bootstrap

bootstrap

Setting up the Exosuit framework for this project.

Interactive UX: Read @.claude/prompts/interactive-ux.md for the shared protocol. Use AskUserQuestion for all closed-choice interactions. Show progress between major steps. Read references/question-scaffolding.md (in the discover skill) for question formatting rules — Rules 7-8 apply here too.

Process Flow (authoritative — prose below is supporting detail)

START → 0. Detect Installation Mode
  → [Plugin mode?]
    → YES: CLAUDE_PLUGIN_ROOT is set, skip .claude/ setup
    → NO: Template mode, .claude/ already in project
  → 0.5. README Management (rename framework README → FRAMEWORK_README.md)
  → 1. Detect Project State
    → [Source files exist?]
      → YES: Path A (Existing Repository)
        → A1-A3: Detect stack, commands, assess docs/coverage/architecture, measure codebase
          → A2.8: Assess type checking → A2.85: Offer quality tooling installation
            → A2.9: Stack best practices research (optional, quick depth)
              → A3.1: LLM-readiness assessment → A3.2: Technical debt assessment
                → A3.5: Generate architecture → A3.5b: Establish ground rules
                  → A3.7: Detect default branch
                    → A3.8: Profile detection (recommend lean/standard/strict)
                      → [Lean?] → Skip A3.1-A3.5c, A5-A5.9, generate minimal docs
                      → A4: Generate config + populate TESTING_STRATEGY.md
                        → A4.2: Generate or update project README.md
                      → A5: Run /skill-create → A5.5-A5.6: Configure hooks/rules + assess pre-commit + CI/CD
                        → A5.8: Framework Readiness Report → A5.9: Generate foundation backlog
                          → A6: Clean up → A7: Present summary → DONE
      → NO: Path B (New Project)
        → Read references/new-project.md for Phase 0 (Idea Capture) ONLY
          → Phase 0: Idea Capture (braindump file / inline description / fast-track)
            → After Phase 0: invoke /discover
              → [Lean profile or --quick?] → /discover --quick
              → [Otherwise] → /discover (auto-detects mode from scale)
              → /discover handles: classification, elicitation, research, vision, backlog, README
            → After /discover: continue with scaffold generation + summary → DONE

0. Detect Installation Mode

Determine whether the framework is running as a plugin or as a template:

# Plugin mode: CLAUDE_PLUGIN_ROOT is set by Claude Code
if [ -n "${CLAUDE_PLUGIN_ROOT:-}" ]; then
    echo "Plugin mode: core at $CLAUDE_PLUGIN_ROOT"
else
    echo "Template mode: core at .claude/"
fi

Plugin mode (CLAUDE_PLUGIN_ROOT set): Core framework (hooks, skills, agents, rules, prompts) is installed as a Claude Code plugin. Only scaffold files (docs/, vision/, CLAUDE.md) need to be in the project.

Template mode (default): Full framework cloned into the project. Both core and scaffold files are in the project directory.

This affects Path A steps A5.5 (hook configuration) and A5.6 (rule configuration) — in plugin mode, hook and rule configuration is managed by the plugin, not project-level settings.json.

0.5. README Management

Detect and handle the framework's own README before proceeding:

# Check if README.md is the framework's own README (not a project README)
grep -qE "Exosuit|JD-LLM Development Framework" README.md 2>/dev/null && \
grep -q "drop-in development framework" README.md 2>/dev/null

If framework README detected: Rename to preserve it as a reference:

mv README.md FRAMEWORK_README.md

Report: "Renamed framework README to FRAMEWORK_README.md — reference it anytime for framework documentation."

If README.md is a scaffold template (contains [Project Name] and [Brief description): Leave it — it will be populated in step A4.2 (Path A) or Phase 7D (Path B).

If README.md is a real project README (neither framework nor scaffold template): Preserve it unchanged. It will be reviewed for completeness in A4.2.

If no README.md exists: One will be generated in step A4.2 (Path A) or Phase 7D (Path B).

1. Detect Project State

Determine which path to follow:

# Count non-framework source files
find . -type f \
  -not -path './.git/*' \
  -not -path './.claude/*' \
  -not -path './vision/*' \
  -not -path './docs/*' \
  -not -path './scripts/*' \
  -not -path './CLAUDE.md' \
  -not -path './CLAUDE.local.md*' \
  -not -path './README.md' \
  -not -path './FRAMEWORK_README.md' \
  -not -path './AGENTS.md' \
  -not -path './llms.txt' \
  -not -path './install.sh' \
  -not -path './.gitignore' \
  -not -path './.gitkeep' \
  -not -name '.DS_Store' | head -20

If source files exist: → Path A (Existing Repository) If no source files (or only framework files): → Path B — Read references/new-project.md for Phase 0 (Idea Capture), then invoke /discover for deep guided elicitation (replaces legacy Phases 1-4).

Path A: Existing Repository

---
**Bootstrap** | Step 1 of 8: Stack Detection
[=>..................] 1 of 8 steps
Coming up: Detecting your technology stack, tools, and codebase metrics
---

Analyzing your project to detect the tech stack, available tools, and
codebase structure. This is automatic — no input needed yet.

A1-A3. Detect Stack, Commands, and Measure Codebase

Run scripts/detect-stack.sh — execute directly, do NOT read source first.

