…pt fallback

…ted script\n\nReplace broken UV_PYTHON_SPEC preview with neutral Python stack preview.\nRoute uv install to scripts/install_uv.sh reconcile.

…ilities

- Show npm, pnpm, yarn prompts unconditionally (outside Node block)
- Update via Corepack; fallback to npm global installs
- Re-audit after each action
- Include black in Python utilities prompt

… prefer yarn@stable

- Ensure corepack enable on update
- corepack prepare pnpm@latest --activate || npm i -g pnpm@latest
- corepack prepare yarn@stable --activate || npm i -g yarn@latest
- Keep npm/eslint/prettier updated

…e/rename.ul

- Skip Corepack shim package.json; invoke real pnpm/yarn for versions
- Prefer Yarn stable and Yarn tags endpoint; upstream_method=yarn-tags
- Detect uv-managed tools via 'uv tool list' and symlink targets; report 'uv tool'
- Separate perl 'prename' and util-linux 'rename.ul' and parse versions

…d via official installer

Detect ~/.local/bin/uv and label as 'github binary'; keep pipx/user for pipx venv symlinks.

Detect pipx-installed Python CLIs and prompt to reinstall with 'uv tool', uninstalling pipx version to avoid shim conflicts; re-audit after action.

- audit: show upstream_method as 'uv tool' for PyPI tools
- guide: migrate any pipx/pip-installed Python CLIs (incl. pip/pipx/ansible-core) to uv tool with uninstall of old shims

…y as 'uv venv'/'uv python'\n\n- Prefer ~/.venvs/dev/bin/python or /home/sme/.local/share/uv/python/cpython-3.13.6-linux-x86_64-gnu/bin/python3.13 for installed Python\n- Show proper installed_method for uv-managed Python\n- Keeps PATH scan fallback for non-uv setups

…- Prefer ansible-community for community version; keep ansible-core CLI present\n- Ensure install_ansible.sh also installs ansible-core via uv to retain ansible shim\n- Detect uv-managed tools via real target path; refine pipx detection\n- Classify npm global installs (user/system) via node_modules real path\n- Improve unknown -> /home/.local/bin classification where appropriate

…Add installed_path_resolved and classification_reason in JSON output\n- Introduce CLI_AUDIT_DEBUG to surface suppressed exceptions\n- Refresh AUDIT_JSON after Ansible install in guide.sh\n- Refactor classification into helper for transparency

…asdf/shims and installs as 'asdf'\n- Classify ~/.nodenv/shims and versions as 'nodenv'

…t DPKG path/owner/version caches to CLI_AUDIT_DPKG_CACHE_LIMIT (default 1024)\n- Prevent unbounded growth during repeated audits

…nown paths

…mpty selections

…install-method classifiers

…on' to avoid engine version

…ble; remove dead constant

…th fields

…-origin caps; delegate http_get

… prefer pipx/uv

…ual normalization

… Introduce COLLECT_ONLY/RENDER_ONLY env modes\n- Add snapshot write/read (tools_snapshot.json) with __meta__\n- Render audit strictly from snapshot in render-only mode\n- Persist upstream lookup method to latest_versions.json on success\n- Improve version detection flags (jq, fzf, ctags, ripgrep, ast-grep) and filter error/usage lines\n- Narrow state column and remove subheaders for compact table\n- Add readiness summary and optional streaming rows

Add comprehensive root agent guide covering:
- Overview (Phase 1 complete, Phase 2 planned)
- Setup with Python 3.10+ requirements
- Build & tests (make audit, update, lint)
- Code style (PEP 8, type hints, frozen dataclasses)
- Security (HTTPS-only, no secrets, rate limiting)
- PR/commit checklist (Conventional Commits)
- Good vs bad examples (dataclasses, locks, parallelization)
- When stuck (troubleshooting workflows)
- House Rules (SOLID, DRY, KISS, testing, docs currency)

