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Project Bootstrap Guide

Load this guide when setting up a new project for AI-assisted development.

Overview

This guide covers how to bootstrap a project so AI agents (Claude, Codex, etc.) can work on it effectively. Proper bootstrapping ensures:

  1. Agents understand the project structure and conventions
  2. Orchestration works correctly with quality gates
  3. Independent code review and security review are configured
  4. Issue tracking is consistent across projects
  5. Documentation standards and API contracts are enforced from day one
  6. PRD requirements are established before coding begins
  7. Branching/merging is consistent: branch -> main via PR with squash-only merges
  8. Steered-autonomy execution is enabled so agents can run end-to-end with escalation-only human intervention

Quick Start

# Automated bootstrap (recommended)
~/.config/mosaic/rails/bootstrap/init-project.sh \
  --name "my-project" \
  --type "nestjs-nextjs" \
  --repo "https://git.mosaicstack.dev/owner/repo"

# Or manually using templates
export PROJECT_NAME="My Project"
export PROJECT_DESCRIPTION="What this project does"
export TASK_PREFIX="MP"
envsubst < ~/.config/mosaic/templates/agent/AGENTS.md.template > AGENTS.md
envsubst < ~/.config/mosaic/templates/agent/CLAUDE.md.template > CLAUDE.md

Step 0: Enforce Sequential-Thinking MCP (Hard Requirement)

sequential-thinking MCP must be installed and configured before project bootstrapping.

# Auto-configure sequential-thinking MCP for installed runtimes
~/.config/mosaic/bin/mosaic-ensure-sequential-thinking

# Verification-only check
~/.config/mosaic/bin/mosaic-ensure-sequential-thinking --check

If this step fails, STOP and remediate Mosaic runtime configuration before continuing.

Step 1: Detect Project Type

Check what files exist in the project root to determine the type:

File Present Project Type Template
package.json + pnpm-workspace.yaml + NestJS+Next.js NestJS + Next.js Monorepo projects/nestjs-nextjs/
pyproject.toml + manage.py Django projects/django/
pyproject.toml (no Django) Python (generic) Generic template
package.json (no monorepo) Node.js (generic) Generic template
Other Generic Generic template 
# Auto-detect project type
detect_project_type() {
  if [[ -f "pnpm-workspace.yaml" ]] && [[ -f "turbo.json" ]]; then
    # Check for NestJS + Next.js
    if grep -q "nestjs" package.json 2>/dev/null && grep -q "next" package.json 2>/dev/null; then
      echo "nestjs-nextjs"
      return
    fi
  fi
  if [[ -f "manage.py" ]] && [[ -f "pyproject.toml" ]]; then
    echo "django"
    return
  fi
  if [[ -f "pyproject.toml" ]]; then
    echo "python"
    return
  fi
  if [[ -f "package.json" ]]; then
    echo "nodejs"
    return
  fi
  echo "generic"
}

Step 2: Create AGENTS.md (Primary Project Contract)

AGENTS.md is the primary project-level contract for all agent runtimes. It defines project-specific requirements, quality gates, patterns, and testing expectations.

Using a Tech-Stack Template

# Set variables
export PROJECT_NAME="My Project"
export PROJECT_DESCRIPTION="Multi-tenant SaaS platform"
export PROJECT_DIR="my-project"
export REPO_URL="https://git.mosaicstack.dev/owner/repo"
export TASK_PREFIX="MP"

# Use tech-stack-specific template if available
TYPE=$(detect_project_type)
TEMPLATE_DIR="$HOME/.config/mosaic/templates/agent/projects/$TYPE"

if [[ -d "$TEMPLATE_DIR" ]]; then
  envsubst < "$TEMPLATE_DIR/AGENTS.md.template" > AGENTS.md
else
  envsubst < "$HOME/.config/mosaic/templates/agent/AGENTS.md.template" > AGENTS.md
fi

Using the Generic Template

# Set all required variables
export PROJECT_NAME="My Project"
export PROJECT_DESCRIPTION="What this project does"
export REPO_URL="https://git.mosaicstack.dev/owner/repo"
export PROJECT_DIR="my-project"
export SOURCE_DIR="src"
export CONFIG_FILES="pyproject.toml / package.json"
export FRONTEND_STACK="N/A"
export BACKEND_STACK="Python / FastAPI"
export DATABASE_STACK="PostgreSQL"
export TESTING_STACK="pytest"
export DEPLOYMENT_STACK="Docker"
export BUILD_COMMAND="pip install -e ."
export TEST_COMMAND="pytest tests/"
export LINT_COMMAND="ruff check ."
export TYPECHECK_COMMAND="mypy ."
export QUALITY_GATES="ruff check . && mypy . && pytest tests/"

envsubst < ~/.config/mosaic/templates/agent/AGENTS.md.template > AGENTS.md

Required Sections

Every AGENTS.md should contain:

