refactor(skills): migrate to runtime registry install architecture

[senamakel]

Summary

• Replaced submodule-based/bundled skill sourcing with a runtime registry installer model.
• Added Rust registry services and new Tauri commands for core sync, catalog listing, install/update, and uninstall.
• Switched runtime discovery source to installed workspace skills (.../skills/installed) and added startup core sync before auto-start.
• Updated Skills UI to expose a registry section with core/contributor entries and install/update/uninstall actions.
• Removed bundled skills resource and submodule wiring (.gitmodules, tracked gitlink), and adjusted path/script assumptions accordingly.

Problem

• Skills were effectively compile-time/submodule-coupled, making contribution and distribution centralized and heavyweight.
• There was no first-class runtime registry workflow for mandatory core skills vs user-installed contributor skills.
• Existing runtime path resolution depended on legacy skills/skills layouts.

Solution

• Implemented src-tauri/src/runtime/registry.rs to:
  • pull/refresh the skills source repo (skills/),
  • parse registry/manifest.json,
  • verify directory hashes,
  • install/update atomically into runtime install directory,
  • persist install state.
• Added new commands in runtime command surface:
  • registry_sync_core
  • registry_list_catalog
  • registry_install_skill
  • registry_update_skill
  • registry_uninstall_skill
• Updated runtime engine fallback source dir to managed install output and wired startup core sync in app boot before auto_start_skills().
• Updated frontend/provider/pages to consume registry commands and show install/update controls in UI.
• Removed submodule/bundle assumptions from Tauri resources and scripts.

Testing

• yarn -s compile
• cargo check --manifest-path src-tauri/Cargo.toml
• Other checks run (list commands)
• yarn -s tsc --noEmit
• yarn -s prettier --check . (via push hook)
• yarn -s eslint . --ext .ts,.tsx (via push hook)
• Manual validation completed (list scenarios)

Impact

• Desktop runtime behavior changes: skills are now runtime-installed/synced from registry entries instead of bundled/submodule lookup.
• Improves extensibility for contributor skills and enforces integrity checks via hash verification.
• Introduces migration impact for developers relying on old skills/skills discovery/resource bundling assumptions.

Breaking Changes

• None
• Yes (describe clearly, including migration steps)
• Removed tracked skills submodule/gitlink and .gitmodules.
• Removed bundled ../skills/skills Tauri resource entry.
• Runtime now expects installed skills in managed install directory and registry metadata in skills/registry/manifest.json.

Related

• Issue(s): N/A
• Follow-up PR(s)/TODOs:
• Add registry schema/version validation and stronger trust metadata handling.
• Add automated integration tests for install/update/uninstall command flows.
• Add explicit migration docs for maintainers and contributors.