Thin root file references scoped AGENTS.md files.
Follows https://github.com/anthropics/claude-code convention.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Add comprehensive guide for 13+ installation scripts:
- Overview (install/update/uninstall/reconcile actions)
- Setup (INSTALL_PREFIX, FORCE_INSTALL, DEBUG)
- Build & tests (individual scripts, Make targets, debug mode)
- Code style (Bash 4.0+, set -euo pipefail, error handling)
- Security (HTTPS downloads, checksum verification, sudo safety)
- PR/commit checklist (shellcheck, test all actions)
- Good vs bad examples (robust downloads, version comparison, cleanup)
- When stuck (debug workflows, PATH issues, reconciliation)
- House Rules (vendor tools preferred, parallel reconciliation)

References Phase 2 ADRs for installation strategy decisions.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Update .envrc to follow AGENTS.md convention:
- Export PROJECT_NAME from basename
- Display welcome message with quick start commands
- Show first-time user guidance

Maintains compatibility with existing Makefile env loading.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Improvements:
- Replace custom help with awk-based format (AGENTS.md convention)
- Add ## annotations to all targets for help display
- Document all audit, install, update, uninstall, reconcile targets

Example output:
  audit                   Render audit from snapshot (no network, <100ms)
  install-python          Install Python toolchain via uv
  update-python           Update Python toolchain
  reconcile-node          Reconcile Node.js to nvm-managed

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Phase 2 Planning (PRD & ADRs):
- PRD.md (29KB): Product requirements, Phase 1 summary, Phase 2 spec
- PHASE2_IMPLEMENTATION.md (58KB): 8-week roadmap, 5 phases
- CONFIGURATION_SPEC.md (33KB): .cli-audit.yml schema reference
- adr/README.md: ADR process and index
- ADR-001: Context-aware installation (workstation/server/ci modes)
- ADR-002: Package manager hierarchy (vendor→GitHub→system)
- ADR-003: Parallel installation approach (keep both, PATH ordering)
- ADR-004: Always-latest version policy (warn on major upgrades)
- ADR-005: Environment detection logic (CI/server/workstation)
- ADR-006: Configuration file format (YAML, multi-location precedence)

Technical Documentation Updates:
- INDEX.md: Added Phase 2 planning section, navigation updates
- QUICK_REFERENCE.md: One-liners, env vars, jq queries
- ARCHITECTURE.md: System design, threading model, cache hierarchy
- API_REFERENCE.md: 50+ functions, environment variables
- FUNCTION_REFERENCE.md: Categorized function catalog
- DEVELOPER_GUIDE.md: Contributing guide, testing strategies
- TOOL_ECOSYSTEM.md: 50+ tool catalog with categories
- DEPLOYMENT.md: Makefile targets, CI/CD integration
- TROUBLESHOOTING.md: Common issues and solutions

AI Agent Context:
- claudedocs/project_context.md: Quick reference for AI agents
- claudedocs/session_summary.md: Session documentation and insights

Total: 12 docs files (189KB), 8 ADRs (71KB), 2 AI context files (19KB)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Document all 13+ installation scripts:
- Overview of multi-action support (install/update/uninstall/reconcile)
- Per-script detailed documentation
- Actions explained (install, update, uninstall, reconcile)
- Usage examples via Make targets
- Troubleshooting per script
- Shared utilities (lib/ directory)
- Best practices and patterns

Scripts covered:
- install_core.sh: fd, fzf, ripgrep, jq, yq, bat, delta, just
- install_python.sh: uv-based Python toolchain
- install_node.sh: nvm-based Node.js
- install_rust.sh: rustup-based Rust
- install_go.sh, install_aws.sh, install_kubectl.sh
- install_terraform.sh, install_ansible.sh, install_docker.sh
- install_brew.sh, install_uv.sh
- guide.sh: Interactive upgrade guide
- test_smoke.sh: Smoke testing

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Add @anthropic-ai/claude-code ^2.0.11 for AI agent integration.

This dependency ensures AI coding agents (like Claude Code) have
proper tooling support. Package required for AI agent context
and project integration.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Mode enhancements:
- Add COLLECT_ONLY mode (CLI_AUDIT_COLLECT=1): write snapshot, no output
- Add RENDER_ONLY mode (CLI_AUDIT_RENDER=1): read snapshot, no network
- Snapshot includes __meta__ (schema_version, created_at, count)
- write_snapshot() now returns meta dict

Tracing and diagnostics:
- Add CLI_AUDIT_TRACE for ultra-verbose output
- Add CLI_AUDIT_TRACE_NET for HTTP request tracing
- Add _vlog(), _tlog() helper functions
- Add SLOW_MS threshold for performance tracking

HTTP improvements:
- Make http_fetch() retry parameters configurable via env vars
- Add HTTP_RETRIES, HTTP_BACKOFF_BASE, HTTP_BACKOFF_JITTER
- Add network tracing (request status, retries, errors)

Version detection improvements:
- Filter error/usage lines from version output
- Improve jq, fzf, ctags, ripgrep, ast-grep version detection
- Handle --help output that contains version info

Performance:
- Persist upstream lookup method to latest_versions.json on success
- Narrow state column in table output
- Remove subheaders for more compact display
- Add readiness summary
- Optional streaming rows

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Version updates:
- npm: 10.8.3 → 11.6.2
- pipx: 1.7.1 → 1.8.0
- poetry: 1.8.3 → 2.2.1
- yarn: 4.5.1 → 4.9.4

Method persistence:
- Add __methods__ section tracking upstream lookup methods
- Persist successful lookup methods for faster future queries

This cache update improves performance by recording which
upstream API (pypi, npm, github, crates) successfully resolved
each tool's latest version.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Ignore node_modules/ directory from @anthropic-ai/claude-code
dependency. Minimal Node.js usage (AI agent integration only).

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Major documentation reorganization following best practices:

Documentation Organization:
- Move PROJECT_GUIDE.md to docs/ for proper organization
- Move ARCHITECTURE_DIAGRAM.md to docs/ for technical documentation
- Move DEVELOPMENT_QUICKSTART.md to docs/ for developer resources
- Preserve important claudedocs/ content in committed docs/
  - logging_framework.md → docs/LOGGING.md
  - phase2_completion_report.md → docs/PHASE2_COMPLETION_REPORT.md
  - comprehensive_code_review.md → docs/CODE_REVIEW.md
- Add docs/DOCUMENTATION_ORGANIZATION.md for organization rationale
- Update .gitignore to exclude claudedocs/ (AI agent session context)

Phase 2 Implementation (Complete):
- Add cli_audit package with 11 modules (5,338 LOC)
- Phase 2.1: Foundation (environment, config, package_managers, install_plan)
- Phase 2.2: Core installation (installer with retry and validation)
- Phase 2.3: Bulk operations (parallel installation with progress tracking)
- Phase 2.4: Upgrade management (version comparison, breaking changes)
- Phase 2.5: Reconciliation (multi-installation detection and management)
- Phase 2.6: Logging framework (structured logging with console/file output)

Testing Infrastructure:
- Add comprehensive test suite (292 tests, 4,907 LOC)
- Unit tests for all 11 Phase 2 modules
- Integration tests for end-to-end workflows
- Test fixtures for configuration validation

Development Infrastructure:
- Add CI/CD workflows (GitHub Actions)
  - ci.yml: Matrix testing (Python 3.10-3.12, Linux/macOS)
  - release.yml: Automated releases with PyPI publishing
  - dependabot.yml: Automated dependency updates
- Add development tooling configuration
  - .flake8: Linting rules
  - mypy.ini: Type checking configuration
  - pytest.ini: Test configuration
  - pyproject.toml: Package metadata and dependencies
- Add CONTRIBUTING.md with comprehensive contributor guide

Documentation:
- Add docs/PHASE2_API_REFERENCE.md (78 API symbols across 11 modules)
- Add docs/phase2_api/environment.md (detailed module documentation)
- Add docs/CODE_REVIEW.md (comprehensive quality assessment: 9.3/10)
- Add docs/LOGGING.md (logging framework documentation)
- Update README.md with Phase 2 features and code examples

Quality:
- Zero circular dependencies across 11 modules
- Comprehensive type hints throughout
- Frozen dataclasses for immutability
- Thread-safe progress tracking
- Retry logic with exponential backoff
- Checksum verification for downloads
- Breaking change detection and warnings
- System tool safelist (26 protected tools)

Cross-references updated in PHASE2_API_REFERENCE.md and environment.md
to reflect new documentation locations.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](codecov/codecov-action@v4...v5)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>