Read references/stack-detection.md for detailed detection tables and commands. This covers:

• Technology stack detection (A1)
• Command detection (A2)
• Documentation state assessment (A2.5)
• API surface detection (A2.55) — Scan for API spec files (OpenAPI, AsyncAPI, GraphQL, Proto) and API framework indicators. Record API type, spec files, contract-first status. Feeds into Readiness Report and foundation backlog.
• Test coverage assessment (A2.6) — Read references/coverage-assessment.md for the full flow: detect coverage tool → offer installation if missing → run coverage → record baseline → flag zero-coverage areas. This data feeds into the Readiness Report (A5.8).
• Architecture assessment (A2.7)
• Codebase metrics (A3)

A2.8. Assess Type Checking Readiness

Detect whether a type checker is configured for the detected stack:

• If built-in: Mark as ready, no action needed.
• If config found: Mark as ready, record the type checker in use.
• If no config found (and not built-in): Record gap for the Readiness Report and quality tooling offer (A2.85).

A2.85. Offer Quality Tooling Installation

---
**Bootstrap** | Step 3 of 8: Quality Tooling
[=====>..............] 3 of 8 steps
Coming up: Installing recommended development tools
---

Read references/quality-tooling.md for the complete flow. After detecting the stack and its available tools (including type checker from A2.8), present missing-but-recommended quality tools via AskUserQuestion with multiSelect:

header: "Dev tools"
question: "These tools are recommended for your [language] project but aren't
           installed yet. Select which to install now. Skipped tools become
           backlog stories you can tackle later."
multiSelect: true
options:
  - label: "[tool] ([category]) (Recommended)"
    description: "[what it does]. Install: `[command]`. Used by quality gates
                  during development."
  - label: "[tool] ([category]) (Recommended)"
    description: "[what it does]. Install: `[command]`."
  - label: "[tool] ([category])"
    description: "[what it does]. Install: `[command]`. Optional but improves
                  code reliability."

If all tools are already available, skip this step with a note: "All recommended tools detected."

For stacks with built-in tools (Go, Rust, Dart): note as available, skip the offer for those categories.

Also check for architecture enforcement tools per references/quality-tooling.md — Architecture Enforcement Tools section. If the project has clear layered architecture (detected in A2.7) but no enforcement tool, mention it as an informational recommendation (not blocking).

A2.9. Stack Best Practices Research (Optional)

After detecting the stack, perform a quick research pass to identify current best practices for comparison with the project's actual state.

Compose the deep-research methodology (.claude/prompts/deep-research.md) at QUICK depth:

• Query: "Current best practices for [detected primary language] + [detected framework] projects"
• Sub-questions (auto-generated from detected stack):
  1. "Recommended testing practices for [framework]"
  2. "Common architecture patterns for [framework] in [current year]"
• Output format: plan-context (compact, feeds into readiness report)

Integrate findings into the Readiness Report (A5.8) as a "Best Practices Comparison" — informational, not blocking.

Skip when: User explicitly requests fast bootstrap (--skip-research or answers "skip" when asked), or no internet access is available.

Allowed tools for this step: WebSearch, WebFetch, Agent (add to skill-level allowed-tools when composing deep-research).

A3.1. LLM-Readiness Assessment

Read references/llm-readiness.md for the complete assessment flow. Using the codebase metrics from A3, assess whether the code structure supports effective LLM-assisted development:

1. File size analysis — flag files exceeding 500 LOC
2. Fan-out analysis — identify high-coupling modules (imported by >5 others)
3. Circular dependency check — detect mutual import patterns (where feasible)

Record metrics in docs/progress.md (codebase size, average file size, largest file, files over threshold). Results feed into the Context-efficient check in the Readiness Report (A5.8). Flagged files generate refactoring stories in the foundation backlog (A5.9).

A3.2. Technical Debt Assessment

Read references/technical-debt-assessment.md for the complete assessment flow. Scan the codebase for common technical debt indicators:

1. Stale markers — count TODO, FIXME, HACK, XXX comments
2. Missing types — detect untyped code (stack-specific: Python functions without hints, TypeScript any usage)
3. Unsafe patterns — detect known risky defaults (stack-specific)
4. Dead code indicators — detect unused imports where tooling is available

Record detected items in docs/technical-debt.md under the matching severity heading, using the full item format (category, severity, origin, location, quantified impact, interest rate, effort, resolution). Set origin to legacy for all bootstrap-detected items. Critical/High-severity items generate foundation stories in the foundation backlog (A5.9).

Seed docs/context/error-patterns.md: For files with 3+ stale markers (TODO/FIXME/HACK) or detected unsafe patterns, add an entry to error-patterns.md noting the affected area and common failure patterns for that module. This gives debug-session and context-prime useful context from day one. Format follows the template in error-patterns.md (Brief description, Affected area, Prevention note). Only seed 3-5 entries maximum from the most problematic areas — this file grows organically via record-failure during normal development.

A3.5. Generate Architecture Overview

Auto-populate docs/architecture/ARCHITECTURE.md from code structure. Apply accuracy safeguards from references/accuracy-safeguards.md — every claim must reference actual files. Generate all sections of the template:

Header: Set project name, one-line purpose, Last Verified date to today.

Tech Stack: Populate from A1 detection results. Only include non-obvious entries — skip what AI can discover from package files.

