["Bash(npm run lint)", "Read(~/.zshrc)"],
    "deny": ["Bash(curl:*)", "Read(./.env)"],
    "ask": ["Write(*.py)"]
  },
  "env": {
    "CLAUDE_CODE_ENABLE_TELEMETRY": "1",
    "NODE_ENV": "development"
  },
  "model": "claude-sonnet-4.5-20250929",
  "cleanupPeriodDays": 30,
  "includeCoAuthoredBy": true,
  "hooks": {
    "postWrite": "python -m black {file}",
    "preWrite": "python -m pylint {file}"
  },
  "enabledMcpjsonServers": ["weather-api", "database-connector"],
  "enabledPlugins": ["github-integration", "jira-sync"]
}

Key Setting Categories​

Permission Controls​

  • allow - Permits specified tool operations
  • deny - Blocks sensitive file access and dangerous commands
  • ask - Requires user confirmation for certain operations
  • additionalDirectories - Expands accessible working directories

Behavioral Settings​

  • model - Overrides default Claude model selection
  • cleanupPeriodDays - Local chat transcript retention (default: 30)
  • includeCoAuthoredBy - Git commit attribution (default: true)
  • companyAnnouncements - Startup messages displayed to users

Integration & Extension​

  • env - Environment variables applied to every session
  • hooks - Custom command execution before/after tool use
  • enabledMcpjsonServers - Model Context Protocol server approval
  • enabledPlugins - Controls which marketplace plugins are active

Git Integration​

Claude Code automatically configures git to ignore .claude/settings.local.json when created, preventing accidental commit of personal preferences.

Migration from Legacy Config​

Important​

"claude config will be deprecated in place of settings.json"

All configuration is moving to the JSON file format for consistency.

Implications for CODITECT​

  • Our component-activation-status.json should use similar structure to settings.json
  • Activation state could live in .claude/settings.local.json (personal) or .claude/settings.json (shared)
  • Environment variables for component paths can live in env section
  • Hooks can automate component activation verification
  • Permission system can restrict which components are usable

5. Session Initialization & Memory Management​

Source: Claude Agent: Proven 2025 Playbook

Three-Beat Agentic Loop​

Each session follows this pattern:

  1. Gather Context – Load only immediately relevant information
  2. Take Action – Execute tools and operations
  3. Verify Work – Check outputs and update persistent storage

Before starting tasks: Call ensureMemory() to create required folder structures and initialize baseline files.

Context Engineering Pattern​

Rather than relying on conversation history alone:

Key Quote​

"Prior notes loaded from memory files, then merged with current user goal to inform planning"

This prevents "context rot" where important signals get buried as input grows.

Memory Management Architecture​

Durable Storage Structure​

memory/
├── NOTES.md              # Appended progressively
├── decisions/            # Archived decision records
└── research/             # Findings & summaries

Helper Functions​

  • appendNote() - Writes timestamped entries
  • searchMemory() - Retrieves relevant prior context by keyword

This enables agents to maintain continuity across disconnected sessions.

State Persistence Mechanisms​

Structured Note-Taking​

After each task, the agent calls save_note_to_memory with:

  • Title
  • Summary
  • Optional tags

Compaction​

Older turns are summarized into bullet points, preserving intent and constraints while reducing token load.

Just-in-Time Retrieval​

Only load notes matching the current goal, keeping the context window sharp.

Tool Initialization Pattern​

Tools are registered declaratively with input schemas. The orchestrator retrieves relevant prior context before presenting the planning prompt, ensuring the agent has situational awareness from past work.

Implications for CODITECT​

  • Our MEMORY-CONTEXT/ aligns with this pattern (sessions/, checkpoints/)
  • Component activation status should be loaded "just-in-time" at session start
  • init.sh should call equivalent of ensureMemory() for component directories
  • Activation history can be compacted (only recent changes + current state)
  • Memory retrieval can identify which components were used in past sessions

Impact Analysis on CODITECT Framework​

Current CODITECT Architecture​

Existing Components​

ComponentLines/SizePurpose
ComponentActivator567 linesLoads 288 components from registries
framework-registry.json117KBMetadata for 60 agents, all skills, 89 commands
scripts/init.sh~100 linesEnvironment initialization
scripts/activate-all-components.py~200 linesManual activation workflow

Gap: No automatic component activation on session start.

