feat(cli)!: replace commands monolith with module-per-command architecture

[eschaar]

BREAKING CHANGE: vstack.cli.commands removed. CommandService and all command classes now live in dedicated modules under vstack.cli (service, install, verify, validate, status, uninstall, manifest, report). Manifest persistence classes moved to new vstack.manifest package.

• Split 596-line commands.py into 12 focused modules: base, catalog, helpers, registry, service, interface, install, verify, validate, status, uninstall, report
• Extract vstack.manifest package (store.py) with schema-versioned Manifest, ManifestFile, ArtifactEntry, content_hash
• Add manifest upgrade --backfill to retroactively compute checksums for legacy manifest entries without checksum
• Fix _version_gt TypeError when existing version is None on first install
• Restructure full test suite: per-module test files, TestClass layout, delete catch-all test_commands.py; test count 288 -> 337
• Add mypy to quality gate (106 files, 0 errors)
• Consolidate e2e tests into tests/vstack/test_integration.py
• Add 4 new ADRs: 014 manifest schema versioning, 015 conservative install defaults, 016 atomic manifest writes, 017 checksum backfill
• Write release notes docs/releases/2026-04-26.md and update CHANGELOG

[Copilot]

Pull request overview

This PR performs a breaking refactor of the vstack CLI from a monolithic command module into a catalog/registry/interface architecture with per-command modules, and extracts manifest persistence into a dedicated vstack.manifest package with schema versioning and checksum backfill support.

Changes:

• Replaced the vstack.cli.commands monolith with a module-per-command CLI (parser/catalog/registry/interface/service + command handlers).
• Introduced vstack.manifest with schema-v2 manifest models, atomic writes, and manifest upgrade --backfill.
• Restructured and expanded the test suite (unit tests per module + consolidated integration tests) and updated user-facing docs/release notes.