Architecture Overview (Mermaid flowchart TD): Generate a diagram showing:

• Detected entry points as top-level nodes
• Major modules/services as labeled boxes (include technology: [API Server<br/>Python FastAPI])
• Data stores with cylinder notation [(PostgreSQL)]
• External integrations and communication protocols on edges (-->|REST|, -->|gRPC|)
• Use subgraph for monorepos with multiple packages/services

Module Map: Map top-level source directories to responsibilities. List key entry point files.

Dependency Rules: Derive imperative rules from the actual import graph:

1. For each top-level module, identify what it imports from other modules
2. Identify the dependency direction (which modules depend on which)
3. Express as MUST/NEVER/MAY rules: "Controllers MUST only call services. Services NEVER import controllers."
4. If no clear layering exists, note: "No strict layer boundaries detected — consider establishing rules in GROUND_RULES.md"

Key Data Flow (Mermaid sequenceDiagram): Identify the primary user-facing operation and trace it through the system. For APIs: the most common endpoint. For CLIs: the main command flow. For libraries: the primary public API usage.

Constraints: Populate from CI config (timeout values → performance constraints), compliance markers in code (GDPR, SOC2, HIPAA references), version constraints (engines, minimum runtime versions). If nothing detected, leave with a guidance comment.

Key Decisions: If docs/adr/ contains ADRs, summarize top 3-5 with trade-offs and populate the ## Architecture Rules section in CLAUDE.md with the most critical ADR-derived constraints (format: - [constraint] (ADR-NNNN)). Otherwise, infer major technology choices from config (ORM, auth library, test framework) and suggest creating retroactive ADRs for undocumented decisions — list 2-3 candidate topics (e.g., "Why PostgreSQL over MongoDB?", "Why REST over GraphQL?") based on detected technologies.

Quality Attributes: Seed from Readiness Report data (A5.8): coverage baseline, CI requirements, type safety status.

Cross-cutting Concerns: Detect from codebase patterns — grep for error handling (try/catch, error middleware), logging (logging/winston/structlog/slog), authentication (auth middleware, JWT, sessions), validation (zod, pydantic, joi), configuration (dotenv, config loaders). One line per concern detected.

Known Landmines: Seed from A3.2 (Technical Debt) and A3.1 (LLM-readiness) data: files with high TODO/FIXME/HACK counts, circular dependencies, files > 500 LOC, @deprecated markers. If nothing detected, leave empty with guidance comment.

Update Triggers: Pre-populated (generic, applies to all projects): new modules/services added, data stores changed, API boundaries changed, dependency rules violated intentionally, deployment topology changed.

A3.55. Generate Project Context Knowledge Base

Populate docs/context/ files by analyzing the codebase. Apply accuracy safeguards from references/accuracy-safeguards.md:

• project-overview.md — What the project does, who it's for, core workflows
• tech-context.md — Stack, key libraries, API contracts, data layer
• system-patterns.md — Populate each section with codebase evidence:
  • Implementation Patterns: Grep for structural patterns (Controller/Service/Repository classes, middleware chains, factory functions, event handlers). For each, cite a reference file.
  • Architectural Conventions: Extract naming conventions from file/class/function names across 10+ files. Note import direction rules from the A3.5 dependency graph.
  • Error Handling Strategy: Grep for try/catch, error middleware, custom error classes, logging calls. Trace error propagation from data layer to user-facing response.
  • Testing Conventions: Analyze test file naming, co-location vs separate dir, assertion library, mock/stub patterns, fixture setup.
  • Implementation Recipes: Identify the most common entity type (API endpoint, service, component) and document the step-by-step to add a new one. Reference exemplar files.
• project-structure.md — Directory layout, module responsibilities, data flow
• product-context.md — Domain terminology, feature areas, constraints
• personas.md — User personas (see below)

Each file: ≤200 lines, evidence-based claims only, update YAML frontmatter timestamps.

Persona Generation (Path A): For projects with user-facing features (web apps, APIs with end users, CLIs with distinct user types), generate docs/context/personas.md:

1. Infer personas from codebase signals: role-based directories (admin/, user/), auth roles in code, distinct UI sections, README user descriptions, existing persona docs
2. Ask the user via AskUserQuestion:

   header: "User personas"
   question: "I've identified these user types from your codebase. Are they correct?
              Uncheck any that don't exist, or select 'Other' to add missing ones."
   multiSelect: true
   options: [one per inferred persona with description]

3. Generate lean persona cards (6-field format) for confirmed user types
4. Ask for primary persona if more than one confirmed
5. Save to docs/context/personas.md

Skip when: Project is a library, internal tool with a single user type, or the user says "no personas needed." In these cases, leave personas.md as the template with a note: "Single user type — personas not applicable."

A3.5b. Establish Project Ground Rules

---
**Bootstrap** | Step 5 of 8: Ground Rules
[========>...........] 5 of 8 steps
Coming up: Defining architectural rules that protect your codebase
---

Ground rules are non-negotiable architectural principles — they prevent
AI and developers from making choices that break your system. These get
checked automatically during every sprint.