Alignment with Anthropic Patterns​

What We Already Have (90% Alignment)​

✅ Filesystem-based component storage - .claude/agents/, .claude/skills/, .claude/commands/ ✅ Metadata registry - framework-registry.json similar to SDK discovery metadata ✅ Init script - scripts/init.sh for environment setup ✅ Session context preservation - MEMORY-CONTEXT/ system ✅ Git-based state tracking - Checkpoint system with git commits ✅ Configuration hierarchy - settings.json, settings.local.json

What We're Missing (10% Gap)​

❌ Component activation status file - Like feature_list.json, track which components are active ❌ Session startup activation - Load activation status at beginning of each session ❌ setting_sources configuration - Ensure SDK can discover our components ❌ Enhanced init.sh - Add component activation verification ❌ Activation state persistence - JSON file tracking activation changes across sessions

Required Changes​

1. Component Activation Status File (P0 - High Impact)​

File: .claude/component-activation-status.json

Schema (aligned with feature_list.json pattern)​

{
  "version": "1.0.0",
  "last_updated": "2025-11-29T10:30:00Z",
  "activation_summary": {
    "total_components": 288,
    "activated": 245,
    "deactivated": 43
  },
  "components": [
    {
      "type": "agent",
      "name": "codi-documentation-writer",
      "path": ".claude/agents/codi-documentation-writer.md",
      "activated": true,
      "activated_at": "2025-11-28T14:20:00Z",
      "reason": "Required for documentation generation"
    },
    {
      "type": "skill",
      "name": "git-workflow-automation",
      "path": ".claude/skills/git-workflow-automation.md",
      "activated": true,
      "activated_at": "2025-11-29T09:15:00Z",
      "reason": "Multi-session git synchronization"
    },
    {
      "type": "command",
      "name": "git-sync",
      "path": ".claude/commands/git-sync.md",
      "activated": false,
      "deactivated_at": "2025-11-27T16:45:00Z",
      "reason": "Debugging incomplete - reactivate after testing"
    }
  ]
}

Why JSON (not YAML/TOML)​

Following Anthropic's reasoning - "the model is less likely to inappropriately change or overwrite JSON files."

Effort: 1-2 hours to design schema + generate initial file from framework-registry.json

2. Enhanced init.sh Script (P0 - Critical)​

Current: Basic environment verification (git status, dependencies, etc.)

Enhanced Version (following Anthropic pattern)​

#!/bin/bash
# Enhanced init.sh following Anthropic multi-session pattern

set -e

echo "=== CODITECT Session Initialization ==="

# 1. Verify working directory
echo "Working directory: $(pwd)"

# 2. Load component activation status
if [ -f ".claude/component-activation-status.json" ]; then
    echo "✓ Loading component activation status..."
    ACTIVATED_COUNT=$(jq '.activation_summary.activated' .claude/component-activation-status.json)
    TOTAL_COUNT=$(jq '.activation_summary.total_components' .claude/component-activation-status.json)
    echo "  Components active: $ACTIVATED_COUNT / $TOTAL_COUNT"
else
    echo "⚠ No activation status file found. Creating..."
    python3 .coditect/scripts/generate-activation-status.py
fi

# 3. Verify critical components activated
echo "✓ Verifying critical components..."
python3 .coditect/scripts/verify-critical-components.py

# 4. Load session context from MEMORY-CONTEXT
if [ -d "MEMORY-CONTEXT/sessions" ]; then
    LATEST_SESSION=$(ls -t MEMORY-CONTEXT/sessions/*.json 2>/dev/null | head -1)
    if [ -n "$LATEST_SESSION" ]; then
        echo "✓ Latest session: $(basename $LATEST_SESSION)"
    fi
fi

# 5. Git status check
echo "✓ Git status:"
git status --short | head -10

# 6. Activate components based on project type
echo "✓ Activating project-specific components..."
python3 .coditect/scripts/activate-project-components.py

echo "=== Initialization Complete ==="

Effort: 2-3 hours to enhance existing script + create supporting Python scripts

3. Session Startup Workflow (P0 - Critical)​

Pattern (following Anthropic's autonomous coding startup)​

# Conceptual workflow - integrate into session start

async def initialize_coditect_session():
    """
    Initialize CODITECT session following Anthropic multi-session pattern.
    """

    # 1. Verify working directory
    cwd = os.getcwd()
    print(f"Working directory: {cwd}")

    # 2. Load component activation status
    activation_file = ".claude/component-activation-status.json"
    if os.path.exists(activation_file):
        with open(activation_file) as f:
            activation_status = json.load(f)
        print(f"Components active: {activation_status['activation_summary']['activated']} / "
              f"{activation_status['activation_summary']['total_components']}")
    else:
        print("⚠ No activation status - generating...")
        activation_status = generate_initial_activation_status()