  1. Project description — One-line summary
  2. Quality gates — Commands that must pass
  3. Codebase patterns — Reusable implementation rules
  4. Common gotchas — Non-obvious constraints
  5. Testing approaches — Project-specific test strategy
  6. Testing policy — Situational-first validation and risk-based TDD
  7. Orchestrator integration — Task prefix, worker checklist
  8. Documentation contract — Required documentation gates and update expectations
  9. PRD requirement — docs/PRD.md or docs/PRD.json required before coding

Step 3: Create Runtime Context File (Runtime-Specific)

Runtime context files are runtime adapters. They are not the primary project contract. Use CLAUDE.md for Claude runtime compatibility. Use other runtime adapters as required by your environment.

Claude runtime mandate (HARD RULE):

  • CLAUDE.md MUST explicitly instruct Claude agents to read and use AGENTS.md.
  • CLAUDE.md MUST treat AGENTS.md as the authoritative project-level contract.
  • If AGENTS.md and runtime wording conflict, AGENTS.md project rules win.
TYPE=$(detect_project_type)
TEMPLATE_DIR="$HOME/.config/mosaic/templates/agent/projects/$TYPE"

if [[ -d "$TEMPLATE_DIR" ]]; then
  envsubst < "$TEMPLATE_DIR/CLAUDE.md.template" > CLAUDE.md
else
  envsubst < "$HOME/.config/mosaic/templates/agent/CLAUDE.md.template" > CLAUDE.md
fi

Required Runtime Sections

Every runtime context file should contain:

  1. AGENTS handoff rule — Runtime MUST direct agents to read/use AGENTS.md
  2. Conditional documentation loading — Required guide loading map
  3. Technology stack — Runtime-facing architecture summary
  4. Repository structure — Important paths
  5. Development workflow — Build/test/lint/typecheck commands
  6. Issue tracking — Issue and commit conventions
  7. Code review — Required review process
  8. Runtime notes — Runtime-specific behavior references
  9. Branch and merge policy — Trunk workflow (branch -> main via PR, squash-only)
  10. Autonomy and escalation policy — Agent owns coding/review/PR/release/deploy lifecycle

Step 4: Create Directory Structure

# Create standard directories
mkdir -p docs/scratchpads
mkdir -p docs/templates
mkdir -p docs/reports/qa-automation/pending
mkdir -p docs/reports/qa-automation/in-progress
mkdir -p docs/reports/qa-automation/done
mkdir -p docs/reports/qa-automation/escalated
mkdir -p docs/reports/deferred
mkdir -p docs/tasks
mkdir -p docs/releases
mkdir -p docs/USER-GUIDE docs/ADMIN-GUIDE docs/DEVELOPER-GUIDE docs/API

# Documentation baseline files
touch docs/USER-GUIDE/README.md
touch docs/ADMIN-GUIDE/README.md
touch docs/DEVELOPER-GUIDE/README.md
touch docs/API/OPENAPI.yaml
touch docs/API/ENDPOINTS.md
touch docs/SITEMAP.md

# PRD baseline file (requirements source before coding)
cp ~/.config/mosaic/templates/docs/PRD.md.template docs/PRD.md

# TASKS baseline file (canonical tracking)
cp ~/.config/mosaic/templates/docs/TASKS.md.template docs/TASKS.md

# Deployment baseline file (target/platform/runbook)
touch docs/DEPLOYMENT.md

Documentation root hygiene (HARD RULE):

  • Keep docs/ root clean.
  • Store reports in docs/reports/, archived task artifacts in docs/tasks/, releases in docs/releases/, and scratchpads in docs/scratchpads/.
  • Do not place ad-hoc report files directly under docs/.