Prompt the user for 3-7 non-negotiable architectural principles. Populate docs/reference/GROUND_RULES.md:

• Fill the Architecture Summary with 2-3 sentences describing the pattern and key technology choices
• Select categories — use AskUserQuestion with multiSelect to let the user pick which categories matter:

header: "Categories"
question: "Which ground rule categories matter for your project?
           The first 3 are recommended for all projects."
multiSelect: true
options:
  - label: "Dependencies + Boundaries + Data-flow (Recommended)"
    description: "Essential for all projects. Controls what imports what,
                  where logic lives, and how data moves."
  - label: "Security"
    description: "For apps handling auth, payments, or personal data.
                  Locks down credential handling and data access patterns."
  - label: "Technology"
    description: "Locks tech choices to prevent AI from introducing unapproved
                  libraries. Recommended for AI-assisted development."
  - label: "API design / Operational"
    description: "For APIs, microservices, or production systems with SLOs.
                  Enforces contract-first design and operational standards."

• Ask conversationally: "What architectural rules should NEVER be broken in this project?" Give examples from the BOOTSTRAP DEFAULTS comment in GROUND_RULES.md, selecting the section matching the detected architecture
• For each principle, use the GR-NNN format with fields: Level (MUST/SHOULD), Category (dependencies/boundaries/data-flow/security/technology/operational), Statement (one sentence with RFC 2119 keyword), Rationale (what breaks if violated), Enforced-by (ai/review/auto check), Exceptions (process or "None")
• If the user has no strong preferences, suggest 3-5 principles from the matching architecture defaults plus universal defaults
• Brownfield baseline (Path A only): If a new rule is defined but existing code already violates it, document existing violations in the Exception Log with scope "pre-existing", and suggest a foundation story to remediate incrementally. Rules that can't be enforced today are aspirational, not ground rules.
• The ground rules are checked during /story-cycle planning (Phase 1e), /sprint-end quality gates, /architecture-check, /code-quality, and /weekly-maintenance

A3.5c. Team Detection

Check for team indicators:

• .github/CODEOWNERS exists → team project
• Multiple contributors in git log → team project
• Branch protection rules configured → team project

CONTRIBUTORS=$(git log --format="%aE" | sort -u | wc -l | tr -d ' ')
if [ "$CONTRIBUTORS" -gt 1 ] || [ -f ".github/CODEOWNERS" ]; then
    echo "Team project detected ($CONTRIBUTORS contributors)"
fi

If team detected:

• Suggest configuring CODEOWNERS if it doesn't exist
• Mention docs/reference/TEAM_WORKFLOW.md in the summary
• Add "Team coordination" to the readiness report
• Size-based guidance (based on $CONTRIBUTORS count):
  • 2–5 contributors: "Small team — shared CLAUDE.md and informal review are sufficient. See TEAM_WORKFLOW.md for lightweight coordination patterns."
  • 6–15 contributors: "Medium team — formal CODEOWNERS, 200-line PR caps, mandatory AI disclosure, and weekly architecture syncs recommended. See TEAM_WORKFLOW.md scaling guide."
  • 16+ contributors: "Large team — sub-team decomposition, rotating AI review lead, and architecture fitness functions needed. See TEAM_WORKFLOW.md."

A3.7. Detect Default Branch

Detect the repository's default branch name and store it in CLAUDE.md so all skills can reference it without guessing:

# Try remote HEAD first (most reliable for repos with a remote)
DEFAULT_BRANCH=$(git symbolic-ref refs/remotes/origin/HEAD 2>/dev/null | sed 's@^refs/remotes/origin/@@')

if [ -z "$DEFAULT_BRANCH" ]; then
    # No remote HEAD — check common branch names
    for branch in main master develop; do
        if git show-ref --verify --quiet "refs/heads/$branch"; then
            DEFAULT_BRANCH="$branch"
            break
        fi
    done
fi

# Final fallback: use current branch
if [ -z "$DEFAULT_BRANCH" ]; then
    DEFAULT_BRANCH=$(git branch --show-current)
fi

echo "Default branch: $DEFAULT_BRANCH"

Update CLAUDE.md's Git Workflow section: replace the <!-- Detected by /bootstrap --> comment with the detected branch name.

Also update docs/reference/GIT_WORKFLOW.md: replace generic main references in the Branching Model section with the detected default branch name (e.g., if the project uses develop as its default branch, update accordingly). This ensures sprint-end and framework-upgrade read the correct branch name from this reference file.

A3.8. Profile Detection

---
**Bootstrap** | Step 4 of 8: Development Profile
[======>.............] 4 of 8 steps
Coming up: Choosing how much ceremony the framework applies
---

Analyze project characteristics to recommend a complexity profile. This determines the ceremony level for all framework skills.

Strict indicators (2+ present = recommend Strict):

• Compliance/regulatory references: grep for HIPAA, SOC2, PCI-DSS, GDPR, FDA, FedRAMP in any file
• Domain markers: fintech, healthcare, insurance, payments, banking in README or package description
• Multi-service architecture: docker-compose.yml with 3+ services, kubernetes/ or k8s/ directory, terraform/ directory
• Production infrastructure: k8s manifests, terraform configs, multiple deployment environment configs
• Strict CI: branch protection rules, required reviewers, mandatory status checks

Standard indicators (default when not clearly Lean or Strict):

• CI/CD configured (.github/workflows/, .gitlab-ci.yml, Jenkinsfile, etc.)
• Test framework detected (from A2)
• Established codebase (>5K LOC from A3 metrics)
• Production deployment target (Dockerfile, deployment configs, CDN configs)