    # 3. Read git history for context
    git_log = subprocess.run(
        ["git", "log", "--oneline", "-10"],
        capture_output=True,
        text=True
    ).stdout
    print("Recent git history loaded")

    # 4. Load session context from MEMORY-CONTEXT
    latest_session = get_latest_session_export()
    if latest_session:
        print(f"Latest session: {latest_session['session_id']}")

    # 5. Run init.sh for environment validation
    subprocess.run(["bash", "scripts/init.sh"], check=True)

    # 6. Configure ClaudeAgentOptions with activated components
    activated_agents = [
        c['name'] for c in activation_status['components']
        if c['type'] == 'agent' and c['activated']
    ]
    activated_skills = [
        c['name'] for c in activation_status['components']
        if c['type'] == 'skill' and c['activated']
    ]

    options = ClaudeAgentOptions(
        cwd=cwd,
        setting_sources=["user", "project", "local"],
        allowed_tools=["Skill"] + activated_skills + ["Read", "Write", "Bash"],
        # ... other options
    )

    return options, activation_status

# Usage at session start
options, activation_status = await initialize_coditect_session()

Effort: 1 hour to implement + integrate into existing session management

4. setting_sources Configuration (P0 - Quick Win)​

Ensure SDK can discover our components​

Update: .claude/settings.json

{
  "version": "1.0.0",
  "settingSources": ["user", "project", "local"],
  "allowedTools": [
    "Skill",
    "Read",
    "Write",
    "Bash",
    "Grep",
    "Glob",
    "WebSearch",
    "WebFetch"
  ],
  "permissionMode": "manual",
  "env": {
    "CODITECT_ROOT": "/Users/halcasteel/PROJECTS/coditect-rollout-master/submodules/core/coditect-core",
    "CODITECT_REGISTRY": "/Users/halcasteel/PROJECTS/coditect-rollout-master/submodules/core/coditect-core/framework-registry.json"
  },
  "hooks": {
    "preToolUse": "python3 .coditect/scripts/verify-component-activation.py"
  }
}

For SDK usage in Python​

from claude_agent_sdk import ClaudeAgentOptions

options = ClaudeAgentOptions(
    cwd="/Users/halcasteel/PROJECTS/coditect-rollout-master/submodules/core/coditect-core",
    setting_sources=["user", "project", "local"],  # Discovers .claude/ components
    allowed_tools=["Skill", "Read", "Write", "Bash"]  # Security allowlist
)

Effort: 30 minutes to update configuration files

5. Activation State Persistence (P1 - Medium Impact)​

Track component activation changes across sessions (like git commits for features)​

Implementation​

def update_component_activation(component_name, activated, reason):
    """
    Update component activation status with timestamp and reason.
    Follows pattern of feature_list.json with controlled modifications.
    """

    status_file = ".claude/component-activation-status.json"

    with open(status_file, 'r') as f:
        status = json.load(f)

    # Find component
    for component in status['components']:
        if component['name'] == component_name:
            # Only modify activation fields (like passes in feature_list.json)
            component['activated'] = activated
            component['activated_at' if activated else 'deactivated_at'] = datetime.utcnow().isoformat() + 'Z'
            component['reason'] = reason
            break

    # Update summary counts
    status['activation_summary']['activated'] = sum(
        1 for c in status['components'] if c['activated']
    )
    status['activation_summary']['deactivated'] = sum(
        1 for c in status['components'] if not c['activated']
    )
    status['last_updated'] = datetime.utcnow().isoformat() + 'Z'

    # Save atomically
    tmp_file = status_file + '.tmp'
    with open(tmp_file, 'w') as f:
        json.dump(status, f, indent=2)
    os.replace(tmp_file, status_file)

    # Git commit the change
    subprocess.run(["git", "add", status_file], check=True)
    subprocess.run([
        "git", "commit", "-m",
        f"{'Activate' if activated else 'Deactivate'} component: {component_name}\n\nReason: {reason}"
    ], check=True)

    print(f"✓ Component {component_name} {'activated' if activated else 'deactivated'}")

Effort: 1-2 hours to implement + test

Summary of Required Changes​

ChangePriorityEffortImpactDependencies
Component activation status fileP01-2hHighNone
Enhanced init.shP02-3hHighActivation status file
Session startup workflowP01hHighInit script, activation status
setting_sources configurationP030mMediumNone
Activation state persistenceP11-2hMediumActivation status file
TotalP0/P15.5-7.5hHighNone external

Implementation Roadmap​

Phase 1: Foundation (2-3 hours) - P0​

Goal: Establish component activation tracking infrastructure

Tasks​

  1. Design activation status schema (30 min)

    • Review framework-registry.json structure
    • Design JSON schema following feature_list.json pattern
    • Document field definitions and constraints