Step 5: Initialize Repository Labels & Milestones

# Use the init script
~/.config/mosaic/rails/bootstrap/init-repo-labels.sh

# Or manually create standard labels
~/.config/mosaic/rails/git/issue-create.sh  # (labels are created on first use)

Standard Labels

Label Color Purpose
epic #3E4B9E Large feature spanning multiple issues
feature #0E8A16 New functionality
bug #D73A4A Defect fix
task #0075CA General work item
documentation #0075CA Documentation updates
security #B60205 Security-related
breaking #D93F0B Breaking change

Initial Milestone (Hard Rule)

Create the first pre-MVP milestone at 0.0.1. Reserve 0.1.0 for the MVP release milestone.

~/.config/mosaic/rails/git/milestone-create.sh -t "0.0.1" -d "Pre-MVP - Foundation Sprint"

# Create when MVP scope is complete and release-ready:
~/.config/mosaic/rails/git/milestone-create.sh -t "0.1.0" -d "MVP - Minimum Viable Product"

Step 5b: Configure Main Branch Protection (Hard Rule)

Apply equivalent settings in Gitea, GitHub, or GitLab:

  1. Protect main from direct pushes.
  2. Require pull requests to merge into main.
  3. Require required CI/status checks to pass before merge.
  4. Require code review approval before merge.
  5. Allow squash merge only for PRs into main (disable merge commits and rebase merges for main).

This enforces one merge strategy across human and agent workflows.

Step 6: Set Up CI/CD Review Pipeline

Woodpecker CI

# Copy Codex review pipeline
mkdir -p .woodpecker/schemas
cp ~/.config/mosaic/rails/codex/woodpecker/codex-review.yml .woodpecker/
cp ~/.config/mosaic/rails/codex/schemas/*.json .woodpecker/schemas/

# Add codex_api_key secret to Woodpecker CI dashboard

GitHub Actions

For GitHub repos, use the official Codex GitHub Action instead:

# .github/workflows/codex-review.yml
uses: openai/codex-action@v1

Python Package Publishing (Gitea PyPI)

If the project publishes Python packages, use Gitea's PyPI registry.

# Build and publish
python -m pip install --upgrade build twine
python -m build
python -m twine upload \
  --repository-url "https://GITEA_HOST/api/packages/ORG/pypi" \
  --username "$GITEA_USERNAME" \
  --password "$GITEA_TOKEN" \
  dist/*

Use the same gitea_username and gitea_token CI secrets used for container and npm publishing.

Step 7: Verify Bootstrap

After bootstrapping, verify everything works:

# Check files exist
ls AGENTS.md docs/scratchpads/
ls docs/reports/qa-automation/pending docs/reports/deferred docs/tasks docs/releases
ls docs/USER-GUIDE/README.md docs/ADMIN-GUIDE/README.md docs/DEVELOPER-GUIDE/README.md
ls docs/API/OPENAPI.yaml docs/API/ENDPOINTS.md docs/SITEMAP.md
ls docs/PRD.md
ls docs/TASKS.md

# Verify AGENTS.md has required sections
grep -c "Quality Gates" AGENTS.md
grep -c "Orchestrator Integration" AGENTS.md
grep -c "Testing Approaches" AGENTS.md
grep -c "Testing Policy" AGENTS.md
grep -c "Documentation Contract" AGENTS.md
grep -c "PRD Requirement" AGENTS.md

# Verify runtime context file has required sections
if [[ -f CLAUDE.md ]]; then
  grep -c "AGENTS.md" CLAUDE.md
  grep -c "Conditional Documentation Loading" CLAUDE.md
  grep -c "Technology Stack" CLAUDE.md
  grep -c "Code Review" CLAUDE.md
elif [[ -f RUNTIME.md ]]; then
  grep -c "Conditional Documentation Loading" RUNTIME.md
  grep -c "Technology Stack" RUNTIME.md
  grep -c "Code Review" RUNTIME.md
else
  echo "Missing runtime context file (CLAUDE.md or RUNTIME.md)" >&2
  exit 1
fi

# Run quality gates from AGENTS.md
# (execute the command block under "Quality Gates")

# Test Codex review (if configured)
~/.config/mosaic/rails/codex/codex-code-review.sh --help

# Verify sequential-thinking MCP remains configured
~/.config/mosaic/bin/mosaic-ensure-sequential-thinking --check

Available Templates

Generic Templates

Template Path Purpose
AGENTS.md.template ~/.config/mosaic/templates/agent/ Primary project agent contract
CLAUDE.md.template ~/.config/mosaic/templates/agent/ Runtime compatibility context (Claude)
DOCUMENTATION-CHECKLIST.md ~/.config/mosaic/templates/docs/ Documentation completion gate
PRD.md.template ~/.config/mosaic/templates/docs/ Requirements source template
TASKS.md.template ~/.config/mosaic/templates/docs/ Canonical task and issue tracking template

