Refactor FS access to bounded-context repositories

[danielbdyer]

Motivation

• Reduce broad path+FS coupling by introducing context-specific repository contracts for intent, knowledge, control, resolution, execution, and governance so application code depends on narrow persistence ports instead of raw file operations.
• Keep a single canonical filesystem implementation/export and deprecate duplicate barrel usage to centralize filesystem behavior and error mapping.

Description

• Added repository ports and Effect tags in lib/application/ports.ts for IntentRepository, KnowledgeRepository, ControlRepository, ResolutionTaskRepository, ExecutionRepository, and GovernanceRepository and their contracts.
• Implemented local adapters in lib/infrastructure/repositories/local-context-repositories.ts that encapsulate path resolution and (de)serialization (YAML for knowledge, JSON for tasks/runs) while delegating I/O to the canonical lib/infrastructure/fs/local-fs.ts FS adapter.
• Wired repository services into the local service composition and layers (lib/composition/local-services.ts, lib/composition/layers.ts) so repositories are provided alongside the FileSystem service.
• Migrated application flows to repositories: buildInterpretationSurfaceProjection/task projection now uses ResolutionTaskRepository, applyDriftEvents uses KnowledgeRepository, and run persistence uses ExecutionRepository.writeRunArtifacts(...) (lib/application/task.ts, lib/application/drift.ts, lib/application/run.ts).
• Removed the duplicate FS barrel lib/infrastructure/local-fs.ts so lib/infrastructure/fs/local-fs.ts is the single canonical export, and added focused repository contract tests in tests/repository-contracts.spec.ts.

Testing

• Ran npm run build and confirmed the build completed successfully.
• Ran the focused repository contract suite with npx playwright test tests/repository-contracts.spec.ts and all tests passed (3 passed).
• Note: npm run typecheck surfaced pre-existing repository-wide diagnostics unrelated to this change; those are baseline issues (typecheck report at .tesseract/reports/typecheck-report.json) and did not block the targeted build/tests above.

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Codex Task