Lean indicators (ALL must be true to recommend Lean):

• No CI/CD configuration detected
• No test framework detected OR zero test files
• Small codebase (<2K LOC from A3 metrics)
• No deployment configuration (no Dockerfile, no hosting configs)

Present the recommendation with matched indicators, then use AskUserQuestion:

header: "Profile"
question: "Based on your project ([list matched indicators]), I recommend
           [profile]. This controls how much ceremony the framework applies.
           You can change this anytime in CLAUDE.md."
options:
  - label: "[Recommended profile] (Recommended)"
    description: "[Full description]. [Why this fits based on matched indicators]."
  - label: "Lean"
    description: "Minimal ceremony. Fast iteration. Best for prototypes, MVPs,
                  internal tools. Fewer quality gates, less documentation."
  - label: "Standard"
    description: "Balanced quality gates + documentation. Best for production apps
                  and APIs. TDD enforced, PR reviews, sprint workflow."
  - label: "Strict"
    description: "Maximum rigor with audit trail. Best for regulated, high-stakes,
                  or compliance-sensitive projects. All gates mandatory, ADRs required."

Note: Show the recommended profile first with (Recommended). The remaining 2 options are the other profiles (don't repeat the recommended one).

Store the chosen profile: write **Profile:** <choice> to CLAUDE.md in step A4.

Generate only:

• CLAUDE.md with commands section populated (test, lint, format, build, typecheck from A2)
• README.md (project README from detected info — A4.2 still runs in lean mode)
• docs/progress.md (minimal template)
• .gitignore with stack-specific patterns

Still perform: A1 (stack detection), A2 (command detection), A2.85 (quality tooling offer), A3.7 (default branch), A4 (CLAUDE.md configuration — lean subset), A4.2 (README generation). </IF>

A4. Generate Configuration

Update these files with detected information:

1. CLAUDE.md — Fill in Project Overview, Commands, Architecture one-liner, Default branch (from A3.7), Tech Stack (language + framework + key library versions from lockfiles), Critical Rules (promote 3-5 most damaging violations from CODING_STANDARDS.md)
2. docs/reference/CODING_STANDARDS.md — Fill in language-specific sections following the <!-- /bootstrap guidance --> comments in the template. For each detected language:
   • Reference the authoritative base standard (see references/language-standards.md)
   • Extract version pins from lockfiles/config (package.json, pyproject.toml, go.mod, Cargo.toml)
   • Fill the naming convention table with language-specific constructs
   • Add 2-3 do/don't code pairs from patterns observed in the existing codebase
   • List detected formatter, linter, and type checker in the Tooling subsection
   • Fill Quality Gates table with thresholds the project can actually enforce
   • Fill Key Commands table from A2 detected commands
3. docs/progress.md — Initialize with baseline metrics (including LLM-readiness metrics from A3.1)
4. docs/reference/TESTING_STRATEGY.md — Populate the "Test Infrastructure" section with detected test tooling:

## Test Infrastructure

**Test Runner:** {test_framework} {version}
**Test Command:** `{test_command}`
**Fast Feedback:** `{fast_test_command}` (e.g., pytest -x --tb=short, npm test -- --bail)
**Coverage:** `{coverage_command}` (or "Not configured — see foundation backlog")
**Test Location:** {test_directory} (e.g., tests/, __tests__/, alongside source)
**Naming Convention:** {test_pattern} (e.g., test_*.py, *.test.ts, *_test.go)
**Fixtures:** {fixture_files_if_any} (e.g., tests/conftest.py — database session, test client)

All data comes from A2 (detect commands) and A2.6 (coverage assessment). If test setup files exist (conftest.py, jest.config., vitest.config., etc.), document key fixtures and configuration.

A4.2. Generate or Update Project README

Ensure the project has a proper README.md using information gathered in A1-A3.

If no README.md exists (or only the scaffold template with [Project Name] placeholders): Generate a complete README with these sections (cognitive funnel — broadest first):

1. Title: Project name from package.json name, pyproject.toml [project] name, go.mod module, Cargo.toml [package] name, or git remote / directory name as fallback
2. Description: From package.json description, pyproject.toml description, Cargo.toml description, or go.doc comment. If none found, write a one-liner from the Project Overview in CLAUDE.md
3. Prerequisites: Detected runtime + version from A1 (e.g., "Python 3.11+", "Node 20+"). Include required system tools
4. Getting Started: Clone URL (from git remote get-url origin), install command, and dev/run command from A2
5. Development: Table of commands from A2 — test, lint, format, build, typecheck. Only include commands that were actually detected
6. Project Structure: Top-level directory overview from A2.7 architecture assessment. List each top-level source directory with a one-line description of its responsibility. In lean mode (A2.7 skipped), use a basic ls of top-level directories instead
7. Contributing: Link to CONTRIBUTING.md if it exists. Otherwise: "See docs/reference/CODING_STANDARDS.md for conventions and docs/reference/GIT_WORKFLOW.md for branch/commit rules."
8. License: Detect from LICENSE, LICENSE.md, or LICENSE.txt. Show the license type (MIT, Apache-2.0, etc.). If no license file found, leave as a placeholder

If project has an existing README.md (real content, not scaffold template): Do NOT overwrite. Check for these standard sections and note missing ones in the A7 summary:

• Prerequisites / Installation / Getting Started
• Development commands (test, lint, build)
• Project structure
• Contributing
• License

Report: "Existing README preserved. Consider adding: [list of missing sections]."