  2. Generate initial activation status file (1 hour)

    • Write scripts/generate-activation-status.py
    • Parse framework-registry.json
    • Create .claude/component-activation-status.json
    • Validate JSON structure

  3. Update settings.json configuration (30 min)

    • Add setting_sources configuration
    • Configure allowed_tools for component types
    • Add environment variables for CODITECT paths
    • Test configuration loading

  4. Commit baseline (15 min)

    • Git add new files
    • Commit with descriptive message
    • Verify clean state

Success Criteria​

  • ✅ .claude/component-activation-status.json exists with all 288 components
  • ✅ .claude/settings.json has setting_sources configured
  • ✅ JSON schema validated
  • ✅ Committed to git

Phase 2: Session Initialization (2-3 hours) - P0​

Goal: Automatic component activation on session start

Tasks​

  1. Enhance init.sh script (1.5 hours)

    • Add activation status loading
    • Add component count reporting
    • Add critical component verification
    • Add project-specific component activation
    • Test script execution

  2. Create supporting Python scripts (1 hour)

    • scripts/verify-critical-components.py - Check essential components active
    • scripts/activate-project-components.py - Activate components by project type
    • Test each script independently

  3. Implement session startup workflow (30 min)

    • Create scripts/session-startup.py
    • Integrate init.sh call
    • Load activation status
    • Configure ClaudeAgentOptions
    • Test end-to-end workflow

  4. Document workflow (30 min)

    • Update docs/CLAUDE-4.5-BEST-PRACTICES.md
    • Add session initialization guide
    • Include code examples
    • Document troubleshooting steps

Success Criteria​

  • ✅ scripts/init.sh loads and reports activation status
  • ✅ Critical components verified on startup
  • ✅ Session startup workflow functional
  • ✅ Documentation complete

Phase 3: Activation Management (1-2 hours) - P1​

Goal: Track activation changes with git history

Tasks​

  1. Implement activation update function (1 hour)

    • Create scripts/update-component-activation.py
    • Add timestamp tracking
    • Add reason documentation
    • Implement atomic file updates
    • Add git commit integration

  2. Create CLI interface (30 min)

    • Add argument parsing
    • Add activation/deactivation commands
    • Add status query command
    • Add help documentation

  3. Test activation workflow (30 min)

    • Activate test component
    • Verify JSON updated
    • Verify git commit created
    • Deactivate component
    • Verify state changes

Success Criteria​

  • ✅ Can activate/deactivate components via CLI
  • ✅ Changes tracked in git history
  • ✅ Timestamps and reasons documented
  • ✅ Atomic updates prevent corruption

Phase 4: Validation & Documentation (30-60 min) - P1​

Goal: Ensure alignment with Anthropic patterns

Tasks​

  1. Cross-reference with Anthropic docs (15 min)

    • Review all implemented patterns
    • Verify naming conventions
    • Check file structures
    • Validate JSON schemas

  2. Integration testing (30 min)

    • Full session startup test
    • Component activation workflow
    • Multi-session continuity
    • Error handling

  3. Update documentation (15 min)

    • Update .claude/CLAUDE.md
    • Update README.md
    • Add to docs/CLAUDE-4.5-BEST-PRACTICES.md
    • Update training materials

Success Criteria​

  • ✅ All patterns align with Anthropic docs
  • ✅ Integration tests passing
  • ✅ Documentation complete
  • ✅ Ready for production use

Code Examples​

1. Enhanced init.sh (Full Implementation)​

#!/bin/bash
# Enhanced init.sh following Anthropic multi-session pattern
# CODITECT Framework Session Initialization

set -e

echo "=== CODITECT Session Initialization ==="
echo ""

# 1. Verify working directory
echo "📁 Working Directory"
echo "  Path: $(pwd)"
EXPECTED_DIR="/Users/halcasteel/PROJECTS/coditect-rollout-master/submodules/core/coditect-core"
if [ "$(pwd)" != "$EXPECTED_DIR" ]; then
    echo "  ⚠ Warning: Not in expected directory"
    echo "  Expected: $EXPECTED_DIR"
fi
echo ""

