[Change] Module package separation for command implementations

[djm81]

Why

The modular command registry exists, but command implementations still live in src/specfact_cli/commands/. Module packages are mostly re-export shells, which keeps command ownership centralized and increases merge conflict risk.

What Changes

• Move command implementations into module-local src/commands.py files under src/specfact_cli/modules/<name>/src/.
• Update each module src/app.py to import app from local commands.
• Keep backward-compatible re-export shims in src/specfact_cli/commands/.
• Execute migration in tiers (small to heavyweight) with verification gates.
• Update architecture and contributor docs that reference old command implementation locations.

Acceptance Criteria

• Each migrated module has local command implementation and local app wiring.
• Legacy imports from specfact_cli.commands.* continue to work via shims.
• Tier-by-tier tests, contract checks, and representative CLI help checks pass.
• Documentation reflects module-local command implementation model.

OpenSpec Change Proposal: arch-02-module-package-separation