A4.4. Update llms.txt

Update llms.txt with project-specific information from bootstrap results. Replace the generic framework description with: project name, one-line purpose (from CLAUDE.md Project Overview), detected tech stack, and key documentation paths. This file is consumed by /framework-upgrade for version comparisons and serves as an external LLM context entry point.

A4.5. Detect MCP Servers (Optional)

Check if any MCP servers are available in the Claude Code environment. If detected, note them in CLAUDE.md under a ## MCP Servers section so skills can conditionally leverage them. See docs/reference/MCP_INTEGRATION.md for server categories and integration guidance.

If no MCP servers are detected, skip this step — all skills function without them.

A5. Run /skill-create

---
**Bootstrap** | Step 6 of 8: Configuration
[===========>........] 6 of 8 steps
Coming up: Generating skills, configuring hooks, and setting up CI/CD
---

Generate technology-specific skills for the detected stack.

A5.5. Configure Hooks

Based on detected stack, configure hooks:

• Formatter detected → uncomment/configure post-edit-format.sh for the language
• Linter + test runner detected → configure quality rules in .claude/hooks/rules/quality.yaml
• Safety hooks → always enabled (already in settings.json)

Update .claude/settings.json if adding PostToolUse or Stop hooks.

A5.6. Configure Rules

Generate path-scoped rules for detected file types:

• If detected language has specific patterns, add to existing rules or create new ones
• Ensure .claude/rules/testing.md paths match the project's test file patterns
• Ensure .claude/rules/dependencies.md paths match the project's dependency files

A5.62. Environment Variable Template

Check for .env usage and manage the template:

1. Detect .env usage:

# Check for .env references in code
grep -rl 'process\.env\.\|os\.environ\|os\.getenv\|ENV\[' --include='*.py' --include='*.ts' --include='*.js' --include='*.rb' --include='*.go' . 2>/dev/null | head -5
# Check for existing .env files
ls .env .env.* 2>/dev/null

2. If .env is used but .env.example doesn't exist:
   • Parse .env (if exists) to extract variable names (NOT values)
   • Generate .env.example with variable names and placeholder values
   • Add .env to .gitignore if not already present
   • Report: "Created .env.example with [N] variables. Review and customize."
3. If .env.example exists: Verify it covers all variables used in code. Report gaps if any.
4. If no .env usage detected: Skip silently.
5. Populate SECRETS_INVENTORY.md (if .env usage detected): Create docs/reference/SECRETS_INVENTORY.md from the scaffold template. For each detected environment variable, add a row with: variable name, inferred type (api_key, database_credential, jwt_signing, config — based on naming patterns), environment (all), storage (env_file), classification (critical if name contains SECRET/KEY/TOKEN/PASSWORD, standard otherwise). Leave Last Rotated, Next Due, and Rotation Method as "—" for the user to fill. This enables weekly-maintenance's secret rotation checking from day one.

A5.65. Assess Pre-Commit Hook Readiness

Check for existing pre-commit hook infrastructure:

# Check for pre-commit tools (language-agnostic)
ls .pre-commit-config.yaml 2>/dev/null    # pre-commit (Python ecosystem)
ls -d .husky/ 2>/dev/null                  # Husky (Node.js ecosystem)
ls lefthook.yml 2>/dev/null                # Lefthook (any stack)
ls .git/hooks/pre-commit 2>/dev/null       # Raw git hook

• If found: Record the tool in use. Mark as ready for the Readiness Report.
• If not found: Offer to set up Lefthook via AskUserQuestion:

header: "Git hooks"
question: "No pre-commit hooks detected. Lefthook can enforce conventional
           commits and block direct pushes to main — protecting manual
           commits (the framework already protects AI sessions via its own hooks)."
options:
  - label: "Yes, set up Lefthook (Recommended)"
    description: "Installs Lefthook with conventional commit validation and
                  branch protection. Takes ~1 minute."
  - label: "Skip for now"
    description: "No pre-commit hooks. A low-priority backlog story will be
                  created. The framework's own hooks still protect AI sessions."
  - label: "I use a different tool"
    description: "Tell me which tool (Husky, pre-commit, etc.) and I'll
                  configure it instead."

If user accepts:

1. Check for Lefthook: lefthook version 2>/dev/null
2. If available, create lefthook.yml:

   commit-msg:
     commands:
       conventional:
         run: |
           MSG=$(head -1 {1})
           if ! echo "$MSG" | grep -qE '^(feat|fix|docs|style|refactor|perf|test|build|ci|chore)(\(.+\))?!?:\ .+'; then
             echo "Commit message must follow Conventional Commits: <type>(<scope>): <description>"
             exit 1
           fi
   pre-push:
     commands:
       branch-check:
         run: |
           BRANCH=$(git rev-parse --abbrev-ref HEAD)
           if [ "$BRANCH" = "main" ] || [ "$BRANCH" = "master" ]; then
             echo "Direct push to $BRANCH blocked. Create a pull request instead."
             exit 1
           fi

3. If Gitleaks is detected (gitleaks version 2>/dev/null), add pre-commit secret scanning:

   pre-commit:
     parallel: true
     commands:
       secrets:
         run: gitleaks detect --staged --no-banner

4. Run lefthook install
5. Record as "Ready" in the Readiness Report

• If Lefthook not available: suggest installing it (go install github.com/evilmartians/lefthook@latest or brew install lefthook), generate a foundation story for setup

If user declines: Record gap for the Readiness Report. Generate a low-priority foundation story. The framework's Claude Code hooks protect during AI sessions, but pre-commit hooks protect manual commits too.