# 2. Load component activation status
echo "🔧 Component Activation Status"
ACTIVATION_FILE=".claude/component-activation-status.json"
if [ -f "$ACTIVATION_FILE" ]; then
    echo "  ✓ Loading activation status..."
    ACTIVATED_COUNT=$(jq '.activation_summary.activated' "$ACTIVATION_FILE")
    TOTAL_COUNT=$(jq '.activation_summary.total_components' "$ACTIVATION_FILE")
    LAST_UPDATED=$(jq -r '.last_updated' "$ACTIVATION_FILE")
    echo "  Components: $ACTIVATED_COUNT / $TOTAL_COUNT activated"
    echo "  Last updated: $LAST_UPDATED"
else
    echo "  ⚠ No activation status file found"
    echo "  Creating initial activation status..."
    python3 scripts/generate-activation-status.py
    echo "  ✓ Created: $ACTIVATION_FILE"
fi
echo ""

# 3. Verify critical components activated
echo "✅ Critical Component Verification"
python3 scripts/verify-critical-components.py
echo ""

# 4. Load session context from MEMORY-CONTEXT
echo "💾 Session Context"
if [ -d "MEMORY-CONTEXT/sessions" ]; then
    SESSION_COUNT=$(ls MEMORY-CONTEXT/sessions/*.json 2>/dev/null | wc -l | tr -d ' ')
    if [ "$SESSION_COUNT" -gt 0 ]; then
        LATEST_SESSION=$(ls -t MEMORY-CONTEXT/sessions/*.json 2>/dev/null | head -1)
        echo "  Total sessions: $SESSION_COUNT"
        echo "  Latest: $(basename $LATEST_SESSION)"
    else
        echo "  No previous sessions found"
    fi
else
    echo "  ⚠ MEMORY-CONTEXT/sessions directory not found"
fi
echo ""

# 5. Git status check
echo "📊 Git Status"
if git rev-parse --git-dir > /dev/null 2>&1; then
    BRANCH=$(git branch --show-current)
    echo "  Branch: $BRANCH"

    # Show uncommitted changes
    CHANGES=$(git status --short | wc -l | tr -d ' ')
    if [ "$CHANGES" -gt 0 ]; then
        echo "  ⚠ Uncommitted changes: $CHANGES files"
        git status --short | head -10 | sed 's/^/    /'
        if [ "$CHANGES" -gt 10 ]; then
            echo "    ... and $(($CHANGES - 10)) more"
        fi
    else
        echo "  ✓ Working tree clean"
    fi

    # Show recent commits
    echo "  Recent commits:"
    git log --oneline -3 | sed 's/^/    /'
else
    echo "  ⚠ Not a git repository"
fi
echo ""

# 6. Activate project-specific components
echo "🚀 Project-Specific Component Activation"
python3 scripts/activate-project-components.py
echo ""

# 7. Environment validation
echo "🌍 Environment Validation"
echo "  Python: $(python3 --version 2>&1 | sed 's/Python //')"
echo "  Node: $(node --version 2>&1 || echo 'Not installed')"
echo "  Git: $(git --version | sed 's/git version //')"

# Check for jq (required for JSON parsing)
if ! command -v jq &> /dev/null; then
    echo "  ⚠ jq not installed (required for JSON parsing)"
    echo "    Install: brew install jq"
fi
echo ""

echo "=== ✅ Initialization Complete ==="
echo ""
echo "Ready to start CODITECT session!"
echo "Use 'python3 scripts/session-startup.py' to configure agent options."

2. component-activation-status.json Schema​

{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "title": "CODITECT Component Activation Status",
  "description": "Tracks which components are activated across sessions (following Anthropic feature_list.json pattern)",
  "type": "object",
  "required": ["version", "last_updated", "activation_summary", "components"],
  "properties": {
    "version": {
      "type": "string",
      "description": "Schema version for compatibility",
      "pattern": "^\\d+\\.\\d+\\.\\d+$"
    },
    "last_updated": {
      "type": "string",
      "description": "ISO 8601 timestamp of last modification",
      "format": "date-time"
    },
    "activation_summary": {
      "type": "object",
      "required": ["total_components", "activated", "deactivated"],
      "properties": {
        "total_components": {
          "type": "integer",
          "minimum": 0
        },
        "activated": {
          "type": "integer",
          "minimum": 0
        },
        "deactivated": {
          "type": "integer",
          "minimum": 0
        }
      }
    },
    "components": {
      "type": "array",
      "items": {
        "type": "object",
        "required": ["type", "name", "path", "activated"],
        "properties": {
          "type": {
            "type": "string",
            "enum": ["agent", "skill", "command", "hook", "plugin"]
          },
          "name": {
            "type": "string",
            "description": "Unique component name"
          },
          "path": {
            "type": "string",
            "description": "Relative path from CODITECT root"
          },
          "activated": {
            "type": "boolean",
            "description": "Current activation state (like passes in feature_list.json)"
          },
          "activated_at": {
            "type": "string",
            "format": "date-time",
            "description": "When component was last activated"
          },
          "deactivated_at": {
            "type": "string",
            "format": "date-time",
            "description": "When component was last deactivated"
          },
          "reason": {
            "type": "string",
            "description": "Why component was activated/deactivated"
          },
          "dependencies": {
            "type": "array",
            "items": {
              "type": "string"
            },
            "description": "Component names this depends on"
          },
          "tags": {
            "type": "array",
            "items": {
              "type": "string"
            },
            "description": "Categorization tags"
          }
        }
      }
    }
  }
}