Tech-Stack Templates

Stack Path Includes
NestJS + Next.js ~/.config/mosaic/templates/agent/projects/nestjs-nextjs/ AGENTS.md + runtime context template
Django ~/.config/mosaic/templates/agent/projects/django/ AGENTS.md + runtime context template

Orchestrator Templates

Template Path Purpose
tasks.md.template ~/src/jarvis-brain/docs/templates/orchestrator/ Task tracking
orchestrator-learnings.json.template ~/src/jarvis-brain/docs/templates/orchestrator/ Variance tracking
phase-issue-body.md.template ~/src/jarvis-brain/docs/templates/orchestrator/ Git provider issue body
scratchpad.md.template ~/src/jarvis-brain/docs/templates/ Per-task working doc

Variables Reference

Variable Description Example
${PROJECT_NAME} Human-readable project name "Mosaic Stack"
${PROJECT_DESCRIPTION} One-line description "Multi-tenant platform"
${PROJECT_DIR} Directory name "mosaic-stack"
${PROJECT_SLUG} Python package slug "mosaic_stack"
${REPO_URL} Git remote URL "https://git.mosaicstack.dev/mosaic/stack"
${TASK_PREFIX} Orchestrator task prefix "MS"
${SOURCE_DIR} Source code directory "src" or "apps"
${QUALITY_GATES} Quality gate commands "pnpm typecheck && pnpm lint && pnpm test"
${BUILD_COMMAND} Build command "pnpm build"
${TEST_COMMAND} Test command "pnpm test"
${LINT_COMMAND} Lint command "pnpm lint"
${TYPECHECK_COMMAND} Type check command "pnpm typecheck"
${FRONTEND_STACK} Frontend technologies "Next.js + React"
${BACKEND_STACK} Backend technologies "NestJS + Prisma"
${DATABASE_STACK} Database technologies "PostgreSQL"
${TESTING_STACK} Testing technologies "Vitest + Playwright"
${DEPLOYMENT_STACK} Deployment technologies "Docker"
${CONFIG_FILES} Key config files "package.json, tsconfig.json"

Bootstrap Scripts

init-project.sh

Full project bootstrap with interactive and flag-based modes:

~/.config/mosaic/rails/bootstrap/init-project.sh \
  --name "My Project" \
  --type "nestjs-nextjs" \
  --repo "https://git.mosaicstack.dev/owner/repo" \
  --prefix "MP" \
  --description "Multi-tenant platform"

init-repo-labels.sh

Initialize standard labels and the first pre-MVP milestone:

~/.config/mosaic/rails/bootstrap/init-repo-labels.sh

Checklist

After bootstrapping, verify:

  • AGENTS.md exists and is the primary project contract
  • Runtime context file exists (CLAUDE.md or RUNTIME.md)
  • docs/scratchpads/ directory exists
  • docs/reports/qa-automation/pending directory exists
  • docs/reports/deferred/ directory exists
  • docs/tasks/ directory exists
  • docs/releases/ directory exists
  • docs/USER-GUIDE/README.md exists
  • docs/ADMIN-GUIDE/README.md exists
  • docs/DEVELOPER-GUIDE/README.md exists
  • docs/API/OPENAPI.yaml exists
  • docs/API/ENDPOINTS.md exists
  • docs/SITEMAP.md exists
  • docs/PRD.md or docs/PRD.json exists
  • docs/TASKS.md exists and is ready for active tracking
  • docs/DEPLOYMENT.md exists with target platform and rollback notes
  • sequential-thinking MCP is configured and verification check passes
  • Git labels created (epic, feature, bug, task, etc.)
  • Initial pre-MVP milestone created (0.0.1)
  • MVP milestone reserved for release (0.1.0)
  • main is protected from direct pushes
  • PRs into main are required
  • Merge method for main is squash-only
  • Quality gates run successfully
  • .env.example exists (if project uses env vars)
  • CI/CD pipeline configured (if using Woodpecker/GitHub Actions)
  • Python publish path configured in CI (if project ships Python packages)
  • Codex review scripts accessible (~/.config/mosaic/rails/codex/)
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