A5.7. Assess CI/CD Foundation

Check for existing CI/CD configuration:

# Check for CI/CD providers
ls .github/workflows/*.yml 2>/dev/null     # GitHub Actions
ls .gitlab-ci.yml 2>/dev/null              # GitLab CI
ls Jenkinsfile 2>/dev/null                 # Jenkins
ls .circleci/config.yml 2>/dev/null        # CircleCI
ls bitbucket-pipelines.yml 2>/dev/null     # Bitbucket Pipelines
ls .travis.yml 2>/dev/null                 # Travis CI

• If CI/CD found: Check if the framework's claude-pr-review.yml workflow is included. If not, note separately — existing CI exists but framework PR review is missing.
• If no CI/CD found: Use AskUserQuestion:

header: "CI/CD"
question: "No CI/CD pipeline detected. The framework includes a GitHub Actions
           workflow for automated PR review — it checks code quality on every
           pull request."
options:
  - label: "Install GitHub Actions (Recommended)"
    description: "Adds claude-pr-review.yml to .github/workflows/. Runs
                  quality checks on every PR automatically."
  - label: "Skip for now"
    description: "No CI/CD. A backlog story will be created. Quality checks
                  will only run locally during AI sessions."
  - label: "I use a different CI"
    description: "Tell me your CI provider (GitLab CI, CircleCI, etc.)
                  and I'll note it for manual setup."

• If user accepts: Copy the workflow to .github/workflows/claude-pr-review.yml.
• If user declines: Generate a foundation story in the backlog.
• Feed CI/CD status into the Readiness Report (A5.8) under "CI-enforced".

A5.75. Document Quality Check

After generating ARCHITECTURE.md, dispatch a fresh sub-agent to test the document from a reader's perspective:

• Agent type: Explore (read-only, forked context)
• Input: ONLY the generated docs/architecture/ARCHITECTURE.md — no conversation history
• Instructions: "You are a new developer reading this architecture document for the first time. List: (1) What questions would you have? (2) What's ambiguous or unclear? (3) What context does this assume the reader already has? (4) What's missing that a developer would need?"

Review findings. Fix genuine gaps before presenting the summary to the user.

A5.8. Framework Readiness Report

---
**Bootstrap** | Step 7 of 8: Readiness Assessment
[===============>....] 7 of 8 steps
Coming up: Assessing how ready your project is for framework-powered development
---

Read references/readiness-report.md for the complete check definitions and classification rules.

Using data collected in earlier steps (A1-A3, A2.6, A2.8, A2.9, A3.1, A3.2, A3.5b, A3.7, A4, A5.5, A5.65, A5.7), assess each framework principle against the project's actual state. For each principle, classify as ✓ Ready, ⚠️ Risk, or ✗ Missing with a brief explanation.

Output:

1. Display the readiness report table in the A7 summary
2. Save to docs/reference/READINESS_REPORT.md
3. Pass Risk and Missing items to A5.9 for foundation story generation

A5.9. Generate Foundation Backlog & Initialize BACKLOG_INDEX.md

---
**Bootstrap** | Step 7 of 8: Foundation Backlog
[=================>..] 7 of 8 steps
Coming up: Generating stories for gaps found in the readiness report
---

Read references/foundation-backlog.md for story generation templates.

Based on the Readiness Report (A5.8), auto-generate dependency-ordered foundation stories for Risk and Missing items. Stories are organized into four dependency levels:

• Level 0: Install missing tools (test framework, formatter, linter, coverage, type checker)
• Level 1: Configure commands and fix baselines (CLAUDE.md commands, failing tests, type checker config)
• Level 2: Measurable improvements (coverage ≥60%, lint warnings→0, type errors→0, ground rules, pre-commit)
• Level 3: Structural improvements (split oversized files, break circular deps, CI pipeline) — optional for starting features

Stories at Level N require all Level N-1 stories to be complete. Level 2+ stories with measurable targets include an /optimize execution method with metric command, target, and direction from the Readiness Report's Optimization Metrics section. A Framework Ready Gate is inserted between Levels 2 and 3, defining minimum thresholds for starting feature development.

Each story has a type, priority, level, description, execution method, and acceptance criteria. Present stories to the user and use AskUserQuestion for approval:

header: "Foundation"
question: "I've generated [N] foundation stories across [L] levels based on
           the readiness gaps. Review the stories above. Ready to finalize?"
options:
  - label: "Accept all (Recommended)"
    description: "Write all stories to the foundation backlog. You can
                  modify individual stories later during sprint planning."
  - label: "I want to remove some"
    description: "Tell me which stories to drop — I'll adjust dependencies."
  - label: "Skip foundation backlog"
    description: "No foundation stories. Go straight to feature work.
                  Note: some framework features won't work without foundation."

Write accepted stories to docs/reference/backlog/E00-foundation.md.