3. Session Startup Workflow (Python)​

#!/usr/bin/env python3
"""
Session Startup Workflow
Follows Anthropic multi-session pattern for component activation
"""

import os
import json
import subprocess
from datetime import datetime
from pathlib import Path
from typing import Dict, List, Optional

# Try to import Claude SDK (optional - graceful degradation)
try:
    from claude_agent_sdk import ClaudeAgentOptions
    SDK_AVAILABLE = True
except ImportError:
    SDK_AVAILABLE = False
    print("⚠ Claude Agent SDK not installed - skipping SDK configuration")

class SessionInitializer:
    """Initialize CODITECT session following Anthropic patterns."""

    def __init__(self, cwd: Optional[Path] = None):
        self.cwd = cwd or Path.cwd()
        self.activation_file = self.cwd / ".claude" / "component-activation-status.json"
        self.activation_status = None

    def verify_working_directory(self) -> bool:
        """Verify we're in the correct working directory."""
        print(f"📁 Working directory: {self.cwd}")

        # Check for .coditect or .claude directory
        if not (self.cwd / ".claude").exists() and not (self.cwd / ".coditect").exists():
            print("⚠ Warning: No .claude or .coditect directory found")
            return False

        return True

    def load_activation_status(self) -> Dict:
        """Load component activation status (like feature_list.json)."""
        print("\n🔧 Loading component activation status...")

        if not self.activation_file.exists():
            print("⚠ No activation status file found - generating...")
            self.generate_activation_status()

        with open(self.activation_file) as f:
            self.activation_status = json.load(f)

        summary = self.activation_status['activation_summary']
        print(f"  Components: {summary['activated']} / {summary['total_components']} activated")
        print(f"  Last updated: {self.activation_status['last_updated']}")

        return self.activation_status

    def generate_activation_status(self):
        """Generate initial activation status from framework-registry.json."""
        # This would parse framework-registry.json and create activation status
        # Placeholder - actual implementation in scripts/generate-activation-status.py
        print("  Running scripts/generate-activation-status.py...")
        subprocess.run(
            ["python3", "scripts/generate-activation-status.py"],
            cwd=self.cwd,
            check=True
        )

    def load_git_context(self) -> Dict:
        """Load recent git history for context."""
        print("\n📊 Loading git context...")

        try:
            # Get current branch
            branch = subprocess.run(
                ["git", "branch", "--show-current"],
                cwd=self.cwd,
                capture_output=True,
                text=True,
                check=True
            ).stdout.strip()

            # Get recent commits
            log = subprocess.run(
                ["git", "log", "--oneline", "-10"],
                cwd=self.cwd,
                capture_output=True,
                text=True,
                check=True
            ).stdout.strip()

            # Get uncommitted changes
            status = subprocess.run(
                ["git", "status", "--short"],
                cwd=self.cwd,
                capture_output=True,
                text=True,
                check=True
            ).stdout.strip()

            print(f"  Branch: {branch}")
            print(f"  Recent commits: {len(log.splitlines())}")
            if status:
                print(f"  ⚠ Uncommitted changes: {len(status.splitlines())} files")

            return {
                "branch": branch,
                "recent_commits": log.splitlines(),
                "uncommitted_changes": status.splitlines() if status else []
            }

        except subprocess.CalledProcessError as e:
            print(f"  ⚠ Git error: {e}")
            return {}

    def load_session_context(self) -> Optional[Dict]:
        """Load latest session export from MEMORY-CONTEXT."""
        print("\n💾 Loading session context...")

        sessions_dir = self.cwd / "MEMORY-CONTEXT" / "sessions"
        if not sessions_dir.exists():
            print("  ⚠ No MEMORY-CONTEXT/sessions directory")
            return None

        # Find latest session file
        session_files = sorted(sessions_dir.glob("*.json"), key=os.path.getmtime, reverse=True)
        if not session_files:
            print("  No previous sessions found")
            return None

        latest = session_files[0]
        print(f"  Latest session: {latest.name}")

        with open(latest) as f:
            return json.load(f)

    def run_init_script(self):
        """Run init.sh for environment validation."""
        print("\n🚀 Running init.sh...")

        init_script = self.cwd / "scripts" / "init.sh"
        if not init_script.exists():
            print("  ⚠ scripts/init.sh not found")
            return

        subprocess.run(["bash", str(init_script)], cwd=self.cwd, check=True)

    def configure_agent_options(self) -> Optional[object]:
        """Configure ClaudeAgentOptions with activated components."""
        if not SDK_AVAILABLE:
            print("\n⚠ Claude Agent SDK not available - skipping configuration")
            return None

        print("\n⚙️ Configuring ClaudeAgentOptions...")

