Add universal Zoo Code setup, doctor, and uninstall commands

[tbitcs]

Goal

Make Specsmith the canonical distribution point for the portable Zoo Code integration currently prototyped in layer1labs/chronocortex.

Decision

Do not create a separate repository. Specsmith already owns the public specsmith zoo-code CLI group, is distributed through pipx/PyPI, and already documents Zoo Code/Roo Code integration. A separate repository would duplicate release/versioning, compatibility testing, and documentation.

Required CLI

specsmith zoo-code setup --project-dir .
specsmith zoo-code doctor --project-dir .
specsmith zoo-code uninstall --project-dir .

Options:

• --global-roo PATH with default ROO_GLOBAL_DIR or ~/.roo
• --scope both|global|project
• --dry-run
• --preserve-existing for users who do not want reserved Specsmith paths adopted

Ownership boundary

Specsmith package owns

• reusable global Zoo Code rules under ~/.roo/rules*
• reusable slash commands under ~/.roo/commands
• reusable skills under ~/.roo/skills
• managed-file marker and manifest
• safe backup/adoption of reserved Specsmith paths
• stale managed-asset cleanup
• project MCP merge for specsmith-governance
• removal of generic Specsmith rules duplicated inside project .roo
• setup, doctor, and uninstall lifecycle
• package tests and documentation

Project repositories own

• project-specific .roo/rules*
• project-specific .roo/commands
• project-specific .roo/skills
• local provider/model settings and custom modes
• any project-specific wrapper that invokes specsmith zoo-code setup

ChronoCortex should retain only ChronoCortex-specific assets and its model/settings configurator.

Safety requirements

• Never delete an unmanaged file solely because its path resembles a Specsmith asset.
• Managed files must contain a versioned marker.
• Back up an existing file before adopting a reserved Specsmith path.
• Preserve unrelated MCP servers while merging/removing specsmith-governance.
• Uninstall removes only marker/manifest-owned files.
• Doctor fails on missing, mismatched, duplicated, or stale managed assets.
• Commands must be idempotent.

Universal assets

Global rules:

• rules/00-specsmith-source-of-truth.md
• rules/10-specsmith-governance.md
• rules/20-context-continuity.md
• rules/30-security-and-secrets.md
• rules/40-context-efficiency.md
• mode-specific planning, evidence, implementation, debugging, orchestration, and review rules

Global slash commands:

• /specsmith-intake
• /specsmith-plan
• /specsmith-implement
• /specsmith-debug
• /specsmith-review
• /specsmith-checkpoint

Global skills:

• specsmith-governed-work
• specsmith-evidence-debugging
• specsmith-context-continuity

Tests

At minimum:

1. clean setup followed by doctor
2. repeat setup is idempotent
3. existing reserved path is backed up and adopted
4. --preserve-existing reports a conflict without modifying it
5. MCP merge preserves unrelated servers
6. recognized workspace duplicates are removed
7. customized workspace files are preserved and reported
8. stale marker-owned assets are removed
9. uninstall removes only managed assets
10. Linux, macOS, and Windows path behavior

ChronoCortex migration

After a Specsmith release contains this feature:

pipx upgrade specsmith
specsmith zoo-code setup --project-dir ~/chronocortex
specsmith zoo-code doctor --project-dir ~/chronocortex

Then replace ChronoCortex's embedded universal installer/cleanup scripts with a thin call to the packaged CLI. Keep the ChronoCortex-specific .roo profile and Zoo/LiteLLM settings scripts in ChronoCortex.