Initialize BACKLOG_INDEX.md — remove template comments and populate with actual content:

# Backlog Index

**Last Updated:** {date}

## Status Summary

| Epic | Total | Done | In Progress | TODO |
|------|-------|------|-------------|------|
| E00-foundation | {n} | 0 | 0 | {n} |

## Current Focus

Foundation work: infrastructure and tooling gaps identified by the Framework Readiness Report.

## Epic Files

- @docs/reference/backlog/E00-foundation.md — Foundation (infrastructure + tooling)

## Story ID → Epic Mapping

| Story Range | Epic File |
|-------------|-----------|
| E00-S01 — E00-S{nn} | E00-foundation.md |

## Next Steps

- Run `/sprint-start` to begin foundation work
- Run `/ideate` to generate feature stories after foundation is complete

If no foundation stories were generated (all principles Ready), still initialize BACKLOG_INDEX.md with an empty status table and point the user to /ideate.

A5.95. Scaffold Solutions Directory

Create docs/solutions/ with a .gitkeep file. This directory stores structured learnings from completed stories (see capture-learnings micro-component). Each solution document has searchable YAML frontmatter (title, tags, module, component) so future story-cycle Phase 1b can grep for prior learnings on affected modules.

Also create docs/brainstorms/ with a .gitkeep file. This directory stores design exploration documents from /brainstorm sessions for reference during /ideate.

Also create docs/research/ with a .gitkeep file. This directory stores structured research reports from /research sessions and spike stories. Reports have searchable YAML frontmatter (title, tags, confidence, date) so future research and story-cycle Phase 1 can check for prior findings.

Also create docs/reviews/ with a .gitkeep file. This directory stores phase review findings from /phase-review sessions (walkthrough results, direction decisions). Required by Phase Transition Stories.

A6. Clean Up

• Delete vision/ directory (not needed for existing repos)
• Delete scaffold/ directory if present (template-mode artifact, contents already installed)
• Remove template placeholder comments from populated docs
• Delete any empty template sections that weren't filled

A7. Present Summary

---
**Bootstrap** | Step 8 of 8: Complete!
[====================] 8 of 8 steps
---

### Bootstrap Complete (Existing Repository)

**Detected Stack:**
- Languages: [list]
- Package Manager: [name]
- Test Framework: [name] ([count] tests, [coverage]% coverage)
- Linter: [name]
- Formatter: [name]
- Type Checker: [name or "not configured"]
- CI/CD: [provider or "not found"]
- Pre-commit: [tool or "not configured"]

**Commands Configured:**
| Operation | Command |
|-----------|---------|
| Test      | [cmd]   |
| Lint      | [cmd]   |
| Format    | [cmd]   |
| Build     | [cmd]   |
| TypeCheck | [cmd]   |

**Codebase Health:**
- Total: [N] LOC across [N] files (avg [N] LOC/file)
- Largest file: [path] ([N] LOC)
- Files over 500 LOC: [N]
- Technical debt items: [N] critical / [N] high / [N] medium / [N] low

**Stack Research:** [summary of best practices findings from A2.9, or "Skipped" if not run]

**Framework Readiness Report:**
| Principle | Status | Detail |
|-----------|--------|--------|
| [principle] | [✓/⚠️/✗] | [explanation] |
| ... | ... | ... |

**Summary:** [N] of [assessed] principles ready, [N] at risk, [N] missing ([N] skipped as not applicable)

**Foundation Backlog:** [N] stories across [L] levels in E00-foundation (Framework Ready Gate after Level 2: [N] checks) — or "No gaps found — project is ready"

**Files Updated:**
- README.md (project README — generated or existing preserved)
- FRAMEWORK_README.md (framework documentation — renamed from original README.md, if applicable)
- CLAUDE.md (project overview, commands, architecture, profile, default branch)
- docs/reference/CODING_STANDARDS.md (language standards)
- docs/architecture/ARCHITECTURE.md (module overview)
- docs/context/* (project knowledge base — 5-6 files)
- docs/reference/GROUND_RULES.md (architectural principles)
- docs/reference/TESTING_STRATEGY.md (test infrastructure)
- docs/reference/READINESS_REPORT.md (principle assessment)
- docs/reference/GIT_WORKFLOW.md (personalized with default branch)
- docs/reference/SECRETS_INVENTORY.md (if .env usage detected)
- docs/reference/backlog/E00-foundation.md (if gaps found)
- docs/reference/BACKLOG_INDEX.md (initialized)
- docs/progress.md (baseline metrics)
- docs/technical-debt.md (detected debt items)
- docs/context/error-patterns.md (seeded from debt scan)
- llms.txt (project-specific summary)

**Hooks Configured:**
- [list of enabled hooks]

**Technology Skills Generated:** [count]

**Next Steps:**
- Foundation work needed? → Run `/sprint-start` to begin with E00-foundation Level 0 stories, then work through levels in order. Use `/optimize` for Level 2+ measurable improvement stories. After passing the Framework Ready Gate, you can start feature work while completing optional Level 3 stories in parallel.
- No foundation work? → Run `/ideate` to plan your next feature, then `/sprint-start`

Graceful Degradation

Rules

• NEVER overwrite files that have user content (check for non-template content first)
• ALWAYS show what will be changed before writing
• ALWAYS present a summary with next steps
• Follow coding standards in docs/reference/CODING_STANDARDS.md