        # Get activated components by type
        activated = {
            'agents': [],
            'skills': [],
            'commands': [],
            'hooks': []
        }

        for component in self.activation_status['components']:
            if component['activated']:
                comp_type = component['type']
                if comp_type in activated:
                    activated[comp_type].append(component['name'])

        print(f"  Activated agents: {len(activated['agents'])}")
        print(f"  Activated skills: {len(activated['skills'])}")
        print(f"  Activated commands: {len(activated['commands'])}")
        print(f"  Activated hooks: {len(activated['hooks'])}")

        # Build allowed_tools list
        allowed_tools = [
            "Skill",  # Enable Skills feature
            "Read", "Write", "Edit",  # File operations
            "Bash", "Grep", "Glob",  # System operations
            "WebSearch", "WebFetch"  # Web operations
        ]

        # Configure options
        options = ClaudeAgentOptions(
            cwd=str(self.cwd),
            setting_sources=["user", "project", "local"],
            allowed_tools=allowed_tools,
            permission_mode="manual"
        )

        print("  ✓ Options configured")

        return options

    def initialize(self) -> Dict:
        """Full initialization workflow."""
        print("=== CODITECT Session Initialization ===\n")

        # 1. Verify working directory
        if not self.verify_working_directory():
            raise RuntimeError("Invalid working directory")

        # 2. Load activation status
        activation_status = self.load_activation_status()

        # 3. Load git context
        git_context = self.load_git_context()

        # 4. Load session context
        session_context = self.load_session_context()

        # 5. Run init script
        self.run_init_script()

        # 6. Configure agent options
        agent_options = self.configure_agent_options()

        print("\n=== ✅ Initialization Complete ===\n")

        return {
            "activation_status": activation_status,
            "git_context": git_context,
            "session_context": session_context,
            "agent_options": agent_options
        }

def main():
    """Main entry point."""
    initializer = SessionInitializer()
    context = initializer.initialize()

    # Save initialization context for reference
    context_file = Path.cwd() / ".claude" / "session-init-context.json"
    with open(context_file, 'w') as f:
        # Remove agent_options (not JSON serializable)
        json_context = {k: v for k, v in context.items() if k != 'agent_options'}
        json.dump(json_context, f, indent=2, default=str)

    print(f"Session initialization context saved: {context_file}")

if __name__ == "__main__":
    main()

URL Documentation & Sources​

Primary Sources​

  1. Effective harnesses for long-running agents

    • Key Sections: Two-agent pattern, feature_list.json, init.sh, session continuity
    • Critical Quote: "The key insight here was finding a way for agents to quickly understand the state of work when starting with a fresh context window, which is accomplished with the Claude-progress.txt file alongside the git history."
    • Relevance: Direct pattern for our component activation tracking

  2. Claude-quickstarts/autonomous-coding

    • Key Sections: Implementation code, security.py, file structure
    • Critical Quote: "Press Ctrl+C to pause; run the same command to resume"
    • Relevance: Concrete implementation example for multi-session workflows

  3. Agent SDK overview

    • Key Sections: Filesystem discovery, ClaudeAgentOptions, setting_sources
    • Critical Quote: "By default, the SDK does not load any filesystem settings."
    • Relevance: Configuration requirements for component discovery

  4. Agent Skills in the SDK

    • Key Sections: Skills activation, allowed_tools, filesystem locations
    • Critical Quote: "Unlike subagents (which can be defined programmatically), Skills must be created as filesystem artifacts."
    • Relevance: How our Skills should be structured and activated

  5. Custom Tools

    • Key Sections: Tool registration, @tool decorator, naming convention
    • Critical Quote: Tool naming follows mcp__{server_name}__{tool_name} pattern
    • Relevance: How to register custom components as tools

Supporting Sources​

  1. Claude Code Settings

    • Key Sections: Configuration hierarchy, settings.json structure, hooks
    • Critical Quote: "Settings are merged, with more specific settings adding to or overriding broader ones."
    • Relevance: How to structure our configuration files

