Add learned-skill substrate foundation

[adriandemian]

Context

This PR repairs ralphx/ralphx/agent-88af9c08 after the original ideation/task branch lost the expected learned-skill work. It also merges the recovered unsquashed adapter history so the visible branch contains the work that was previously only present in task/worktree history.

What Landed

• Recovered the unsquashed adapter/injection history into this PR branch.
• Added the Phase 1 persistence substrate:
  • task_outcomes
  • project_skills
  • skill_usage_events
  • domain entities, repository traits, SQLite repos, memory repos, services, AppState wiring, and focused tests.
• Added read-only Rust HTTP/API-key project skill surfaces:
  • POST /api/project_skills/list
  • POST /api/project_skills/get
  • project-scope enforcement for learned project skill list/get paths.
• Added read-only MCP learned skill tools:
  • list_project_skills
  • get_project_skill
  • plugin server dispatch, MCP-side project scope validation, canonical agent allowlists, generated build output, and MCP tests.
• Added Agent Composer learned skill read support:
  • backend catalog includes approved repository-backed project-wide learned skills;
  • frontend schema accepts source: "learned";
  • selected learned skills serialize stable ralphx_project_skill directives carrying project_skill_id.
• Added a repository-backed service resolver for Composer learned-skill directives that returns citations only for same-project, approved, non-archived skills.

Decisions

• This PR does not pretend Phase 4 curator/import/promotion is complete. The earlier substrate was absent, so this branch first lands the prerequisite substrate/read surface.
• Path-scoped learned skills are intentionally hidden from Agent Composer until Composer sends an explicit active path/scope contract.
• The task-e471f6fc adapter work is treated as follow-up adapter logic, not the substrate itself.
• Lifecycle and directive eligibility live in backend services, not only UI controls.

Remaining Gaps

• Phase 0 dark memory capture validation/repair is still open.
• Runtime prompt composition still needs to call the repository-backed directive resolver and record selected learned-skill usage through SkillUsageService after AgentRun creation.
• Distillation, approval workflow, reviewer flagship, task-pipeline/PR outcome capture, export to target .claude/skills, reporting/scoring, curator/import/promotion, and AgentProfile overlays remain follow-on milestones.
• Usage-dependent reporting/curation must remain gated until Claude and Codex usage attribution is wired and tested.

Validation

• cargo check --manifest-path src-tauri/Cargo.toml --lib
• cargo test --manifest-path src-tauri/Cargo.toml learned_skill --lib
• cargo test --manifest-path src-tauri/Cargo.toml project_skill_scope_guard --lib
• cargo test --manifest-path src-tauri/Cargo.toml agent_composer --lib
• cargo test --manifest-path src-tauri/Cargo.toml prompt_selected_citations_resolve_only_approved_same_project_skills --lib
• cd plugins/app/ralphx-mcp-server && npm run build
• cd plugins/app/ralphx-mcp-server && npm run test
• cd frontend && npm run test:run -- src/components/agents/composer/agentComposerCore.test.ts src/components/agents/AgentComposerSurface.test.tsx
• cd frontend && npm run typecheck
• git diff --check

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[codecov]

Codecov Report

❌ Patch coverage is 91.07629% with 393 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
.../application/chat_service/chat_service_handlers.rs	52.31%	103 Missing ⚠️
src-tauri/src/application/memory_orchestration.rs	80.61%	57 Missing ⚠️
...c-tauri/src/application/task_transition_service.rs	23.33%	46 Missing ⚠️
...ri/src/application/project_skill_export_service.rs	94.13%	22 Missing ⚠️
...nents/project-skills/ProjectSkillsCuratorPanel.tsx	92.72%	20 Missing ⚠️
...tauri/src/infrastructure/agents/internal_skills.rs	95.25%	17 Missing ⚠️
...nfrastructure/sqlite/sqlite_learned_skill_repos.rs	97.71%	17 Missing ⚠️
...uri/src/commands/agent_composer_commands/skills.rs	89.80%	16 Missing ⚠️
...ri/src/domain/services/agent_workspace_outcomes.rs	95.62%	13 Missing ⚠️
...ation/chat_service/chat_service_send_background.rs	72.50%	11 Missing ⚠️
... and 23 more

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