Reviewed changes

Copilot reviewed 62 out of 62 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
tests/vstack/test_main.py	Updates entrypoint tests to exercise the new CommandLineInterface-based main() behavior.
tests/vstack/test_integration.py	Adds end-to-end subprocess coverage for verify/status/manifest upgrade/backfill flows.
tests/vstack/prompts/test_constants.py	Adds prompt constant tests aligning with new prompt module structure.
tests/vstack/prompts/test_config.py	Adds prompt artifact type config tests.
tests/vstack/prompts/test___init__.py	Adds prompts package public API export tests.
tests/vstack/manifest/test_store.py	Adds comprehensive tests for manifest schema v2 parsing, upgrade, backfill, and atomic write behaviors.
tests/vstack/instructions/test_constants.py	Adds instruction constant tests.
tests/vstack/instructions/test_config.py	Adds instruction artifact type config tests.
tests/vstack/instructions/test___init__.py	Adds instructions package public API export tests.
tests/vstack/cli/test_verify.py	Adds VerifyCommand unit tests for manifest error handling and context forwarding.
tests/vstack/cli/test_validate.py	Adds ValidateCommand context-forwarding tests.
tests/vstack/cli/test_uninstall.py	Adds UninstallCommand behavior + context-forwarding tests.
tests/vstack/cli/test_status.py	Adds StatusCommand context-forwarding tests.
tests/vstack/cli/test_report.py	Adds report rendering/YAML serializer tests for status output.
tests/vstack/cli/test_registry.py	Adds registry construction tests for catalog-driven dispatch.
tests/vstack/cli/test_parser.py	Updates parser tests for new command catalog, new flags, and new error behavior (ValueError vs SystemExit).
tests/vstack/cli/test_manifest.py	Replaces manifest model tests with ManifestCommand dispatch tests.
tests/vstack/cli/test_interface.py	Adds interface-level tests for parser/service wiring, scope resolution, and dispatch.
tests/vstack/cli/test_integration_runtime.py	Removes superseded CLI runtime integration test (moved into consolidated integration tests).
tests/vstack/cli/test_install.py	Adds InstallCommand decision/version/backfill-related unit tests and context forwarding.
tests/vstack/cli/test_helpers.py	Adds tests for shared helper normalization logic.
tests/vstack/cli/test_catalog.py	Adds tests ensuring command/subcommand catalog correctness and invariants.
tests/vstack/cli/test_base.py	Adds tests for the new CommandContext and BaseCommand contract.
src/vstack/manifest/store.py	New manifest domain implementation: schema v2, checksum support, backfill, and atomic file persistence.
src/vstack/manifest/init.py	Exposes manifest domain API at package level.
src/vstack/main.py	Switches entrypoint to CommandLineInterface.run() with centralized ValueError handling.
src/vstack/constants.py	Adds explicit bandit suppression comment for safe subprocess.check_output usage.
src/vstack/cli/verify.py	New VerifyCommand handler with manifest checksum + metadata verification paths.
src/vstack/cli/validate.py	New ValidateCommand handler (in-memory render + unresolved placeholder reporting).
src/vstack/cli/uninstall.py	New UninstallCommand handler implementing conservative removal + manifest updates.
src/vstack/cli/status.py	New StatusCommand handler producing text/json/yaml status reports.
src/vstack/cli/service.py	Introduces CommandService as shared CLI coordinator (generators, manifest access, drift checks, wrappers).
src/vstack/cli/report.py	Adds report builders/renderers and a minimal YAML serializer for status output.
src/vstack/cli/registry.py	Adds catalog-driven registry construction for command dispatch.
src/vstack/cli/parser.py	Rebuilds argparse tree from catalogs; target resolution now raises ValueError instead of exiting.
src/vstack/cli/manifest.py	Re-exports manifest symbols for compatibility and adds vstack manifest <action> dispatch command.
src/vstack/cli/interface.py	Adds orchestration facade that wires parser → service → registry → command execution.
src/vstack/cli/install.py	New InstallCommand implementing conservative install/update/adopt/force-name behaviors + manifest writes.
src/vstack/cli/helpers.py	Adds shared CLI helpers (targeted-name normalization).
src/vstack/cli/constants.py	Centralizes CLI constants: ANSI colors, known types, global-only supported types, expected input names, artifact states.
src/vstack/cli/commands.py	Removes the legacy monolithic CLI implementation.
src/vstack/cli/catalog.py	Adds central command/subcommand configuration catalogs and ordering.
src/vstack/cli/base.py	Adds BaseCommand ABC and CommandContext dataclass for unified handler interface.
docs/test-report.md	Adds/updates a consolidated QA report for the refactor and new gates.
docs/security-report.md	Adds/updates security review notes and documents the subprocess suppression decision.
docs/releases/2026-04-26.md	Adds release notes for v2.0.0 and the breaking CLI/manifest changes.
docs/product/roadmap.md	Updates roadmap counts and supporting narrative to match current skill set.
docs/product/requirements.md	Rewrites requirements doc with the new CLI/manifest contracts and conservative install semantics.
docs/performance-baseline.md	Adds a performance baseline document for CLI operations and import time.
docs/architecture/architecture.md	Updates architecture doc to reflect new manifest package and CLI component model.
docs/architecture/adr/017-checksum-backfill-on-upgrade.md	Adds ADR for checksum backfill behavior and its safety model.
docs/architecture/adr/016-atomic-manifest-writes.md	Adds ADR documenting atomic manifest writes.
docs/architecture/adr/015-conservative-install-by-default.md	Adds ADR documenting conservative install semantics and flags.
docs/architecture/adr/014-manifest-schema-versioning.md	Adds ADR documenting manifest schema versioning and explicit upgrade gating.
docs/architecture/adr/012-flat-templates-install-time-generation.md	Updates ADR to reflect conservative install/adopt/force behaviors and checksum usage.
README.md	Updates CLI command documentation and usage guidance for new commands/subcommands and conservative defaults.
README-pypi.md	Updates PyPI-safe README content to include new manifest commands and conservative behavior summary.
CHANGELOG.md	Adds 2.0.0 entry documenting breaking changes, additions, and fixes.
.github/vstack.json	Updates the repo’s installed manifest artifact to schema v2 with checksums (generated output snapshot).