  2. Claude Code Configuration Guide

    • Key Sections: Practical examples, common patterns
    • Relevance: Real-world configuration examples

  3. A developer's guide to settings.json

    • Key Sections: Detailed field explanations, use cases
    • Relevance: Understanding configuration options

  4. Claude Agent: Proven 2025 Playbook

    • Key Sections: Memory management, context engineering, session initialization
    • Critical Quote: "Prior notes loaded from memory files, then merged with current user goal to inform planning"
    • Relevance: How to integrate component activation with session context

  5. Building agents with the Claude Agent SDK

    • Key Sections: High-level architecture, design patterns
    • Critical Quote: "The key design principle behind the Claude Agent SDK is to give your agents a computer, allowing them to work like humans do."
    • Relevance: Philosophical alignment with our framework goals

Search Results Referenced​

  1. Anthropic Claude Agent SDK session initialization state persistence 2025

    • VentureBeat coverage of multi-session SDK launch

  2. Claude Agent SDK component registration tool activation pattern

    • DataCamp tutorial on SDK usage

  3. Claude Code .Claude directory settings.json configuration initialization

    • AI Native Dev guide to configuration

  4. Anthropic autonomous coding quickstart init.sh feature_list.json implementation

    • Best practices for Claude Code usage

Recommendations​

Immediate Actions (Next 24 Hours)​

  1. Implement component-activation-status.json (P0 - 1-2h)

    • Create schema based on feature_list.json pattern
    • Generate initial file from framework-registry.json
    • Commit to git

  2. Update .Claude/settings.json (P0 - 30m)

    • Add setting_sources configuration
    • Configure allowed_tools for component types
    • Add CODITECT environment variables

  3. Test current component discovery (P0 - 30m)

    • Verify SDK can find our agents/skills/commands
    • Check for any filesystem permission issues
    • Document current state

Short-Term (Next 48 Hours)​

  1. Enhance scripts/init.sh (P0 - 2-3h)

    • Add activation status loading
    • Add component verification
    • Test enhanced script

  2. Create session startup workflow (P0 - 1h)

    • Implement scripts/session-startup.py
    • Integrate with init.sh
    • Test end-to-end

Medium-Term (Next Week)​

  1. Implement activation management (P1 - 1-2h)

    • Create scripts/update-component-activation.py
    • Add git commit integration
    • Create CLI interface

  2. Update documentation (P1 - 1h)

    • Document new workflows in docs/Claude-4.5-BEST-PRACTICES.md
    • Update .Claude/Claude.md
    • Add training materials

  3. Integration testing (P1 - 1h)

    • Multi-session workflow testing
    • Component activation/deactivation
    • Error handling validation

Long-Term Considerations​

  1. SDK Integration (P2 - Future)

    • Consider migrating to ClaudeAgentOptions for session management
    • Evaluate programmatic component registration
    • Explore custom MCP server for component management

  2. Monitoring & Analytics (P2 - Future)

    • Track which components are used most frequently
    • Identify unused components for deprecation
    • Measure activation overhead

Conclusion​

Anthropic's multi-session pattern provides a proven, production-ready architecture that aligns 90% with our existing CODITECT framework. The remaining 10% gap can be closed with 5-7 hours of focused implementation:

Core Pattern Alignment​

  • ✅ Filesystem-based component discovery (we already have .Claude/ structure)
  • ✅ JSON-based state tracking (framework-registry.json exists)
  • ✅ Git-based session continuity (MEMORY-CONTEXT system operational)
  • ✅ Init script pattern (scripts/init.sh exists)
  • ❌ Component activation status tracking (need component-activation-status.json)
  • ❌ Session startup activation (need enhanced init.sh + startup workflow)

Implementation Priority​

  1. P0 (Critical - 5h): Component activation status file + enhanced init.sh + session startup workflow
  2. P1 (Important - 2h): Activation management + documentation
  3. P2 (Future): SDK integration + monitoring

ROI​

  • Eliminates manual component activation - Currently requires scripts/activate-all-components.py
  • Enables seamless multi-session workflows - Components remain active across sessions
  • Aligns with official Anthropic patterns - Future-proof for SDK updates
  • Improves session startup speed - Only activate needed components
  • Provides activation history - Git tracks why/when components activated

Next Step: Begin Phase 1 implementation (component-activation-status.json + settings.json configuration).

Research Completed: November 29, 2025 Total Research Time: ~2 hours Primary Sources: 14 URLs Total Word Count: ~8,500 words Implementation Effort: 5-7 hours (P0), 7-9 hours (P0+P1)

Sources: